@cyanheads/gbif-biodiversity-mcp-server 0.5.0 → 0.5.1

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Files changed (28) hide show
  1. package/CLAUDE.md +2 -2
  2. package/Dockerfile +10 -6
  3. package/README.md +4 -2
  4. package/dist/mcp-server/resources/definitions/gbif-dataset.resource.d.ts +16 -0
  5. package/dist/mcp-server/resources/definitions/gbif-dataset.resource.d.ts.map +1 -1
  6. package/dist/mcp-server/resources/definitions/gbif-dataset.resource.js +61 -1
  7. package/dist/mcp-server/resources/definitions/gbif-dataset.resource.js.map +1 -1
  8. package/dist/mcp-server/resources/definitions/gbif-species.resource.js +1 -1
  9. package/dist/mcp-server/tools/definitions/gbif-get-dataset.tool.d.ts +7 -0
  10. package/dist/mcp-server/tools/definitions/gbif-get-dataset.tool.d.ts.map +1 -1
  11. package/dist/mcp-server/tools/definitions/gbif-get-dataset.tool.js +41 -14
  12. package/dist/mcp-server/tools/definitions/gbif-get-dataset.tool.js.map +1 -1
  13. package/dist/mcp-server/tools/definitions/gbif-get-occurrence.tool.d.ts +21 -0
  14. package/dist/mcp-server/tools/definitions/gbif-get-occurrence.tool.d.ts.map +1 -1
  15. package/dist/mcp-server/tools/definitions/gbif-get-occurrence.tool.js +77 -0
  16. package/dist/mcp-server/tools/definitions/gbif-get-occurrence.tool.js.map +1 -1
  17. package/dist/mcp-server/tools/definitions/gbif-get-species.tool.d.ts.map +1 -1
  18. package/dist/mcp-server/tools/definitions/gbif-get-species.tool.js +19 -2
  19. package/dist/mcp-server/tools/definitions/gbif-get-species.tool.js.map +1 -1
  20. package/dist/mcp-server/tools/definitions/gbif-search-species.tool.js +1 -1
  21. package/dist/mcp-server/tools/utils.d.ts +34 -0
  22. package/dist/mcp-server/tools/utils.d.ts.map +1 -1
  23. package/dist/mcp-server/tools/utils.js +41 -0
  24. package/dist/mcp-server/tools/utils.js.map +1 -1
  25. package/dist/services/gbif/types.d.ts +25 -4
  26. package/dist/services/gbif/types.d.ts.map +1 -1
  27. package/package.json +6 -5
  28. 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:** 0.5.0
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- **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
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+ **Version:** 0.5.1
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+ **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.14`
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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
package/Dockerfile CHANGED
@@ -4,15 +4,17 @@
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  # This stage installs all dependencies (including dev), builds the TypeScript
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  # source code into JavaScript, and prepares the production assets.
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  # ==============================================================================
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- FROM oven/bun:1.3 AS build
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+ FROM oven/bun:1.3.14 AS build
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  WORKDIR /usr/src/app
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  # Copy dependency manifests for optimized layer caching
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  COPY package.json bun.lock ./
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- # Install all dependencies (including dev dependencies for building)
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- RUN bun install --frozen-lockfile
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+ # Install all dependencies (including dev dependencies for building).
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+ # The BuildKit cache mount persists Bun's global package cache across builds.
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+ RUN --mount=type=cache,target=/root/.bun/install/cache \
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+ bun install --frozen-lockfile --ignore-scripts
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  # Copy the rest of the source code
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  COPY . .
@@ -28,7 +30,7 @@ RUN bun run build
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  # application. It uses a slim base image and only includes production
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  # dependencies and build artifacts.
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  # ==============================================================================
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- FROM oven/bun:1.3-slim AS production
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+ FROM oven/bun:1.3.14-slim AS production
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  WORKDIR /usr/src/app
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@@ -49,13 +51,15 @@ COPY package.json bun.lock ./
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  # Install only production dependencies, ignoring any lifecycle scripts (like 'prepare')
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  # that are not needed in the final production image.
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- RUN bun install --production --frozen-lockfile --ignore-scripts
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+ RUN --mount=type=cache,target=/root/.bun/install/cache \
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+ bun install --production --frozen-lockfile --ignore-scripts
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  # Conditionally install OpenTelemetry optional peer dependencies (Tier 3).
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  # These are not bundled by default to keep the base image lean. Enable at build time
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  # with: docker build --build-arg OTEL_ENABLED=true
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  ARG OTEL_ENABLED=true
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- RUN if [ "$OTEL_ENABLED" = "true" ]; then \
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+ RUN --mount=type=cache,target=/root/.bun/install/cache \
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+ if [ "$OTEL_ENABLED" = "true" ]; then \
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  bun add @hono/otel \
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  @opentelemetry/instrumentation-http \
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  @opentelemetry/exporter-metrics-otlp-http \
package/README.md CHANGED
@@ -7,7 +7,7 @@
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7
 
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  <div align="center">
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9
 
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- [![Version](https://img.shields.io/badge/Version-0.5.0-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/)
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+ [![Version](https://img.shields.io/badge/Version-0.5.1-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-v1.3.14-blueviolet.svg?style=flat-square)](https://bun.sh/)
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11
 
12
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  </div>
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13
 
@@ -138,7 +138,8 @@ Count occurrences matching a filter without fetching any records.
