@cyanheads/gbif-biodiversity-mcp-server 0.2.5 → 0.2.7
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 +4 -4
- package/Dockerfile +5 -0
- package/README.md +1 -1
- package/dist/index.js +2 -0
- package/dist/index.js.map +1 -1
- package/dist/mcp-server/tools/definitions/gbif-get-species-children.tool.d.ts +8 -1
- package/dist/mcp-server/tools/definitions/gbif-get-species-children.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/gbif-get-species-children.tool.js +27 -3
- package/dist/mcp-server/tools/definitions/gbif-get-species-children.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/gbif-get-species-classification.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/gbif-get-species-classification.tool.js +13 -2
- package/dist/mcp-server/tools/definitions/gbif-get-species-classification.tool.js.map +1 -1
- package/package.json +4 -4
- package/server.json +3 -3
package/CLAUDE.md
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@@ -1,8 +1,8 @@
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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.
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**Version:** 0.2.7
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.6`
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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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@@ -304,13 +304,13 @@ When you complete a skill's checklist, check the boxes and add a completion time
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| `npm run start:http` | Production mode (HTTP) |
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| `npm run changelog:build` | Regenerate `CHANGELOG.md` from `changelog/*.md` |
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| `npm run changelog:check` | Verify `CHANGELOG.md` is in sync (used by devcheck) |
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| `npm run bundle` | Build and
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| `npm run bundle` | Build, pack, and clean a `.mcpb` for one-click Claude Desktop install |
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---
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## Bundling
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`npm run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. MCPB is stdio-only — HTTP and Cloudflare Workers deployments are unaffected. Consumers who don't need it can delete `manifest.json` and `.mcpbignore`; `lint:packaging` skips cleanly.
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`npm run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. The pack step is followed by `scripts/clean-mcpb.ts`, which prunes dev dependencies (`mcpb clean`) and strips dependency-shipped agent docs (`node_modules/**` `skills/`, `.claude/`, `.agents/`, `SKILL.md`) that root-anchored `.mcpbignore` patterns cannot reach. MCPB is stdio-only — HTTP and Cloudflare Workers deployments are unaffected. Consumers who don't need it can delete `manifest.json` and `.mcpbignore`; `lint:packaging` skips cleanly.
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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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package/Dockerfile
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@@ -37,9 +37,11 @@ WORKDIR /usr/src/app
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ENV NODE_ENV=production
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# OCI image metadata (https://github.com/opencontainers/image-spec/blob/main/annotations.md)
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ARG APP_VERSION
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LABEL org.opencontainers.image.title="@cyanheads/gbif-biodiversity-mcp-server"
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LABEL org.opencontainers.image.description="Search GBIF species taxonomy, occurrence records, datasets, and publishers via MCP. STDIO or Streamable HTTP."
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LABEL org.opencontainers.image.licenses="Apache-2.0"
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LABEL org.opencontainers.image.version="${APP_VERSION}"
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LABEL org.opencontainers.image.source="https://github.com/cyanheads/gbif-biodiversity-mcp-server"
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# Copy dependency manifests
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# Expose the port the server listens on
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EXPOSE ${MCP_HTTP_PORT}
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# Health check using a bun-native fetch (slim image ships no curl/wget)
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HEALTHCHECK --interval=30s --timeout=5s --start-period=10s --retries=3 CMD bun -e "fetch('http://localhost:'+(process.env.MCP_HTTP_PORT??'3010')+'/healthz').then((r)=>process.exit(r.ok?0:1)).catch(()=>process.exit(1))"
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# The command to start the server
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CMD ["bun", "run", "dist/index.js"]
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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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@@ -25,6 +25,8 @@ import { gbifSearchPublishers } from './mcp-server/tools/definitions/gbif-search
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import { gbifSearchSpecies } from './mcp-server/tools/definitions/gbif-search-species.tool.js';
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import { initGbifService } from './services/gbif/gbif-service.js';
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await createApp({
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name: 'gbif-biodiversity-mcp-server',
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title: 'gbif-biodiversity-mcp-server',
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tools: [
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gbifMatchSpecies,
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gbifGetSpecies,
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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;SAChC,CAAC,CAAC;IACL,CAAC;CACF,CAAC,CAAC"}
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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,IAAI,EAAE,8BAA8B;IACpC,KAAK,EAAE,8BAA8B;IACrC,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;SAChC,CAAC,CAAC;IACL,CAAC;CACF,CAAC,CAAC"}
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* @module mcp-server/tools/definitions/gbif-get-species-children
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*/
