@cyanheads/gbif-biodiversity-mcp-server 0.2.9 → 0.3.0
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 +1 -1
- package/README.md +1 -1
- package/dist/mcp-server/resources/definitions/gbif-dataset.resource.d.ts +7 -1
- package/dist/mcp-server/resources/definitions/gbif-dataset.resource.d.ts.map +1 -1
- package/dist/mcp-server/resources/definitions/gbif-dataset.resource.js +28 -4
- package/dist/mcp-server/resources/definitions/gbif-dataset.resource.js.map +1 -1
- package/dist/mcp-server/resources/definitions/gbif-species.resource.d.ts +7 -1
- package/dist/mcp-server/resources/definitions/gbif-species.resource.d.ts.map +1 -1
- package/dist/mcp-server/resources/definitions/gbif-species.resource.js +26 -3
- package/dist/mcp-server/resources/definitions/gbif-species.resource.js.map +1 -1
- package/dist/mcp-server/tools/definitions/gbif-get-dataset.tool.d.ts +3 -0
- package/dist/mcp-server/tools/definitions/gbif-get-dataset.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/gbif-get-dataset.tool.js +28 -7
- package/dist/mcp-server/tools/definitions/gbif-get-dataset.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/gbif-get-species.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/gbif-get-species.tool.js +3 -1
- package/dist/mcp-server/tools/definitions/gbif-get-species.tool.js.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
package/CLAUDE.md
CHANGED
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@@ -1,7 +1,7 @@
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# Developer Protocol
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**Server:** @cyanheads/gbif-biodiversity-mcp-server
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**Version:** 0.
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**Version:** 0.3.0
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.9`
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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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package/README.md
CHANGED
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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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* @module mcp-server/resources/definitions/gbif-dataset
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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 gbifDatasetResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
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datasetKey: z.ZodString;
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}, z.core.$strip>, z.ZodObject<{
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@@ -16,5 +17,10 @@ export declare const gbifDatasetResource: import("@cyanheads/mcp-ts-core").Resou
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publishingCountry: z.ZodOptional<z.ZodString>;
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recordCount: z.ZodOptional<z.ZodNumber>;
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numConstituents: z.ZodOptional<z.ZodNumber>;
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}, z.core.$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 datasetKey UUID does not match any dataset in GBIF.";
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readonly recovery: "Use gbif_search_datasets to find valid dataset keys, or check the UUID from an occurrence record's datasetKey field.";
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}]>;
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//# sourceMappingURL=gbif-dataset.resource.d.ts.map
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{"version":3,"file":"gbif-dataset.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gbif-dataset.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;
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{"version":3,"file":"gbif-dataset.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gbif-dataset.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;AAK3E,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;GAqE9B,CAAC"}
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* @module mcp-server/resources/definitions/gbif-dataset
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*/
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import { resource, z } from '@cyanheads/mcp-ts-core';
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import {
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import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
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import { stripHtml } from '../../../mcp-server/tools/utils.js';
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import { getGbifService } from '../../../services/gbif/gbif-service.js';
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export const gbifDatasetResource = resource('gbif://dataset/{datasetKey}', {
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name: 'gbif-dataset',
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recordCount: z.number().optional().describe('Number of records. May be absent.'),
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numConstituents: z.number().optional().describe('Number of sub-datasets. May be absent.'),
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}),
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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 datasetKey UUID does not match any dataset in GBIF.',
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recovery: "Use gbif_search_datasets to find valid dataset keys, or check the UUID from an occurrence record's datasetKey field.",
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},
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],
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async handler(params, ctx) {
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ctx.log.debug('Fetching dataset resource', { datasetKey: params.datasetKey });
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let raw;
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try {
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raw = await getGbifService().getDataset(params.datasetKey, ctx);
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}
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catch (err) {
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// Map the upstream GBIF 404 envelope to a clean domain not_found, mirroring
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// gbif_get_dataset — the service throws before the !raw.key check can run.