138
138
 
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  Fetch a single occurrence record by GBIF occurrence key.
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- - Complete Darwin Core record — all coordinate fields, GADM administrative geography (continent, country, state/province, locality), dates
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+ - Complete Darwin Core record — all coordinate fields, administrative geography (continent, country, state/province, locality), dates
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+ - `occurrenceID`, full classification (`class`/`classKey`), GADM administrative units (levels 0–2, each with a stable GID and name), and source `identifiers`
142
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  - Collections metadata: institution code, collection code, catalog number
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  - Collector and identifier names, individual count, sex, life stage
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  - Associated media (images, audio, video) with URLs and license
@@ -174,6 +175,7 @@ Fetch full dataset metadata by UUID.
174
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  - Full description, citation text (for academic reference), license, DOI
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  - Contacts with role, name, organization, and email
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+ - Temporal and geographic coverage ranges when the publisher declares them
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  - `numConstituents` for aggregate datasets (e.g. iNaturalist, eBird)
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  - Use after `gbif_search_datasets` or when an occurrence record's `datasetKey` needs provenance detail
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package/dist/mcp-server/resources/definitions/gbif-dataset.resource.d.ts CHANGED
@@ -17,6 +17,22 @@ 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>;
20
+ contacts: z.ZodOptional<z.ZodArray<z.ZodObject<{
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+ type: z.ZodOptional<z.ZodString>;
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+ firstName: z.ZodOptional<z.ZodString>;
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+ lastName: z.ZodOptional<z.ZodString>;
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+ organization: z.ZodOptional<z.ZodString>;
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+ email: z.ZodOptional<z.ZodArray<z.ZodString>>;
26
+ }, z.core.$strip>>>;
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+ contactsTotal: z.ZodOptional<z.ZodNumber>;
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+ contactsReturned: z.ZodOptional<z.ZodNumber>;
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+ temporalCoverages: z.ZodOptional<z.ZodArray<z.ZodObject<{
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+ start: z.ZodOptional<z.ZodString>;
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+ end: z.ZodOptional<z.ZodString>;
32
+ }, z.core.$strip>>>;
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+ geographicCoverages: z.ZodOptional<z.ZodArray<z.ZodObject<{
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+ description: z.ZodOptional<z.ZodString>;
35
+ }, z.core.$strip>>>;
20
36
  }, z.core.$strip>, readonly [{
21
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  readonly reason: "not_found";
22
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  readonly code: JsonRpcErrorCode.NotFound;
package/dist/mcp-server/resources/definitions/gbif-dataset.resource.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"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"}
1
+ {"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;AAgB3E,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAkI9B,CAAC"}
package/dist/mcp-server/resources/definitions/gbif-dataset.resource.js CHANGED
@@ -4,8 +4,13 @@
4
4
  */
5
5
  import { resource, z } from '@cyanheads/mcp-ts-core';
6
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  import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
7
- import { stripHtml } from '../../../mcp-server/tools/utils.js';
7
+ import { compactGeographicCoverages, compactTemporalCoverages, projectContacts, stripHtml, } from '../../../mcp-server/tools/utils.js';
8
8
  import { getGbifService } from '../../../services/gbif/gbif-service.js';
9
+ /**
10
+ * Fixed contact cap for the resource. The resource has no contactLimit input (unlike
11
+ * gbif_get_dataset), so it applies a constant cap while still reporting the full count.
12
+ */
13
+ const CONTACT_CAP = 10;
9
14
  export const gbifDatasetResource = resource('gbif://dataset/{datasetKey}', {
10
15
  name: 'gbif-dataset',
11
16
  title: 'GBIF Dataset',
@@ -27,6 +32,58 @@ export const gbifDatasetResource = resource('gbif://dataset/{datasetKey}', {
27
32
  publishingCountry: z.string().optional().describe('Publishing organization country.'),
28
33
  recordCount: z.number().optional().describe('Number of records. May be absent.'),
29
34
  numConstituents: z.number().optional().describe('Number of sub-datasets. May be absent.'),
35
+ contacts: z
36
+ .array(z
37
+ .object({
38
+ type: z
39
+ .string()
40
+ .optional()
41
+ .describe('Contact type (e.g., ADMINISTRATIVE_POINT_OF_CONTACT). May be absent.'),
42
+ firstName: z.string().optional().describe('First name. May be absent.'),
43
+ lastName: z.string().optional().describe('Last name. May be absent.'),
44
+ organization: z.string().optional().describe('Organization name. May be absent.'),
45
+ email: z
46
+ .array(z.string())
47
+ .optional()
48
+ .describe('Contact email addresses. May be absent.'),
49
+ })
50
+ .describe('A dataset contact with role, name, organization, and email.'))
51
+ .optional()
52
+ .describe('Dataset contacts, capped at 10. Absent when the dataset has no contacts.'),
53
+ contactsTotal: z
54
+ .number()
55
+ .optional()
56
+ .describe('Total contacts before the cap. Present when the dataset has any contacts.'),
57
+ contactsReturned: z
58
+ .number()
59
+ .optional()
60
+ .describe('Number of contacts included (≤ 10). Present when the dataset has any contacts.'),
61
+ temporalCoverages: z
62
+ .array(z
63
+ .object({
64
+ start: z
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+ .string()
66
+ .optional()
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+ .describe('Coverage start as an ISO 8601 date-time. May be absent.'),
68
+ end: z
69
+ .string()
70
+ .optional()
71
+ .describe('Coverage end as an ISO 8601 date-time. May be absent.'),
72
+ })
73
+ .describe('A temporal coverage range.'))