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import { z } from '@cyanheads/mcp-ts-core';
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import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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export declare const gbifGetSpeciesChildren: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
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taxonKey: z.ZodNumber;
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limit: z.ZodDefault<z.ZodNumber>;
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numOccurrences: z.ZodOptional<z.ZodNumber>;
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numDescendants: z.ZodOptional<z.ZodNumber>;
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}, z.core.$strip>>;
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}, z.core.$strip>,
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}, z.core.$strip>, readonly [{
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readonly reason: "not_found";
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readonly code: JsonRpcErrorCode.NotFound;
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readonly when: "The taxonKey does not exist in the GBIF backbone.";
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readonly recovery: "Use gbif_match_species to resolve a name to a valid backbone taxon key.";
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}], {
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readonly totalCount: z.ZodNumber;
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readonly offset: z.ZodNumber;
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readonly limit: z.ZodNumber;
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readonly endOfRecords: z.ZodBoolean;
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{"version":3,"file":"gbif-get-species-children.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-species-children.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;
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{"version":3,"file":"gbif-get-species-children.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-species-children.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;AAY3E,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;EA6HjC,CAAC"}
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* @module mcp-server/tools/definitions/gbif-get-species-children
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*/
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import { tool, z } from '@cyanheads/mcp-ts-core';
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import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
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import { getGbifService } from '../../../services/gbif/gbif-service.js';
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/** Pagination guidance when end of records is reached. */
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function buildNotice(args) {
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const { childCount, endOfRecords } = args;
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if (childCount === 0 && endOfRecords) {
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return 'This taxon has no direct children in the GBIF backbone at this rank
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return 'This taxon has no direct children in the GBIF backbone at this rank.';
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}
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}
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// Pagination context and recovery guidance — reaches both structuredContent and content[].
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enrichment: {
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totalCount: z.number().describe('Total direct children before pagination.'),
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offset: z.number().describe('Current pagination offset.'),
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limit: z.number().describe('Records returned in this page.'),
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endOfRecords: z.boolean().describe('True when there are no more results after this page.'),
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notice: z
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.string()
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.optional()
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.describe('Guidance when no children are found
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.describe('Guidance when no children are found for a valid taxon. Absent on successful result pages.'),
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errors: [
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{
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reason: 'not_found',
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code: JsonRpcErrorCode.NotFound,
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when: 'The taxonKey does not exist in the GBIF backbone.',
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recovery: 'Use gbif_match_species to resolve a name to a valid backbone taxon key.',
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},
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],
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async handler(input, ctx) {
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ctx.log.info('Fetching species children', { taxonKey: input.taxonKey });
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const raw = await getGbifService().getSpeciesChildren(input.taxonKey, { limit: input.limit, offset: input.offset }, ctx);
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numOccurrences: r.numOccurrences,
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numDescendants: r.numDescendants,
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}));
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const totalCount = raw.count ?? 0;
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const offset = raw.offset ?? input.offset;
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const limit = raw.limit ?? input.limit;
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const endOfRecords = raw.endOfRecords ?? true;
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// GBIF /species/{key}/children returns [] for both nonexistent keys and taxa with no children.
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// When empty and end of records, verify the taxon exists to distinguish the two cases.