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if (err instanceof McpError && err.code === JsonRpcErrorCode.NotFound) {
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throw ctx.fail('not_found', `Dataset ${params.datasetKey} not found in GBIF.`, {
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...ctx.recoveryFor('not_found'),
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});
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}
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throw err;
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}
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if (!raw.key) {
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throw
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throw ctx.fail('not_found', `Dataset ${params.datasetKey} not found in GBIF.`, {
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...ctx.recoveryFor('not_found'),
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});
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}
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return {
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key: raw.key,
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title: raw.title,
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type: raw.type,
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description: raw.description,
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description: raw.description ? stripHtml(raw.description) : undefined,
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license: raw.license,
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doi: raw.doi,
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citationText: raw.citation?.text,
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{"version":3,"file":"gbif-dataset.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gbif-dataset.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;
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{"version":3,"file":"gbif-dataset.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gbif-dataset.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,SAAS,EAAE,MAAM,6BAA6B,CAAC;AACxD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAGjE,MAAM,CAAC,MAAM,mBAAmB,GAAG,QAAQ,CAAC,6BAA6B,EAAE;IACzE,IAAI,EAAE,cAAc;IACpB,KAAK,EAAE,cAAc;IACrB,WAAW,EACT,gFAAgF;QAChF,uFAAuF;QACvF,0CAA0C;IAC5C,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;KACjD,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;QACpD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;QACvD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;QACrD,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QAClF,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oCAAoC,CAAC;QAC7E,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QACvE,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oCAAoC,CAAC;QAClF,iBAAiB,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QACrF,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;QAChF,eAAe,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;KAC1F,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,yDAAyD;YAC/D,QAAQ,EACN,sHAAsH;SACzH;KACF;IAED,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2BAA2B,EAAE,EAAE,UAAU,EAAE,MAAM,CAAC,UAAU,EAAE,CAAC,CAAC;QAC9E,IAAI,GAAqB,CAAC;QAC1B,IAAI,CAAC;YACH,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,UAAU,CAAC,MAAM,CAAC,UAAU,EAAE,GAAG,CAAC,CAAC;QAClE,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,4EAA4E;YAC5E,2EAA2E;YAC3E,IAAI,GAAG,YAAY,QAAQ,IAAI,GAAG,CAAC,IAAI,KAAK,gBAAgB,CAAC,QAAQ,EAAE,CAAC;gBACtE,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,WAAW,MAAM,CAAC,UAAU,qBAAqB,EAAE;oBAC7E,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;iBAChC,CAAC,CAAC;YACL,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC;QAED,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC;YACb,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,WAAW,MAAM,CAAC,UAAU,qBAAqB,EAAE;gBAC7E,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;aAChC,CAAC,CAAC;QACL,CAAC;QAED,OAAO;YACL,GAAG,EAAE,GAAG,CAAC,GAAG;YACZ,KAAK,EAAE,GAAG,CAAC,KAAK;YAChB,IAAI,EAAE,GAAG,CAAC,IAAI;YACd,WAAW,EAAE,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAC,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS;YACrE,OAAO,EAAE,GAAG,CAAC,OAAO;YACpB,GAAG,EAAE,GAAG,CAAC,GAAG;YACZ,YAAY,EAAE,GAAG,CAAC,QAAQ,EAAE,IAAI;YAChC,iBAAiB,EAAE,GAAG,CAAC,iBAAiB;YACxC,WAAW,EAAE,GAAG,CAAC,UAAU,IAAI,GAAG,CAAC,WAAW;YAC9C,eAAe,EAAE,GAAG,CAAC,eAAe;SACrC,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
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* @module mcp-server/resources/definitions/gbif-species
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*/
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import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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export declare const gbifSpeciesResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
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taxonKey: z.ZodString;
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}, z.core.$strip>, z.ZodObject<{
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extinct: z.ZodOptional<z.ZodBoolean>;
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acceptedKey: z.ZodOptional<z.ZodNumber>;
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accepted: z.ZodOptional<z.ZodString>;
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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 key, or gbif_search_species to browse.";
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}]>;
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//# sourceMappingURL=gbif-species.resource.d.ts.map
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{"version":3,"file":"gbif-species.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gbif-species.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;
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{"version":3,"file":"gbif-species.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gbif-species.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAA6B,MAAM,+BAA+B,CAAC;AAI5F,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;GAwF9B,CAAC"}
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* @module mcp-server/resources/definitions/gbif-species
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import { JsonRpcErrorCode, McpError, validationError } from '@cyanheads/mcp-ts-core/errors';
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import { getGbifService } from '../../../services/gbif/gbif-service.js';
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export const gbifSpeciesResource = resource('gbif://species/{taxonKey}', {
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name: 'gbif-species',
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acceptedKey: z.number().optional().describe('Accepted taxon key when synonym.'),