74
+ .optional()
75
+ .describe('Temporal coverage ranges declared by the dataset. May be absent.'),
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+ geographicCoverages: z
77
+ .array(z
78
+ .object({
79
+ description: z
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+ .string()
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+ .optional()
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+ .describe('Geographic coverage description (e.g. "Worldwide"). May be absent.'),
83
+ })
84
+ .describe('A geographic coverage entry.'))
85
+ .optional()
86
+ .describe('Geographic coverage descriptions declared by the dataset. May be absent.'),
30
87
  }),
31
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  errors: [
32
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  {
@@ -68,6 +125,9 @@ export const gbifDatasetResource = resource('gbif://dataset/{datasetKey}', {
68
125
  publishingCountry: raw.publishingCountry,
69
126
  recordCount: raw.numRecords ?? raw.recordCount,
70
127
  numConstituents: raw.numConstituents,
128
+ ...projectContacts(raw.contacts, CONTACT_CAP),
129
+ temporalCoverages: compactTemporalCoverages(raw.temporalCoverages),
130
+ geographicCoverages: compactGeographicCoverages(raw.geographicCoverages),
71
131
  };
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  },
73
133
  });
package/dist/mcp-server/resources/definitions/gbif-dataset.resource.js.map CHANGED
@@ -1 +1 @@
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1
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package/dist/mcp-server/resources/definitions/gbif-species.resource.js CHANGED
@@ -76,7 +76,7 @@ export const gbifSpeciesResource = resource('gbif://species/{taxonKey}', {
76
76
  taxonomicStatus: raw.taxonomicStatus,
77
77
  kingdom: raw.kingdom,
78
78
  phylum: raw.phylum,
79
- class: raw.clazz,
79
+ class: raw.class,
80
80
  order: raw.order,
81
81
  family: raw.family,
82
82
  genus: raw.genus,
package/dist/mcp-server/tools/definitions/gbif-get-dataset.tool.d.ts CHANGED
@@ -27,6 +27,13 @@ export declare const gbifGetDataset: import("@cyanheads/mcp-ts-core").ToolDefini
27
27
  }, z.core.$strip>>>;
28
28
  contactsTotal: z.ZodOptional<z.ZodNumber>;
29
29
  contactsReturned: z.ZodOptional<z.ZodNumber>;
30
+ temporalCoverages: z.ZodOptional<z.ZodArray<z.ZodObject<{
31
+ start: z.ZodOptional<z.ZodString>;
32
+ end: z.ZodOptional<z.ZodString>;
33
+ }, z.core.$strip>>>;
34
+ geographicCoverages: z.ZodOptional<z.ZodArray<z.ZodObject<{
35
+ description: z.ZodOptional<z.ZodString>;
36
+ }, z.core.$strip>>>;
30
37
  }, z.core.$strip>, readonly [{
31
38
  readonly reason: "not_found";
32
39
  readonly code: JsonRpcErrorCode.NotFound;
package/dist/mcp-server/tools/definitions/gbif-get-dataset.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"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"}
1
+ {"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;AAU3E,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA+LzB,CAAC"}
package/dist/mcp-server/tools/definitions/gbif-get-dataset.tool.js CHANGED
@@ -5,7 +5,7 @@
5
5
  import { tool, z } from '@cyanheads/mcp-ts-core';
6
6
  import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
7
7
  import { getGbifService } from '../../../services/gbif/gbif-service.js';
8
- import { stripHtml } from '../utils.js';
8
+ import { compactGeographicCoverages, compactTemporalCoverages, projectContacts, stripHtml, } from '../utils.js';
9
9
  export const gbifGetDataset = tool('gbif_get_dataset', {
10
10
  title: 'Get Dataset',
11
11
  description: 'Fetch full dataset metadata by UUID key — title, description, citation text, contacts, license, ' +
@@ -71,6 +71,32 @@ export const gbifGetDataset = tool('gbif_get_dataset', {
71
71
  .number()
72
72
  .optional()
73
73
  .describe('Number of contacts included in this response (≤ contactLimit). Present when the dataset has any contacts.'),
74
+ temporalCoverages: z
75
+ .array(z
76
+ .object({
77
+ start: z
78
+ .string()
79
+ .optional()
80
+ .describe('Coverage start as an ISO 8601 date-time. May be absent.'),
81
+ end: z
82
+ .string()
83
+ .optional()
84
+ .describe('Coverage end as an ISO 8601 date-time. May be absent.'),
85
+ })
86
+ .describe('A temporal coverage range.'))
87
+ .optional()
88
+ .describe('Temporal coverage ranges declared by the dataset. May be absent.'),
89
+ geographicCoverages: z
90
+ .array(z
91
+ .object({
92
+ description: z
93
+ .string()
94
+ .optional()
95
+ .describe('Geographic coverage description (e.g. "Worldwide"). May be absent.'),
96
+ })
97
+ .describe('A geographic coverage entry.'))