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if (children.length === 0 && endOfRecords) {
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try {
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await getGbifService().getSpecies(input.taxonKey, ctx);
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}
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catch (err) {
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if (err instanceof McpError && err.code === JsonRpcErrorCode.NotFound) {
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throw ctx.fail('not_found', `Taxon key ${input.taxonKey} not found in the GBIF backbone.`, { ...ctx.recoveryFor('not_found') });
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}
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throw err;
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}
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}
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ctx.enrich({ totalCount, offset, limit, endOfRecords });
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const notice = buildNotice({ childCount: children.length, endOfRecords });
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if (notice)
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ctx.enrich.notice(notice);
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{"version":3,"file":"gbif-get-species-children.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-species-children.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,0DAA0D;AAC1D,SAAS,WAAW,CAAC,IAAmD;IACtE,MAAM,EAAE,UAAU,EAAE,YAAY,EAAE,GAAG,IAAI,CAAC;IAC1C,IAAI,UAAU,KAAK,CAAC,IAAI,YAAY,EAAE,CAAC;QACrC,OAAO,
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|
+
{"version":3,"file":"gbif-get-species-children.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-species-children.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,0DAA0D;AAC1D,SAAS,WAAW,CAAC,IAAmD;IACtE,MAAM,EAAE,UAAU,EAAE,YAAY,EAAE,GAAG,IAAI,CAAC;IAC1C,IAAI,UAAU,KAAK,CAAC,IAAI,YAAY,EAAE,CAAC;QACrC,OAAO,sEAAsE,CAAC;IAChF,CAAC;IACD,OAAO;AACT,CAAC;AAED,MAAM,CAAC,MAAM,sBAAsB,GAAG,IAAI,CAAC,2BAA2B,EAAE;IACtE,KAAK,EAAE,sBAAsB;IAC7B,WAAW,EACT,6FAA6F;QAC7F,4FAA4F;QAC5F,4CAA4C;IAC9C,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE,aAAa,EAAE,KAAK,EAAE;IAC/E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,QAAQ,CAAC,2EAA2E,CAAC;QACxF,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,IAAI,CAAC;aACT,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CAAC,sDAAsD,CAAC;QACnE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;KACpE,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC;aACR,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;YAC/D,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;YACvF,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;YACpF,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;YACvD,eAAe,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;YACpF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;YAC7E,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;YAC1E,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;SACvF,CAAC;aACD,QAAQ,CAAC,wDAAwD,CAAC,CACtE;aACA,QAAQ,CAAC,oBAAoB,CAAC;KAClC,CAAC;IAEF,2FAA2F;IAC3F,UAAU,EAAE;QACV,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,0CAA0C,CAAC;QAC3E,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4BAA4B,CAAC;QACzD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;QAC5D,YAAY,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;QAC1F,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