@cyanheads/gbif-biodiversity-mcp-server 0.2.0

package/LICENSE

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package/README.md

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+<div align="center">
+  <h1>@cyanheads/gbif-biodiversity-mcp-server</h1>
+  <p><b>Search GBIF species taxonomy, occurrence records, datasets, and publishers via MCP. STDIO or Streamable HTTP.</b>
+  <div>12 Tools • 2 Resources</div>
+  </p>
+</div>
+
+<div align="center">
+
+[![Version](https://img.shields.io/badge/Version-0.2.0-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/)
+
+</div>
+
+<div align="center">
+
+[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/gbif-biodiversity-mcp-server/releases/latest/download/gbif-biodiversity-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=gbif-biodiversity-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvZ2JpZi1iaW9kaXZlcnNpdHktbWNwLXNlcnZlciJdfQ==) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22gbif-biodiversity-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads%2Fgbif-biodiversity-mcp-server%22%5D%7D)
+
+[![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
+
+**Public Hosted Server:** [https://gbif-biodiversity.caseyjhand.com/mcp](https://gbif-biodiversity.caseyjhand.com/mcp)
+
+</div>
+
+---
+
+## Tools
+
+12 tools for working with GBIF species taxonomy, occurrence records, datasets, and publishers:
+
+| Tool | Description |
+|:---|:---|
+| `gbif_match_species` | Match a species name against the GBIF backbone taxonomy — returns taxonKey, confidence score, and full classification |
+| `gbif_get_species` | Fetch a single backbone taxon by key — full classification, authorship, synonymy, vernacular name, descendant count |
+| `gbif_search_species` | Search or browse the GBIF backbone taxonomy by name fragment, rank, kingdom, family, or genus |
+| `gbif_get_species_classification` | Return the complete parent chain for a taxon — root-first ordered array from kingdom to immediate parent |
+| `gbif_get_species_children` | List direct children of a backbone taxon — genera within a family, species within a genus |
+| `gbif_search_occurrences` | Search 2.4B+ GBIF occurrence records with Darwin Core filters — country, bounding box, WKT geometry, year, month, basis of record |
+| `gbif_count_occurrences` | Count occurrences matching a filter without fetching records — fast single-number response |
+| `gbif_get_occurrence` | Fetch a single occurrence record by key — full Darwin Core record with GADM geography, media, and quality flags |
+| `gbif_occurrence_facets` | Aggregate occurrence counts by a dimension — country, year, basis of record, dataset, kingdom, and more |
+| `gbif_search_datasets` | Search GBIF datasets by keyword, type, country, or publishing organization |
+| `gbif_get_dataset` | Fetch full dataset metadata by UUID — title, description, citation, contacts, license, DOI, coverage |
+| `gbif_search_publishers` | Search GBIF-registered publishing organizations by name fragment or country |
+
+### `gbif_match_species`
+
+Match a scientific or common name against the GBIF backbone taxonomy.
+
+- Fuzzy matching handles minor typos and vernacular names; set `strict: true` for exact-only matching
+- Returns `taxonKey` — the backbone key required by `gbif_search_occurrences`, `gbif_count_occurrences`, and `gbif_occurrence_facets`
+- Confidence score 0–100; below 80 warrants review
+- Full classification hierarchy with keys at each rank: kingdom, phylum, class, order, family, genus, species
+- `matchType NONE` indicates no usable match — try removing strict mode or broadening the name
+- Resolves synonyms: always returns the accepted backbone key regardless of which name form was queried
+
+---
+
+### `gbif_get_species`
+
+Fetch a complete taxon record by GBIF backbone key.
+
+- Full classification, authorship string, and vernacular (English) name when available
+- `taxonomicStatus`: ACCEPTED, SYNONYM, DOUBTFUL — when SYNONYM, `acceptedKey` and `accepted` identify the current name
+- `numDescendants` and `numOccurrences` for scope at a glance
+- `extinct` field present only when explicitly flagged — not false on unlabeled taxa
+- `publishedIn` carries the original description citation when available
+
+---
+
+### `gbif_search_species`
+
+Search or browse the GBIF backbone taxonomy.
+
+- Accepts name fragments matching scientific and vernacular names
+- Filter by rank, kingdom, family, or genus to scope browsing
+- `isExtinct` filter for extinct vs. extant taxa
+- Scope to a specific checklist dataset with `datasetKey` (omit for the GBIF backbone)
+- Paginated — limit up to 1000, use offset to walk through large groups
+
+---
+
+### `gbif_get_species_classification`
+
+Return the full parent chain for a taxon as an ordered array.
+
+- Root-first (kingdom → phylum → class → order → family → genus → species → up to parent of queried taxon)
+- Each entry: rank, canonical name, scientific name, taxon key