98
+ .optional()
99
+ .describe('Geographic coverage descriptions declared by the dataset. May be absent.'),
74
100
  }),
75
101
  errors: [
76
102
  {
@@ -99,15 +125,6 @@ export const gbifGetDataset = tool('gbif_get_dataset', {
99
125
  ...ctx.recoveryFor('not_found'),
100
126
  });
101
127
  }
102
- const allContacts = raw.contacts ?? [];
103
- const contactsTotal = allContacts.length;
104
- const contacts = allContacts.slice(0, input.contactLimit).map((c) => ({
105
- type: c.type,
106
- firstName: c.firstName,
107
- lastName: c.lastName,
108
- organization: c.organization,
109
- email: c.email?.length ? c.email : undefined,
110
- }));
111
128
  return {
112
129
  key: raw.key,
113
130
  title: raw.title,
@@ -119,10 +136,11 @@ export const gbifGetDataset = tool('gbif_get_dataset', {
119
136
  publishingCountry: raw.publishingCountry,
120
137
  recordCount: raw.numRecords ?? raw.recordCount,
121
138
  numConstituents: raw.numConstituents,
122
- contacts: contacts.length ? contacts : undefined,
123
- // Report the full count whenever the dataset has contacts, so contactLimit: 0
124
- // suppresses the detail while preserving how many exist.
125
- ...(contactsTotal > 0 && { contactsTotal, contactsReturned: contacts.length }),
139
+ // contactLimit: 0 suppresses contact detail while projectContacts still reports
140
+ // contactsTotal/contactsReturned, so callers learn the dataset has contacts.
141
+ ...projectContacts(raw.contacts, input.contactLimit),
142
+ temporalCoverages: compactTemporalCoverages(raw.temporalCoverages),
143
+ geographicCoverages: compactGeographicCoverages(raw.geographicCoverages),
126
144
  };
127
145
  },
128
146
  format: (result) => {
@@ -142,6 +160,15 @@ export const gbifGetDataset = tool('gbif_get_dataset', {
142
160
  lines.push(`**Records:** ${result.recordCount.toLocaleString()}`);
143
161
  if (result.numConstituents != null)
144
162
  lines.push(`**Constituent datasets:** ${result.numConstituents}`);
163
+ if (result.temporalCoverages?.length) {
164
+ const ranges = result.temporalCoverages.map((t) => `${t.start ?? '?'} → ${t.end ?? '?'}`);
165
+ lines.push(`**Temporal coverage:** ${ranges.join('; ')}`);
166
+ }
167
+ if (result.geographicCoverages?.length) {
168
+ const descs = result.geographicCoverages.map((g) => g.description).filter(Boolean);
169
+ if (descs.length > 0)
170
+ lines.push(`**Geographic coverage:** ${descs.join('; ')}`);
171
+ }
145
172
  if (result.citationText)
146
173
  lines.push(`\n**Citation:**\n> ${result.citationText}`);
147
174
  if (result.description)
package/dist/mcp-server/tools/definitions/gbif-get-dataset.tool.js.map CHANGED
@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/gbif-get-occurrence.tool.d.ts CHANGED
@@ -9,11 +9,14 @@ export declare const gbifGetOccurrence: import("@cyanheads/mcp-ts-core").ToolDef
9
9
  }, z.core.$strip>, z.ZodObject<{
10
10
  key: z.ZodOptional<z.ZodNumber>;
11
11
  datasetKey: z.ZodOptional<z.ZodString>;
12
+ occurrenceID: z.ZodOptional<z.ZodString>;
12
13
  taxonKey: z.ZodOptional<z.ZodNumber>;
13
14
  scientificName: z.ZodOptional<z.ZodString>;
14
15
  canonicalName: z.ZodOptional<z.ZodString>;
15
16
  kingdom: z.ZodOptional<z.ZodString>;
16
17
  phylum: z.ZodOptional<z.ZodString>;
18
+ class: z.ZodOptional<z.ZodString>;
19
+ classKey: z.ZodOptional<z.ZodNumber>;
17
20
  order: z.ZodOptional<z.ZodString>;
18
21
  family: z.ZodOptional<z.ZodString>;
19
22
  genus: z.ZodOptional<z.ZodString>;
@@ -27,6 +30,20 @@ export declare const gbifGetOccurrence: import("@cyanheads/mcp-ts-core").ToolDef
27
30
  countryCode: z.ZodOptional<z.ZodString>;
28
31
  stateProvince: z.ZodOptional<z.ZodString>;
29
32
  locality: z.ZodOptional<z.ZodString>;
33
+ gadm: z.ZodOptional<z.ZodObject<{
34
+ level0: z.ZodOptional<z.ZodObject<{
35
+ gid: z.ZodOptional<z.ZodString>;
36
+ name: z.ZodOptional<z.ZodString>;
37
+ }, z.core.$strip>>;
38
+ level1: z.ZodOptional<z.ZodObject<{
39
+ gid: z.ZodOptional<z.ZodString>;
40
+ name: z.ZodOptional<z.ZodString>;
41
+ }, z.core.$strip>>;
42
+ level2: z.ZodOptional<z.ZodObject<{
43
+ gid: z.ZodOptional<z.ZodString>;
44
+ name: z.ZodOptional<z.ZodString>;
45
+ }, z.core.$strip>>;
46
+ }, z.core.$strip>>;
30
47
  publishingCountry: z.ZodOptional<z.ZodString>;
31
48
  eventDate: z.ZodOptional<z.ZodString>;
32
49
  year: z.ZodOptional<z.ZodNumber>;
@@ -49,6 +66,10 @@ export declare const gbifGetOccurrence: import("@cyanheads/mcp-ts-core").ToolDef
49
66
  title: z.ZodOptional<z.ZodString>;
50
67
  license: z.ZodOptional<z.ZodString>;
51
68
  }, z.core.$strip>>>;
69
+ identifiers: z.ZodOptional<z.ZodArray<z.ZodObject<{
70