,2FAA2F,CAC5F;KACJ;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,mDAAmD;YACzD,QAAQ,EAAE,yEAAyE;SACpF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,2BAA2B,EAAE,EAAE,QAAQ,EAAE,KAAK,CAAC,QAAQ,EAAE,CAAC,CAAC;QACxE,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,kBAAkB,CACnD,KAAK,CAAC,QAAQ,EACd,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,EAC5C,GAAG,CACJ,CAAC;QAEF,MAAM,QAAQ,GAAG,CAAC,GAAG,CAAC,OAAO,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC/C,GAAG,EAAE,CAAC,CAAC,GAAG;YACV,cAAc,EAAE,CAAC,CAAC,cAAc;YAChC,aAAa,EAAE,CAAC,CAAC,aAAa;YAC9B,IAAI,EAAE,CAAC,CAAC,IAAI;YACZ,eAAe,EAAE,CAAC,CAAC,eAAe;YAClC,cAAc,EAAE,CAAC,CAAC,cAAc;YAChC,cAAc,EAAE,CAAC,CAAC,cAAc;YAChC,cAAc,EAAE,CAAC,CAAC,cAAc;SACjC,CAAC,CAAC,CAAC;QAEJ,MAAM,UAAU,GAAG,GAAG,CAAC,KAAK,IAAI,CAAC,CAAC;QAClC,MAAM,MAAM,GAAG,GAAG,CAAC,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC;QAC1C,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,IAAI,KAAK,CAAC,KAAK,CAAC;QACvC,MAAM,YAAY,GAAG,GAAG,CAAC,YAAY,IAAI,IAAI,CAAC;QAE9C,+FAA+F;QAC/F,uFAAuF;QACvF,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,IAAI,YAAY,EAAE,CAAC;YAC1C,IAAI,CAAC;gBACH,MAAM,cAAc,EAAE,CAAC,UAAU,CAAC,KAAK,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC;YACzD,CAAC;YAAC,OAAO,GAAG,EAAE,CAAC;gBACb,IAAI,GAAG,YAAY,QAAQ,IAAI,GAAG,CAAC,IAAI,KAAK,gBAAgB,CAAC,QAAQ,EAAE,CAAC;oBACtE,MAAM,GAAG,CAAC,IAAI,CACZ,WAAW,EACX,aAAa,KAAK,CAAC,QAAQ,kCAAkC,EAC7D,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CACpC,CAAC;gBACJ,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC;QACH,CAAC;QAED,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,MAAM,EAAE,KAAK,EAAE,YAAY,EAAE,CAAC,CAAC;QACxD,MAAM,MAAM,GAAG,WAAW,CAAC,EAAE,UAAU,EAAE,QAAQ,CAAC,MAAM,EAAE,YAAY,EAAE,CAAC,CAAC;QAC1E,IAAI,MAAM;YAAE,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;QAEtC,OAAO,EAAE,QAAQ,EAAE,CAAC;IACtB,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,CAAC,gBAAgB,MAAM,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,CAAC;QACnE,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,QAAQ,EAAE,CAAC;YACpC,MAAM,IAAI,GAAG,KAAK,CAAC,aAAa,IAAI,SAAS,CAAC;YAC9C,MAAM,GAAG,GACP,KAAK,CAAC,cAAc,IAAI,KAAK,CAAC,cAAc,KAAK,IAAI,CAAC,CAAC,CAAC,KAAK,KAAK,CAAC,cAAc,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;YAC5F,KAAK,CAAC,IAAI,CAAC,SAAS,IAAI,KAAK,GAAG,EAAE,CAAC,CAAC;YACpC,IAAI,KAAK,CAAC,GAAG,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,UAAU,KAAK,CAAC,GAAG,EAAE,CAAC,CAAC;YACzD,IAAI,KAAK,CAAC,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,WAAW,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;YACpD,IAAI,KAAK,CAAC,eAAe;gBAAE,KAAK,CAAC,IAAI,CAAC,aAAa,KAAK,CAAC,eAAe,EAAE,CAAC,CAAC;YAC5E,IAAI,KAAK,CAAC,cAAc;gBAAE,KAAK,CAAC,IAAI,CAAC,kBAAkB,KAAK,CAAC,cAAc,EAAE,CAAC,CAAC;YAC/E,IAAI,KAAK,CAAC,cAAc,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,kBAAkB,KAAK,CAAC,cAAc,EAAE,CAAC,CAAC;YACvF,IAAI,KAAK,CAAC,cAAc,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,kBAAkB,KAAK,CAAC,cAAc,EAAE,CAAC,CAAC;QACzF,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"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gbif-get-species-classification.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-species-classification.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;
|
|
1
|
+
{"version":3,"file":"gbif-get-species-classification.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-species-classification.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;AAI3E,eAAO,MAAM,4BAA4B;;;;;;;;;;;;;;cAoGvC,CAAC"}
|
|