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accepted: z.string().optional().describe('Accepted name when synonym.'),
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}),
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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 key, or gbif_search_species to browse.',
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},
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],
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async handler(params, ctx) {
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const taxonKey = parseInt(params.taxonKey, 10);
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if (Number.isNaN(taxonKey)) {
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throw validationError(`Invalid taxon key: "${params.taxonKey}". Must be a numeric backbone key.`);
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}
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ctx.log.debug('Fetching species resource', { taxonKey });
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let raw;
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try {
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raw = await getGbifService().getSpecies(taxonKey, ctx);
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}
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catch (err) {
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// Map the upstream GBIF 404 envelope to a clean domain not_found, mirroring
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// gbif_get_species — the service throws before the !raw.key check can run.
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if (err instanceof McpError && err.code === JsonRpcErrorCode.NotFound) {
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throw ctx.fail('not_found', `Taxon key ${taxonKey} not found in the GBIF backbone.`, {
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...ctx.recoveryFor('not_found'),
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});
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}
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throw err;
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}
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if (!raw.key) {
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throw
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throw ctx.fail('not_found', `Taxon key ${taxonKey} not found in the GBIF backbone.`, {
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...ctx.recoveryFor('not_found'),
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});
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}
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return {
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-
{"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;
|
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1
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+
{"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,gBAAgB,EAAE,QAAQ,EAAE,eAAe,EAAE,MAAM,+BAA+B,CAAC;AAC5F,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAGjE,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,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,mDAAmD;YACzD,QAAQ,EACN,qGAAqG;SACxG;KACF;IAED,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,CACnB,uBAAuB,MAAM,CAAC,QAAQ,oCAAoC,CAC3E,CAAC;QACJ,CAAC;QACD,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2BAA2B,EAAE,EAAE,QAAQ,EAAE,CAAC,CAAC;QACzD,IAAI,GAAqB,CAAC;QAC1B,IAAI,CAAC;YACH,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,UAAU,CAAC,QAAQ,EAAE,GAAG,CAAC,CAAC;QACzD,CAAC;QAAC,OAAO,GAAG,EAAE,CAAC;YACb,4EAA4E;YAC5E,2EAA2E;YAC3E,IAAI,GAAG,YAAY,QAAQ,IAAI,GAAG,CAAC,IAAI,KAAK,gBAAgB,CAAC,QAAQ,EAAE,CAAC;gBACtE,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,aAAa,QAAQ,kCAAkC,EAAE;oBACnF,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;iBAChC,CAAC,CAAC;YACL,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC;QAED,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC;YACb,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,aAAa,QAAQ,kCAAkC,EAAE;gBACnF,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;aAChC,CAAC,CAAC;QACL,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"}
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@@ -6,6 +6,7 @@ import { z } from '@cyanheads/mcp-ts-core';
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6
6
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import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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export declare const gbifGetDataset: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
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datasetKey: z.ZodString;
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contactLimit: z.ZodDefault<z.ZodNumber>;
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}, z.core.$strip>, z.ZodObject<{
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key: z.ZodOptional<z.ZodString>;
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title: z.ZodOptional<z.ZodString>;
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@@ -24,6 +25,8 @@ export declare const gbifGetDataset: import("@cyanheads/mcp-ts-core").ToolDefini
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organization: z.ZodOptional<z.ZodString>;
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email: z.ZodOptional<z.ZodArray<z.ZodString>>;
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}, z.core.$strip>>>;
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contactsTotal: z.ZodOptional<z.ZodNumber>;
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+
contactsReturned: z.ZodOptional<z.ZodNumber>;
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}, z.core.$strip>, readonly [{
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readonly reason: "not_found";
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readonly code: JsonRpcErrorCode.NotFound;
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"gbif-get-dataset.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-dataset.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;AAK3E,eAAO,MAAM,cAAc
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1
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+
{"version":3,"file":"gbif-get-dataset.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-dataset.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;AAK3E,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAkKzB,CAAC"}
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@@ -10,12 +10,20 @@ export const gbifGetDataset = tool('gbif_get_dataset', {
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10
10
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title: 'Get Dataset',