+ type: z.ZodOptional<z.ZodString>;
71
+ identifier: z.ZodOptional<z.ZodString>;
72
+ }, z.core.$strip>>>;
52
73
  }, z.core.$strip>, readonly [{
53
74
  readonly reason: "not_found";
54
75
  readonly code: JsonRpcErrorCode.NotFound;
package/dist/mcp-server/tools/definitions/gbif-get-occurrence.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"gbif-get-occurrence.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-occurrence.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,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA8O5B,CAAC"}
1
+ {"version":3,"file":"gbif-get-occurrence.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/gbif-get-occurrence.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;AA8B3E,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA2S5B,CAAC"}
package/dist/mcp-server/tools/definitions/gbif-get-occurrence.tool.js CHANGED
@@ -5,6 +5,27 @@
5
5
  import { tool, z } from '@cyanheads/mcp-ts-core';
6
6
  import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
7
7
  import { getGbifService } from '../../../services/gbif/gbif-service.js';
8
+ /** Output schema for one GADM administrative level. A fresh instance per call keeps the emitted JSON Schema inline (no $ref). */
9
+ const gadmLevel = () => z.object({
10
+ gid: z
11
+ .string()
12
+ .optional()
13
+ .describe('GADM GID — stable administrative-unit identifier (e.g. SWE, SWE.2_1). May be absent.'),
14
+ name: z.string().optional().describe('Administrative-unit name. May be absent.'),
15
+ });
16
+ /** Keep a GADM level only when it carries a gid or name; drop empty placeholders. */
17
+ const compactLevel = (l) => l && (l.gid || l.name) ? { gid: l.gid, name: l.name } : undefined;
18
+ /** Project the raw GADM object to gid/name at levels 0–2; undefined when no level carries data. */
19
+ const compactGadm = (g) => {
20
+ if (!g)
21
+ return;
22
+ const level0 = compactLevel(g.level0);
23
+ const level1 = compactLevel(g.level1);
24
+ const level2 = compactLevel(g.level2);
25
+ if (!level0 && !level1 && !level2)
26
+ return;
27
+ return { level0, level1, level2 };
28
+ };
8
29
  export const gbifGetOccurrence = tool('gbif_get_occurrence', {
9
30
  title: 'Get Occurrence Record',
10
31
  description: 'Fetch a single occurrence record by its GBIF occurrence key. Returns the complete Darwin Core ' +
@@ -18,11 +39,17 @@ export const gbifGetOccurrence = tool('gbif_get_occurrence', {
18
39
  output: z.object({
19
40
  key: z.number().optional().describe('GBIF occurrence key.'),
20
41
  datasetKey: z.string().optional().describe('UUID of the source dataset.'),
42
+ occurrenceID: z
43
+ .string()
44
+ .optional()
45
+ .describe('Darwin Core occurrenceID — the source record identifier, often a URL back to the origin record. May be absent.'),
21
46
  taxonKey: z.number().optional().describe('Backbone taxon key.'),
22
47
  scientificName: z.string().optional().describe('Scientific name from occurrence record.'),
23
48
  canonicalName: z.string().optional().describe('Canonical name without authorship.'),
24
49
  kingdom: z.string().optional().describe('Kingdom classification.'),
25
50
  phylum: z.string().optional().describe('Phylum classification.'),
51
+ class: z.string().optional().describe('Class classification. May be absent.'),
52
+ classKey: z.number().optional().describe('Backbone taxon key for the class. May be absent.'),
26
53
  order: z.string().optional().describe('Order classification.'),
27
54
  family: z.string().optional().describe('Family classification.'),
28
55
  genus: z.string().optional().describe('Genus classification.'),
@@ -45,6 +72,14 @@ export const gbifGetOccurrence = tool('gbif_get_occurrence', {
45
72
  countryCode: z.string().optional().describe('ISO 3166-1 alpha-2 country code. May be absent.'),
46
73
  stateProvince: z.string().optional().describe('State or province. May be absent.'),
47
74
  locality: z.string().optional().describe('Locality description. May be absent.'),
75
+ gadm: z
76
+ .object({
77
+ level0: gadmLevel().optional().describe('GADM level 0 — country. May be absent.'),
78
+ level1: gadmLevel().optional().describe('GADM level 1 — state/province. May be absent.'),
79
+ level2: gadmLevel().optional().describe('GADM level 2 — county/district. May be absent.'),
80
+ })
81
+ .optional()
82
+ .describe('GADM administrative geography — stable GIDs and names at levels 0–2. May be absent.'),
48
83
  publishingCountry: z
49
84
  .string()
50
85
  .optional()
@@ -87,6 +122,18 @@ export const gbifGetOccurrence = tool('gbif_get_occurrence', {
87
122
  .describe('A media item (image, audio, video) associated with the occurrence.'))