+- Useful for building taxonomic trees or placing an unfamiliar taxon in context without manual backbone navigation
+
+---
+
+### `gbif_get_species_children`
+
+List direct children of a backbone taxon.
+
+- Genera within a family, species within a genus, subspecies within a species
+- Each child: key, name, rank, taxonomic status, common name, occurrence count, descendant count
+- Paginated — limit up to 1000, iterate with offset for large groups like Coleoptera
+
+---
+
+### `gbif_search_occurrences`
+
+Search 2.4B+ GBIF occurrence records with full Darwin Core filtering.
+
+- Use `taxonKey` from `gbif_match_species` for reliable results — resolves synonyms automatically; `scientificName` filter does not
+- Geographic filters: `country` (ISO 3166-1 alpha-2), bounding box (`decimalLatitude`/`decimalLongitude` ranges as "min,max"), or WKT polygon (`geometry`)
+- Temporal filters: `year` as single year or range, `month` (1–12) for seasonal queries
+- `basisOfRecord` enum: `HUMAN_OBSERVATION`, `PRESERVED_SPECIMEN`, `MACHINE_OBSERVATION`, and more
+- `hasCoordinate` to require or exclude georeferenced records
+- Pagination capped at offset+limit ≈ 100,000 — use `gbif_occurrence_facets` for aggregate analysis beyond this
+
+---
+
+### `gbif_count_occurrences`
+
+Count occurrences matching a filter without fetching any records.
+
+- Backed by the lightweight `/occurrence/count` endpoint — fast single-number response
+- Supported filters: `taxonKey`, `country`, `isGeoreferenced`, `datasetKey`, `year`
+- Use to assess result set size before deciding whether to paginate a full search
+
+---
+
+### `gbif_get_occurrence`
+
+Fetch a single occurrence record by GBIF occurrence key.
+
+- Complete Darwin Core record — all coordinate fields, GADM administrative geography (continent, country, state/province, locality), dates
+- Collections metadata: institution code, collection code, catalog number
+- Collector and identifier names, individual count, sex, life stage
+- Associated media (images, audio, video) with URLs and license
+- GBIF data quality issue flags for provenance assessment
+
+---
+
+### `gbif_occurrence_facets`
+
+Aggregate occurrence counts across a dimension.
+
+- Facets: `COUNTRY`, `YEAR`, `BASIS_OF_RECORD`, `DATASET_KEY`, `KINGDOM_KEY`, `PHYLUM_KEY`, `CLASS_KEY`, `ORDER_KEY`, `FAMILY_KEY`, `GENUS_KEY`, `SPECIES_KEY`, `PUBLISHING_COUNTRY`, `MONTH`
+- Scope with `taxonKey`, `country`, `year`, `geometry`, or `basisOfRecord` filters
+- Returns top-N values (up to 100) ranked by count — no record payloads
+- Core tool for distribution analysis ("which countries have the most records?") and trend queries ("how has observation volume changed since 2010?")
+
+---
+
+### `gbif_search_datasets`
+
+Search GBIF datasets by keyword, type, country, or publishing organization.
+
+- Filters: free-text query, dataset type (`OCCURRENCE`, `CHECKLIST`, `METADATA`, `SAMPLING_EVENT`), publishing country, hosting organization UUID
+- Returns title, type, description, license, DOI, and record count
+- Use `hostingOrg` from `gbif_search_publishers` to scope to datasets from one organization
+- Paginated — limit up to 1000
+
+---
+
+### `gbif_get_dataset`
+
+Fetch full dataset metadata by UUID.
+
+- Full description, citation text (for academic reference), license, DOI
+- Contacts with role, name, organization, and email
+- `numConstituents` for aggregate datasets (e.g. iNaturalist, eBird)
+- Use after `gbif_search_datasets` or when an occurrence record's `datasetKey` needs provenance detail
+
+---
+
+### `gbif_search_publishers`
+
+Search organizations registered with GBIF.
+
+- Filter by name fragment or country
+- Returns organization key, title, and country — sufficient to chain into `gbif_search_datasets` with `hostingOrg`
+- Paginated — limit up to 1000
+
+## Resources
+
+| Type | Name | Description |
+|:---|:---|:---|
+| Resource | `gbif://species/{taxonKey}` | Taxon record from the GBIF backbone — classification, authorship, synonymy status, vernacular name |
+| Resource | `gbif://dataset/{datasetKey}` | Dataset metadata — title, description, citation, license, contacts, coverage |
+
+## Features
+
+Built on [`@cyanheads/mcp-ts-core`](https://github.com/cyanheads/mcp-ts-core):
+
+- Declarative tool definitions — single file per tool, framework handles registration and validation
+- Unified error handling across all tools
+- Pluggable auth (`none`, `jwt`, `oauth`)
+- Swappable storage backends: `in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`
+- Structured logging with optional OpenTelemetry tracing
+- Runs locally (stdio/HTTP) or on Cloudflare Workers from the same codebase
+
+GBIF-specific:
+
+- Full GBIF REST API v1 coverage: species taxonomy, occurrences, datasets, and publishers
+- `gbif_match_species` as the entry point — resolves synonyms to backbone taxon keys used throughout
+- Occurrence pagination cap detection with `paginationNote` — redirects to facet aggregation before hitting the ~100,000 row limit