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description: 'Fetch full dataset metadata by UUID key — title, description, citation text, contacts, license, ' +
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12
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'DOI, numConstituents (sub-datasets), and temporal/geographic coverage. Use after gbif_search_datasets ' +
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-
"or when an occurrence record's datasetKey needs provenance detail."
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"or when an occurrence record's datasetKey needs provenance detail. " +
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'Contacts are capped by contactLimit (default 10); contactsTotal and contactsReturned report the full count.',
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annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: false },
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15
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input: z.object({
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datasetKey: z
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.string()
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.describe('Dataset UUID from gbif_search_datasets or an occurrence record.'),
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+
contactLimit: z
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.number()
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+
.int()
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23
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.min(0)
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.max(100)
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+
.default(10)
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+
.describe('Maximum number of contacts to include (default 10, max 100). Set to 0 to omit contact detail while still reporting contactsTotal — useful when citation, license, and record count are all you need from a high-contact dataset like eBird.'),
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27
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}),
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20
28
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output: z.object({
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21
29
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key: z.string().optional().describe('Dataset UUID.'),
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@@ -54,7 +62,15 @@ export const gbifGetDataset = tool('gbif_get_dataset', {
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54
62
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})
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55
63
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.describe('A dataset contact with role, name, organization, and email.'))
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|
.optional()
|
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57
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-
.describe('Dataset contacts.
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65
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+
.describe('Dataset contacts, capped at contactLimit. Absent when the dataset has no contacts or contactLimit is 0.'),
|
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66
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+
contactsTotal: z
|
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67
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+
.number()
|
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68
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+
.optional()
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69
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+
.describe('Total contacts on the dataset before applying contactLimit. Present when the dataset has any contacts.'),
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+
contactsReturned: z
|
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71
|
+
.number()
|
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72
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+
.optional()
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73
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+
.describe('Number of contacts included in this response (≤ contactLimit). Present when the dataset has any contacts.'),
|
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58
74
|
}),
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59
75
|
errors: [
|
|
60
76
|
{
|
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@@ -83,7 +99,9 @@ export const gbifGetDataset = tool('gbif_get_dataset', {
|
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83
99
|
...ctx.recoveryFor('not_found'),
|
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});
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}
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-
const
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102
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+
const allContacts = raw.contacts ?? [];
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103
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+
const contactsTotal = allContacts.length;
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104
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+
const contacts = allContacts.slice(0, input.contactLimit).map((c) => ({
|
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87
105
|
type: c.type,
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88
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firstName: c.firstName,
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89
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lastName: c.lastName,
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@@ -101,7 +119,10 @@ export const gbifGetDataset = tool('gbif_get_dataset', {
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101
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publishingCountry: raw.publishingCountry,
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102
120
|
recordCount: raw.numRecords ?? raw.recordCount,
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103
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|
numConstituents: raw.numConstituents,
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104
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-
contacts: contacts
|
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122
|
+
contacts: contacts.length ? contacts : undefined,
|
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123
|
+
// Report the full count whenever the dataset has contacts, so contactLimit: 0
|
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124
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+
// suppresses the detail while preserving how many exist.