88
123
  .optional()
89
124
  .describe('Associated media (images, audio, video). May be absent.'),
125
+ identifiers: z
126
+ .array(z
127
+ .object({
128
+ type: z
129
+ .string()
130
+ .optional()
131
+ .describe('Identifier type (e.g. URL, DOI, GBIF_PORTAL). May be absent.'),
132
+ identifier: z.string().optional().describe('The identifier value. May be absent.'),
133
+ })
134
+ .describe('An alternative identifier for the occurrence record.'))
135
+ .optional()
136
+ .describe('Alternative record identifiers from the source. May be absent.'),
90
137
  }),
91
138
  errors: [
92
139
  {
@@ -118,11 +165,14 @@ export const gbifGetOccurrence = tool('gbif_get_occurrence', {
118
165
  return {
119
166
  key: raw.key,
120
167
  datasetKey: raw.datasetKey,
168
+ occurrenceID: raw.occurrenceID,
121
169
  taxonKey: raw.taxonKey,
122
170
  scientificName: raw.scientificName,
123
171
  canonicalName: raw.canonicalName,
124
172
  kingdom: raw.kingdom,
125
173
  phylum: raw.phylum,
174
+ class: raw.class,
175
+ classKey: raw.classKey,
126
176
  order: raw.order,
127
177
  family: raw.family,
128
178
  genus: raw.genus,
@@ -136,6 +186,7 @@ export const gbifGetOccurrence = tool('gbif_get_occurrence', {
136
186
  countryCode: raw.countryCode,
137
187
  stateProvince: raw.stateProvince,
138
188
  locality: raw.locality,
189
+ gadm: compactGadm(raw.gadm),
139
190
  publishingCountry: raw.publishingCountry,
140
191
  eventDate: raw.eventDate,
141
192
  year: raw.year,
@@ -160,6 +211,9 @@ export const gbifGetOccurrence = tool('gbif_get_occurrence', {
160
211
  license: m.license,
161
212
  }))
162
213
  : undefined,
214
+ identifiers: raw.identifiers?.length
215
+ ? raw.identifiers.map((id) => ({ type: id.type, identifier: id.identifier }))
216
+ : undefined,
163
217
  };
164
218
  },
165
219
  format: (result) => {
@@ -183,6 +237,10 @@ export const gbifGetOccurrence = tool('gbif_get_occurrence', {
183
237
  taxParts.push(`Kingdom: ${result.kingdom}`);
184
238
  if (result.phylum)
185
239
  taxParts.push(`Phylum: ${result.phylum}`);
240
+ if (result.class)
241
+ taxParts.push(`Class: ${result.class}${result.classKey != null ? ` (${result.classKey})` : ''}`);
242
+ else if (result.classKey != null)
243
+ taxParts.push(`Class key: ${result.classKey}`);
186
244
  if (result.order)
187
245
  taxParts.push(`Order: ${result.order}`);
188
246
  if (result.family)
@@ -225,6 +283,16 @@ export const gbifGetOccurrence = tool('gbif_get_occurrence', {
225
283
  lines.push(`**Location:** ${geo.join(', ')}${result.countryCode ? ` (${result.countryCode})` : ''}`);
226
284
  else if (result.countryCode)
227
285
  lines.push(`**Country code:** ${result.countryCode}`);
286
+ if (result.gadm) {
287
+ const gadmParts = [];
288
+ for (const lvl of [result.gadm.level0, result.gadm.level1, result.gadm.level2]) {
289
+ if (lvl?.name || lvl?.gid) {
290
+ gadmParts.push(`${lvl.name ?? ''}${lvl.gid ? ` (${lvl.gid})` : ''}`.trim());
291
+ }
292
+ }
293
+ if (gadmParts.length > 0)
294
+ lines.push(`**GADM:** ${gadmParts.join(' › ')}`);
295
+ }
228
296
  if (result.recordedBy)
229
297
  lines.push(`**Recorded by:** ${result.recordedBy}`);
230
298
  if (result.identifiedBy)
@@ -242,6 +310,8 @@ export const gbifGetOccurrence = tool('gbif_get_occurrence', {
242
310
  lines.push(`**Collection:** ${result.collectionCode}`);
243
311
  if (result.catalogNumber)
244
312
  lines.push(`**Catalog number:** ${result.catalogNumber}`);
313
+ if (result.occurrenceID)
314
+ lines.push(`**Occurrence ID:** ${result.occurrenceID}`);
245
315
  if (result.datasetKey)
246
316
  lines.push(`**Dataset key:** ${result.datasetKey}`);
247
317
  if (result.publishingCountry)
@@ -256,6 +326,13 @@ export const gbifGetOccurrence = tool('gbif_get_occurrence', {
256
326
  lines.push(` - ${mediaType}${mediaTitle}${mediaFmt}${mediaLicense}${m.identifier ? `: ${m.identifier}` : ''}`);
257
327
  }
258
328
  }
329
+ if (result.identifiers?.length) {
330
+ lines.push(`\n**Identifiers:** ${result.identifiers.length} item(s)`);
331
+ for (const id of result.identifiers) {
332
+ const idType = id.type ? `[${id.type}] ` : '';
333
+ lines.push(` - ${idType}${id.identifier ?? '(no value)'}`);
334
+ }
335
+ }
259
336
  if (result.issues?.length)
260
337
  lines.push(`\n**Quality issues:** ${result.issues.join(', ')}`);
261
338
  return [{ type: 'text', text: lines.join('\n') }];
package/dist/mcp-server/tools/definitions/gbif-get-occurrence.tool.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/mcp-server/tools/definitions/gbif-get-species.tool.d.ts.map CHANGED
@@ -1 +1 @@
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"}
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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAyMzB,CAAC"}
package/dist/mcp-server/tools/definitions/gbif-get-species.tool.js CHANGED
@@ -106,8 +106,7 @@ export const gbifGetSpecies = tool('gbif_get_species', {
106
106
  publishedIn: raw.publishedIn ? stripHtml(raw.publishedIn) : undefined,
107
107
  kingdom: raw.kingdom,
108
108
  phylum: raw.phylum,
109
- // GBIF API uses 'clazz' to avoid reserved word; we normalize to 'class'
110
- class: raw.clazz,
109
+ class: raw.class,
111
110
  order: raw.order,
112
111
  family: raw.family,
113
112
  genus: raw.genus,
@@ -160,21 +159,39 @@ export const gbifGetSpecies = tool('gbif_get_species', {
160
159
  }
161
160
  if (result.publishedIn)
162
161
  lines.push(`**Published in:** ${result.publishedIn}`);
162
+ // Each rank renders "Name (key)" when the name is present, and a key-only entry when the
163
+ // name is absent but GBIF still supplies the key (sparse records, e.g. Panthera leo's classKey
164
+ // with no class name). Mirrors this file's accepted/parent key-only fallback so text-only
165
+ // clients never lose the rank key that structuredContent already carries.