+- WKT polygon geometry support for geographic occurrence queries
+- Darwin Core field mapping with explicit provenance on sparse upstream fields
+
+Agent-friendly output:
+
+- `gbif_match_species` is the mandatory first step — all downstream tools document which key they expect
+- Graceful sparse-field handling — optional fields absent from the API response are omitted rather than null-filled
+- Discriminated error contracts with typed reasons, structured recovery hints, and `when` documentation per tool
+
+## Getting started
+
+### Self-Hosted / Local
+
+Add the following to your MCP client configuration file.
+
+```json
+{
+  "mcpServers": {
+    "gbif": {
+      "type": "stdio",
+      "command": "bunx",
+      "args": ["@cyanheads/gbif-biodiversity-mcp-server@latest"],
+      "env": {
+        "MCP_TRANSPORT_TYPE": "stdio",
+        "MCP_LOG_LEVEL": "info"
+      }
+    }
+  }
+}
+```
+
+Or with npx (no Bun required):
+
+```json
+{
+  "mcpServers": {
+    "gbif": {
+      "type": "stdio",
+      "command": "npx",
+      "args": ["-y", "@cyanheads/gbif-biodiversity-mcp-server@latest"],
+      "env": {
+        "MCP_TRANSPORT_TYPE": "stdio",
+        "MCP_LOG_LEVEL": "info"
+      }
+    }
+  }
+}
+```
+
+Or with Docker:
+
+```json
+{
+  "mcpServers": {
+    "gbif": {
+      "type": "stdio",
+      "command": "docker",
+      "args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/gbif-biodiversity-mcp-server:latest"]
+    }
+  }
+}
+```
+
+For Streamable HTTP, set the transport and start the server:
+
+```sh
+MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
+# Server listens at http://localhost:3010/mcp
+```
+
+### Prerequisites
+
+- [Bun v1.3.2](https://bun.sh/) or higher.
+- Optional: [GBIF API key](https://www.gbif.org/developer/summary) for higher rate limits.
+
+### Installation
+
+1. **Clone the repository:**
+
+```sh
+git clone https://github.com/cyanheads/gbif-biodiversity-mcp-server.git
+```
+
+2. **Navigate into the directory:**
+
+```sh
+cd gbif-biodiversity-mcp-server
+```
+
+3. **Install dependencies:**
+
+```sh
+bun install
+```
+
+## Configuration
+
+All configuration is validated at startup via Zod schemas in `src/config/server-config.ts`. Key environment variables:
+
+| Variable | Description | Default |
+|:---|:---|:---|
+| `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http` | `stdio` |
+| `MCP_HTTP_PORT` | HTTP server port | `3010` |
+| `MCP_HTTP_ENDPOINT_PATH` | HTTP endpoint path where the MCP server is mounted | `/mcp` |
+| `MCP_PUBLIC_URL` | Public origin override for TLS-terminating reverse-proxy deployments | none |
+| `MCP_AUTH_MODE` | Authentication: `none`, `jwt`, or `oauth` | `none` |
+| `MCP_LOG_LEVEL` | Log level (`debug`, `info`, `warning`, `error`, etc.) | `info` |
+| `MCP_GC_PRESSURE_INTERVAL_MS` | Opt-in Bun-only forced-GC pressure loop (ms). Try `60000` if RSS grows under sustained HTTP load. | `0` (disabled) |
+| `LOGS_DIR` | Directory for log files (Node.js only) | `<project-root>/logs` |
+| `STORAGE_PROVIDER_TYPE` | Storage backend: `in-memory`, `filesystem`, `supabase`, `cloudflare-kv/r2/d1` | `in-memory` |
+| `GBIF_API_KEY` | GBIF API key. Sent as HTTP Basic Auth username for higher rate limits. | none |
+| `GBIF_BASE_URL` | GBIF API base URL override | `https://api.gbif.org/v1` |
+| `GBIF_REQUEST_TIMEOUT_MS` | HTTP request timeout in milliseconds | `10000` |
+| `OTEL_ENABLED` | Enable OpenTelemetry | `false` |
+
+## Running the server
+
+### Local development
+
+- **Build and run the production version**:
+
+  ```sh
+  # One-time build
+  bun run rebuild
+
+  # Run the built server
+  bun run start:http
+  # or
+  bun run start:stdio
+  ```
+
+- **Run checks and tests**:
+  ```sh
+  bun run devcheck  # Lints, formats, type-checks, and more
+  bun run test      # Runs the test suite
+  ```
+
+## Project structure
+
+| Directory | Purpose |
+|:---|:---|
+| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). Twelve tools across species taxonomy, occurrences, datasets, and publishers. |
+| `src/mcp-server/resources` | Resource definitions. Species and dataset stable-URI resources. |
+| `src/services/gbif` | GBIF REST API service layer — client, request handling, type definitions. |
+| `src/config` | Server-specific environment variable parsing and validation with Zod. |
+| `tests/` | Unit and integration tests, mirroring the `src/` structure. |
+
+## Development guide
+
+See [`CLAUDE.md`](./CLAUDE.md) for development guidelines and architectural rules. The short version:
+
+- Handlers throw, framework catches — no `try/catch` in tool logic
+- Use `ctx.log` for logging, `ctx.state` for storage
+- Register new tools and resources in the `createApp()` arrays
+
+## Contributing
+
+Issues and pull requests are welcome. Run checks and tests before submitting:
+
+```sh
+bun run devcheck
+bun run test
+```
+
+## License
+
+This project is licensed under the Apache 2.0 License. See the [LICENSE](./LICENSE) file for details.