@@ -39,7 +39,18 @@ export const gbifGetSpeciesClassification = tool('gbif_get_species_classificatio
|
|
|
39
39
|
],
|
|
40
40
|
async handler(input, ctx) {
|
|
41
41
|
ctx.log.info('Fetching species classification', { taxonKey: input.taxonKey });
|
|
42
|
-
|
|
42
|
+
let raw;
|
|
43
|
+
try {
|
|
44
|
+
raw = await getGbifService().getSpeciesParents(input.taxonKey, ctx);
|
|
45
|
+
}
|
|
46
|
+
catch (err) {
|
|
47
|
+
if (err instanceof McpError && err.code === JsonRpcErrorCode.NotFound) {
|
|
48
|
+
throw ctx.fail('not_found', `Taxon key ${input.taxonKey} not found in the GBIF backbone.`, {
|
|
49
|
+
...ctx.recoveryFor('not_found'),
|
|
50
|
+
});
|
|
51
|
+
}
|
|
52
|
+
throw err;
|
|
53
|
+
}
|
|
43
54
|
if (!Array.isArray(raw)) {
|
|
44
55
|
throw ctx.fail('not_found', `Taxon key ${input.taxonKey} not found in the GBIF backbone.`, {
|
|
45
56
|
...ctx.recoveryFor('not_found'),
|
|
@@ -52,7 +63,7 @@ export const gbifGetSpeciesClassification = tool('gbif_get_species_classificatio
|
|
|
52
63
|
await getGbifService().getSpecies(input.taxonKey, ctx);
|
|
53
64
|
}
|
|
54
65
|
catch (err) {
|
|
55
|
-
if (err instanceof McpError && err.code ===
|
|
66
|
+
if (err instanceof McpError && err.code === JsonRpcErrorCode.NotFound) {
|
|
56
67
|
throw ctx.fail('not_found', `Taxon key ${input.taxonKey} not found in the GBIF backbone.`, { ...ctx.recoveryFor('not_found') });
|
|
57
68
|
}
|
|
58
69
|
throw err;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gbif-get-species-classification.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-species-classification.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;
|
|
1
|
+
{"version":3,"file":"gbif-get-species-classification.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-species-classification.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAGjE,MAAM,CAAC,MAAM,4BAA4B,GAAG,IAAI,CAAC,iCAAiC,EAAE;IAClF,KAAK,EAAE,4BAA4B;IACnC,WAAW,EACT,4FAA4F;QAC5F,wFAAwF;QACxF,2FAA2F;QAC3F,gHAAgH;IAClH,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE,aAAa,EAAE,KAAK,EAAE;IAC/E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,QAAQ,CAAC,2EAA2E,CAAC;KACzF,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,cAAc,EAAE,CAAC;aACd,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;YACxE,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;YACtF,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,8BAA8B,CAAC;YACpE,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;SACxF,CAAC;aACD,QAAQ,CAAC,kDAAkD,CAAC,CAChE;aACA,QAAQ,CACP,gGAAgG,CACjG;KACJ,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,mDAAmD;YACzD,QAAQ,EAAE,yEAAyE;SACpF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,iCAAiC,EAAE,EAAE,QAAQ,EAAE,KAAK,CAAC,QAAQ,EAAE,CAAC,CAAC;QAE9E,IAAI,GAAoB,CAAC;QACzB,IAAI,CAAC;YACH,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,iBAAiB,CAAC,KAAK,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC;QACtE,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,IAAI,GAAG,YAAY,QAAQ,IAAI,GAAG,CAAC,IAAI,KAAK,gBAAgB,CAAC,QAAQ,EAAE,CAAC;gBACtE,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,aAAa,KAAK,CAAC,QAAQ,kCAAkC,EAAE;oBACzF,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;iBAChC,CAAC,CAAC;YACL,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC;QAED,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;YACxB,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,aAAa,KAAK,CAAC,QAAQ,kCAAkC,EAAE;gBACzF,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;aAChC,CAAC,CAAC;QACL,CAAC;QAED,2FAA2F;QAC3F,oEAAoE;QACpE,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACrB,IAAI,CAAC;