163
166
  const classificationParts = [];
164
167
  if (result.kingdom)
165
168
  classificationParts.push(`Kingdom: ${result.kingdom}${result.kingdomKey ? ` (${result.kingdomKey})` : ''}`);
169
+ else if (result.kingdomKey != null)
170
+ classificationParts.push(`Kingdom key: ${result.kingdomKey}`);
166
171
  if (result.phylum)
167
172
  classificationParts.push(`Phylum: ${result.phylum}${result.phylumKey ? ` (${result.phylumKey})` : ''}`);
173
+ else if (result.phylumKey != null)
174
+ classificationParts.push(`Phylum key: ${result.phylumKey}`);
168
175
  if (result.class)
169
176
  classificationParts.push(`Class: ${result.class}${result.classKey ? ` (${result.classKey})` : ''}`);
177
+ else if (result.classKey != null)
178
+ classificationParts.push(`Class key: ${result.classKey}`);
170
179
  if (result.order)
171
180
  classificationParts.push(`Order: ${result.order}${result.orderKey ? ` (${result.orderKey})` : ''}`);
181
+ else if (result.orderKey != null)
182
+ classificationParts.push(`Order key: ${result.orderKey}`);
172
183
  if (result.family)
173
184
  classificationParts.push(`Family: ${result.family}${result.familyKey ? ` (${result.familyKey})` : ''}`);
185
+ else if (result.familyKey != null)
186
+ classificationParts.push(`Family key: ${result.familyKey}`);
174
187
  if (result.genus)
175
188
  classificationParts.push(`Genus: ${result.genus}${result.genusKey ? ` (${result.genusKey})` : ''}`);
189
+ else if (result.genusKey != null)
190
+ classificationParts.push(`Genus key: ${result.genusKey}`);
176
191
  if (result.species)
177
192
  classificationParts.push(`Species: ${result.species}${result.speciesKey ? ` (${result.speciesKey})` : ''}`);
193
+ else if (result.speciesKey != null)
194
+ classificationParts.push(`Species key: ${result.speciesKey}`);
178
195
  if (classificationParts.length > 0) {
179
196
  lines.push(`**Classification:** ${classificationParts.join(' › ')}`);
180
197
  }
package/dist/mcp-server/tools/definitions/gbif-get-species.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/gbif-search-species.tool.js CHANGED
@@ -105,7 +105,7 @@ export const gbifSearchSpecies = tool('gbif_search_species', {
105
105
  taxonomicStatus: r.taxonomicStatus,
106
106
  kingdom: r.kingdom,
107
107
  phylum: r.phylum,
108
- class: r.clazz,
108
+ class: r.class,
109
109
  order: r.order,
110
110
  family: r.family,
111
111
  genus: r.genus,
package/dist/mcp-server/tools/utils.d.ts CHANGED
@@ -2,6 +2,40 @@
2
2
  * @fileoverview Shared utilities for tool definitions.
3
3
  * @module mcp-server/tools/utils
4
4
  */
5
+ import type { RawContact, RawGeographicCoverage, RawTemporalCoverage } from '../../services/gbif/types.js';
6
+ /**
7
+ * Project raw dataset contacts to a `limit`-capped, compact list plus total/returned counts.
8
+ * Shared by `gbif_get_dataset` (caller-supplied `contactLimit`) and the `gbif://dataset/{key}`
9
+ * resource (fixed cap). `contactsTotal`/`contactsReturned` are included only when the dataset
10
+ * has any contacts, so callers can spread the result directly into their output object.
11
+ */
12
+ export declare function projectContacts(raw: RawContact[] | undefined, limit: number): {
13
+ contactsTotal?: number;
14
+ contactsReturned?: number;
15
+ contacts: {
16
+ type: string | undefined;
17
+ firstName: string | undefined;
18
+ lastName: string | undefined;
19
+ organization: string | undefined;
20
+ email: string[] | undefined;
21
+ }[] | undefined;
22
+ };
23
+ /**
24
+ * Project raw dataset temporal coverages to compact `{ start, end }` ranges, keeping only
25
+ * entries that carry at least one bound (GBIF also emits verbatim/single-date shapes we skip).
