@cyanheads/gbif-biodiversity-mcp-server 0.2.6 → 0.2.8

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.
Files changed (11) hide show
  1. package/CLAUDE.md +4 -4
  2. package/Dockerfile +5 -0
  3. package/README.md +1 -1
  4. package/dist/index.js +3 -0
  5. package/dist/index.js.map +1 -1
  6. package/dist/mcp-server/tools/definitions/gbif-get-species-children.tool.d.ts +1 -0
  7. package/dist/mcp-server/tools/definitions/gbif-get-species-children.tool.d.ts.map +1 -1
  8. package/dist/mcp-server/tools/definitions/gbif-get-species-children.tool.js +3 -1
  9. package/dist/mcp-server/tools/definitions/gbif-get-species-children.tool.js.map +1 -1
  10. package/package.json +6 -6
  11. package/server.json +3 -3
package/CLAUDE.md CHANGED
@@ -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:** 0.2.6
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- **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
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+ **Version:** 0.2.8
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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
@@ -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 pack as `.mcpb` for one-click Claude Desktop install |
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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 CHANGED
@@ -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
@@ -95,5 +97,8 @@ ENV MCP_FORCE_CONSOLE_LOGGING="true"
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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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+
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  # The command to start the server
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  CMD ["bun", "run", "dist/index.js"]
package/README.md CHANGED
@@ -7,7 +7,7 @@
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  <div align="center">
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- [![Version](https://img.shields.io/badge/Version-0.2.6-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/gbif-biodiversity-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/gbif-biodiversity-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/gbif-biodiversity-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
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+ [![Version](https://img.shields.io/badge/Version-0.2.8-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/gbif-biodiversity-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/gbif-biodiversity-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/gbif-biodiversity-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
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  </div>
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package/dist/index.js CHANGED
@@ -25,6 +25,9 @@ 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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+ instructions: 'Use the gbif_* tools to query species taxonomy, occurrences, datasets, and publishers via the GBIF API. Keyless; an optional API key only raises rate limits. Resolve any name with gbif_match_species first — it returns the backbone taxonKey the occurrence tools expect and resolves synonyms, unlike the raw scientificName filter. Countries use ISO 3166-1 alpha-2; datasets and publishers are keyed by UUID, occurrences by integer key. Occurrence paging caps at offset+limit ≈ 100,000 — switch to gbif_occurrence_facets for larger aggregate analysis.',
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  tools: [
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  gbifMatchSpecies,
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  gbifGetSpecies,
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
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1
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package/dist/mcp-server/tools/definitions/gbif-get-species-children.tool.d.ts CHANGED
@@ -25,6 +25,7 @@ export declare const gbifGetSpeciesChildren: import("@cyanheads/mcp-ts-core").To
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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;
package/dist/mcp-server/tools/definitions/gbif-get-species-children.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
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package/dist/mcp-server/tools/definitions/gbif-get-species-children.tool.js CHANGED
@@ -49,6 +49,7 @@ export const gbifGetSpeciesChildren = tool('gbif_get_species_children', {
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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.'),
@@ -78,6 +79,7 @@ export const gbifGetSpeciesChildren = tool('gbif_get_species_children', {
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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;
@@ -94,7 +96,7 @@ export const gbifGetSpeciesChildren = tool('gbif_get_species_children', {
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  throw err;
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  }
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  }
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- ctx.enrich({ offset, limit, endOfRecords });
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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);
package/dist/mcp-server/tools/definitions/gbif-get-species-children.tool.js.map CHANGED
@@ -1 +1 @@
1
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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": "0.2.6",
3
+ "version": "0.2.8",
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",
@@ -76,17 +76,17 @@
76
76
  "access": "public"
77
77
  },
78
78
  "dependencies": {
79
- "@cyanheads/mcp-ts-core": "^0.9.21",
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
- "@biomejs/biome": "^2.4.16",
85
- "@types/node": "^25.9.1",
84
+ "@biomejs/biome": "^2.5.0",
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",
89
89
  "typescript": "^6.0.3",
90
- "vitest": "^4.1.8"
90
+ "vitest": "^4.1.9"
91
91
  }
92
92
  }
package/server.json CHANGED
@@ -12,14 +12,14 @@
12
12
  "url": "https://gbif-biodiversity.caseyjhand.com/mcp"
13
13
  }
14
14
  ],
15
- "version": "0.2.6",
15
+ "version": "0.2.8",
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": "0.2.6",
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+ "version": "0.2.8",
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  "packageArguments": [
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  {
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  "type": "positional",
@@ -48,7 +48,7 @@
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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",
51
- "version": "0.2.6",
51
+ "version": "0.2.8",
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  "packageArguments": [
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  {
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  "type": "positional",