|
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125
|
+
...(contactsTotal > 0 && { contactsTotal, contactsReturned: contacts.length }),
|
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105
126
|
};
|
|
106
127
|
},
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|
107
128
|
format: (result) => {
|
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@@ -125,9 +146,9 @@ export const gbifGetDataset = tool('gbif_get_dataset', {
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125
146
|
lines.push(`\n**Citation:**\n> ${result.citationText}`);
|
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126
147
|
if (result.description)
|
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127
148
|
lines.push(`\n${result.description}`);
|
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128
|
-
if (result.
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|
129
|
-
lines.push(
|
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130
|
-
for (const c of result.contacts) {
|
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149
|
+
if (result.contactsTotal != null) {
|
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150
|
+
lines.push(`\n**Contacts:** ${result.contactsReturned ?? 0} of ${result.contactsTotal}`);
|
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151
|
+
for (const c of result.contacts ?? []) {
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131
152
|
const name = [c.firstName, c.lastName].filter(Boolean).join(' ');
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153
|
const typeLabel = c.type ? ` [${c.type}]` : '';
|
|
133
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|
lines.push(`- ${name || '(unnamed)'}${typeLabel}`);
|
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"gbif-get-dataset.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-dataset.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,OAAO,EAAE,SAAS,EAAE,MAAM,aAAa,CAAC;AAExC,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,kBAAkB,EAAE;IACrD,KAAK,EAAE,aAAa;IACpB,WAAW,EACT,kGAAkG;QAClG,wGAAwG;QACxG,
|
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1
|
+
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"gbif-get-species.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-species.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;
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1
|
+
{"version":3,"file":"gbif-get-species.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-species.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;AAK3E,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA6LzB,CAAC"}
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@@ -5,6 +5,7 @@
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|
|
5
5
|
import { tool, z } from '@cyanheads/mcp-ts-core';
|
|
6
6
|
import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
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7
7
|
import { getGbifService } from '../../../services/gbif/gbif-service.js';
|
|
8
|
+
import { stripHtml } from '../utils.js';
|
|
8
9
|
export const gbifGetSpecies = tool('gbif_get_species', {
|
|
9
10
|
title: 'Get Species Record',
|
|
10
11
|
description: 'Fetch a single backbone taxon by its GBIF taxon key. Returns full classification, authorship, ' +
|
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@@ -101,7 +102,8 @@ export const gbifGetSpecies = tool('gbif_get_species', {
|
|
|
101
102
|
taxonomicStatus: raw.taxonomicStatus,
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|
102
103
|
numDescendants: raw.numDescendants,
|
|
103
104
|
numOccurrences: raw.numOccurrences,
|
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104
|
-
|
|
105
|
+
// GBIF embeds HTML (e.g. <em>) in the original-description citation; strip to plain text.
|
|
106
|
+
publishedIn: raw.publishedIn ? stripHtml(raw.publishedIn) : undefined,
|
|
105
107
|
kingdom: raw.kingdom,
|
|
106
108
|
phylum: raw.phylum,
|
|
107
109
|
// GBIF API uses 'clazz' to avoid reserved word; we normalize to 'class'
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gbif-get-species.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-species.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
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/gbif-biodiversity-mcp-server",
|
|
3
|
-
"version": "0.
|
|
3
|
+
"version": "0.3.0",
|
|
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",
|
package/server.json
CHANGED
|
@@ -12,14 +12,14 @@
|
|
|
12
12
|
"url": "https://gbif-biodiversity.caseyjhand.com/mcp"
|
|
13
13
|
}
|
|
14
14
|
],
|
|
15
|
-
"version": "0.
|
|
15
|
+
"version": "0.3.0",
|
|
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.
|
|
22
|
+
"version": "0.3.0",
|
|
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.
|
|
51
|
+
"version": "0.3.0",
|
|
52
52
|
"packageArguments": [
|
|
53
53
|
{
|
|
54
54
|
"type": "positional",
|