gBACH,MAAM,cAAc,EAAE,CAAC,UAAU,CAAC,KAAK,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC;YACzD,CAAC;YAAC,OAAO,GAAG,EAAE,CAAC;gBACb,IAAI,GAAG,YAAY,QAAQ,IAAI,GAAG,CAAC,IAAI,KAAK,gBAAgB,CAAC,QAAQ,EAAE,CAAC;oBACtE,MAAM,GAAG,CAAC,IAAI,CACZ,WAAW,EACX,aAAa,KAAK,CAAC,QAAQ,kCAAkC,EAC7D,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CACpC,CAAC;gBACJ,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC;QACH,CAAC;QAED,MAAM,cAAc,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;YACxC,GAAG,EAAE,IAAI,CAAC,GAAG;YACb,IAAI,EAAE,IAAI,CAAC,IAAI;YACf,IAAI,EAAE,IAAI,CAAC,aAAa;YACxB,cAAc,EAAE,IAAI,CAAC,cAAc;SACpC,CAAC,CAAC,CAAC;QAEJ,OAAO,EAAE,cAAc,EAAE,CAAC;IAC5B,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,CAAC,6BAA6B,MAAM,CAAC,cAAc,CAAC,MAAM,YAAY,CAAC,CAAC;QAChG,KAAK,MAAM,CAAC,CAAC,EAAE,IAAI,CAAC,IAAI,MAAM,CAAC,cAAc,CAAC,OAAO,EAAE,EAAE,CAAC;YACxD,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC;YAC9B,MAAM,IAAI,GAAG,IAAI,CAAC,IAAI,IAAI,SAAS,CAAC;YACpC,MAAM,IAAI,GAAG,IAAI,CAAC,IAAI,IAAI,EAAE,CAAC;YAC7B,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,IAAI,IAAI,CAAC,CAAC,CAAC,UAAU,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;YAC1D,MAAM,GAAG,GACP,IAAI,CAAC,cAAc,IAAI,IAAI,CAAC,cAAc,KAAK,IAAI,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,cAAc,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;YACzF,KAAK,CAAC,IAAI,CAAC,GAAG,MAAM,GAAG,IAAI,OAAO,IAAI,KAAK,GAAG,GAAG,GAAG,EAAE,CAAC,CAAC;QAC1D,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": "0.2.7",
|
|
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",
|
|
@@ -22,7 +22,7 @@
|
|
|
22
22
|
"list-skills": "bun run scripts/list-skills.ts",
|
|
23
23
|
"lint:mcp": "bun run scripts/lint-mcp.ts",
|
|
24
24
|
"lint:packaging": "bun run scripts/lint-packaging.ts",
|
|
25
|
-
"bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/gbif-biodiversity-mcp-server.mcpb",
|
|
25
|
+
"bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/gbif-biodiversity-mcp-server.mcpb && bun run scripts/clean-mcpb.ts dist/gbif-biodiversity-mcp-server.mcpb",
|
|
26
26
|
"changelog:build": "bun run scripts/build-changelog.ts",
|
|
27
27
|
"changelog:check": "bun run scripts/build-changelog.ts --check",
|
|
28
28
|
"release:github": "bun run scripts/release-github.ts",
|
|
@@ -76,13 +76,13 @@
|
|
|
76
76
|
"access": "public"
|
|
77
77
|
},
|
|
78
78
|
"dependencies": {
|
|
79
|
-
"@cyanheads/mcp-ts-core": "^0.
|
|
79
|
+
"@cyanheads/mcp-ts-core": "^0.10.6",
|
|
80
80
|
"pino-pretty": "^13.1.3",
|
|
81
81
|
"zod": "^4.4.3"
|
|
82
82
|
},
|
|
83
83
|
"devDependencies": {
|
|
84
84
|
"@biomejs/biome": "^2.4.16",
|
|
85
|
-
"@types/node": "^25.9.
|
|
85
|
+
"@types/node": "^25.9.3",
|
|
86
86
|
"depcheck": "^1.4.7",
|
|
87
87
|
"ignore": "^7.0.5",
|
|
88
88
|
"tsc-alias": "^1.8.17",
|
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": "0.2.7",
|
|
16
16
|
"packages": [
|
|
17
17
|
{
|
|
18
18
|
"registryType": "npm",
|
|
19
19
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
20
20
|
"identifier": "@cyanheads/gbif-biodiversity-mcp-server",
|
|
21
21
|
"runtimeHint": "bun",
|
|
22
|
-
"version": "0.2.
|
|
22
|
+
"version": "0.2.7",
|
|
23
23
|
"packageArguments": [
|
|
24
24
|
{
|
|
25
25
|
"type": "positional",
|
|
@@ -48,7 +48,7 @@
|
|
|
48
48
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
49
49
|
"identifier": "@cyanheads/gbif-biodiversity-mcp-server",
|
|
50
50
|
"runtimeHint": "bun",
|
|
51
|
-
"version": "0.2.
|
|
51
|
+
"version": "0.2.7",
|
|
52
52
|
"packageArguments": [
|
|
53
53
|
{
|
|
54
54
|
"type": "positional",
|