package/dist/config/server-config.d.ts

@@ -0,0 +1,14 @@
+/**
+ * @fileoverview Server-specific configuration for gbif-biodiversity-mcp-server.
+ * @module config/server-config
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+declare const ServerConfigSchema: z.ZodObject<{
+    apiKey: z.ZodOptional<z.ZodString>;
+    baseUrl: z.ZodDefault<z.ZodString>;
+    requestTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+}, z.core.$strip>;
+type ServerConfig = z.infer<typeof ServerConfigSchema>;
+export declare function getServerConfig(): ServerConfig;
+export {};
+//# sourceMappingURL=server-config.d.ts.map

package/dist/config/server-config.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,QAAA,MAAM,kBAAkB;;;;iBAYtB,CAAC;AAEH,KAAK,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAIvD,wBAAgB,eAAe,IAAI,YAAY,CAO9C"}

package/dist/config/server-config.js

@@ -0,0 +1,27 @@
+/**
+ * @fileoverview Server-specific configuration for gbif-biodiversity-mcp-server.
+ * @module config/server-config
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { parseEnvConfig } from '@cyanheads/mcp-ts-core/config';
+const ServerConfigSchema = z.object({
+    apiKey: z
+        .string()
+        .optional()
+        .describe('GBIF API key for higher rate limits. Sent as HTTP Basic Auth username with empty password.'),
+    baseUrl: z.string().default('https://api.gbif.org/v1').describe('GBIF API base URL.'),
+    requestTimeoutMs: z.coerce
+        .number()
+        .default(10_000)
+        .describe('HTTP request timeout in milliseconds.'),
+});
+let _config;
+export function getServerConfig() {
+    _config ??= parseEnvConfig(ServerConfigSchema, {
+        apiKey: 'GBIF_API_KEY',
+        baseUrl: 'GBIF_BASE_URL',
+        requestTimeoutMs: 'GBIF_REQUEST_TIMEOUT_MS',
+    });
+    return _config;
+}
+//# sourceMappingURL=server-config.js.map

package/dist/config/server-config.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"server-config.js","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,+BAA+B,CAAC;AAE/D,MAAM,kBAAkB,GAAG,CAAC,CAAC,MAAM,CAAC;IAClC,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,4FAA4F,CAC7F;IACH,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,CAAC,yBAAyB,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;IACrF,gBAAgB,EAAE,CAAC,CAAC,MAAM;SACvB,MAAM,EAAE;SACR,OAAO,CAAC,MAAM,CAAC;SACf,QAAQ,CAAC,uCAAuC,CAAC;CACrD,CAAC,CAAC;AAIH,IAAI,OAAiC,CAAC;AAEtC,MAAM,UAAU,eAAe;IAC7B,OAAO,KAAK,cAAc,CAAC,kBAAkB,EAAE;QAC7C,MAAM,EAAE,cAAc;QACtB,OAAO,EAAE,eAAe;QACxB,gBAAgB,EAAE,yBAAyB;KAC5C,CAAC,CAAC;IACH,OAAO,OAAO,CAAC;AACjB,CAAC"}

package/dist/index.d.ts

@@ -0,0 +1,7 @@
+#!/usr/bin/env node
+/**
+ * @fileoverview gbif-biodiversity-mcp-server MCP server entry point.
+ * @module index
+ */
+export {};
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;GAGG"}