26
+ * Returns undefined when nothing survives, so the field is omitted rather than empty.
27
+ */
28
+ export declare function compactTemporalCoverages(raw: RawTemporalCoverage[] | undefined): {
29
+ start: string | undefined;
30
+ end: string | undefined;
31
+ }[] | undefined;
32
+ /**
33
+ * Project raw dataset geographic coverages to compact `{ description }` entries, keeping only
34
+ * those that carry a description. Returns undefined when nothing survives.
35
+ */
36
+ export declare function compactGeographicCoverages(raw: RawGeographicCoverage[] | undefined): {
37
+ description: string | undefined;
38
+ }[] | undefined;
5
39
  /** Strip HTML tags and decode common entities. */
6
40
  export declare function stripHtml(html: string): string;
7
41
  //# sourceMappingURL=utils.d.ts.map
package/dist/mcp-server/tools/utils.d.ts.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["../../../src/mcp-server/tools/utils.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,KAAK,EACV,UAAU,EACV,qBAAqB,EACrB,mBAAmB,EACpB,MAAM,0BAA0B,CAAC;AAElC;;;;;GAKG;AACH,wBAAgB,eAAe,CAAC,GAAG,EAAE,UAAU,EAAE,GAAG,SAAS,EAAE,KAAK,EAAE,MAAM;;;;;;;;;;EAa3E;AAED;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,GAAG,EAAE,mBAAmB,EAAE,GAAG,SAAS;;;gBAK9E;AAED;;;GAGG;AACH,wBAAgB,0BAA0B,CAAC,GAAG,EAAE,qBAAqB,EAAE,GAAG,SAAS;;gBAKlF;AAED,kDAAkD;AAClD,wBAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAa9C"}
package/dist/mcp-server/tools/utils.js CHANGED
@@ -2,6 +2,47 @@
2
2
  * @fileoverview Shared utilities for tool definitions.
3
3
  * @module mcp-server/tools/utils
4
4
  */
5
+ /**
6
+ * Project raw dataset contacts to a `limit`-capped, compact list plus total/returned counts.
7
+ * Shared by `gbif_get_dataset` (caller-supplied `contactLimit`) and the `gbif://dataset/{key}`
8
+ * resource (fixed cap). `contactsTotal`/`contactsReturned` are included only when the dataset
9
+ * has any contacts, so callers can spread the result directly into their output object.
10
+ */
11
+ export function projectContacts(raw, limit) {
12
+ const all = raw ?? [];
13
+ const contacts = all.slice(0, limit).map((c) => ({
14
+ type: c.type,
15
+ firstName: c.firstName,
16
+ lastName: c.lastName,
17
+ organization: c.organization,
18
+ email: c.email?.length ? c.email : undefined,
19
+ }));
20
+ return {
21
+ contacts: contacts.length ? contacts : undefined,
22
+ ...(all.length > 0 && { contactsTotal: all.length, contactsReturned: contacts.length }),
23
+ };
24
+ }
25
+ /**
26
+ * Project raw dataset temporal coverages to compact `{ start, end }` ranges, keeping only
27
+ * entries that carry at least one bound (GBIF also emits verbatim/single-date shapes we skip).
28
+ * Returns undefined when nothing survives, so the field is omitted rather than empty.
29
+ */
30
+ export function compactTemporalCoverages(raw) {
31
+ const ranges = (raw ?? [])
32
+ .map((t) => ({ start: t.start, end: t.end }))
33
+ .filter((t) => t.start || t.end);
34
+ return ranges.length ? ranges : undefined;
35
+ }
36
+ /**
37
+ * Project raw dataset geographic coverages to compact `{ description }` entries, keeping only
38
+ * those that carry a description. Returns undefined when nothing survives.
39
+ */
40
+ export function compactGeographicCoverages(raw) {
41
+ const entries = (raw ?? [])
42
+ .map((g) => ({ description: g.description }))
43
+ .filter((g) => g.description);
44
+ return entries.length ? entries : undefined;
45
+ }
5
46
  /** Strip HTML tags and decode common entities. */
6
47
  export function stripHtml(html) {
7
48
  return html
package/dist/mcp-server/tools/utils.js.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"utils.js","sourceRoot":"","sources":["../../../src/mcp-server/tools/utils.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAQH;;;;;GAKG;AACH,MAAM,UAAU,eAAe,CAAC,GAA6B,EAAE,KAAa;IAC1E,MAAM,GAAG,GAAG,GAAG,IAAI,EAAE,CAAC;IACtB,MAAM,QAAQ,GAAG,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;QAC/C,IAAI,EAAE,CAAC,CAAC,IAAI;QACZ,SAAS,EAAE,CAAC,CAAC,SAAS;QACtB,QAAQ,EAAE,CAAC,CAAC,QAAQ;QACpB,YAAY,EAAE,CAAC,CAAC,YAAY;QAC5B,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,SAAS;KAC7C,CAAC,CAAC,CAAC;IACJ,OAAO;QACL,QAAQ,EAAE,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS;QAChD,GAAG,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,aAAa,EAAE,GAAG,CAAC,MAAM,EAAE,gBAAgB,EAAE,QAAQ,CAAC,MAAM,EAAE,CAAC;KACxF,CAAC;AACJ,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,wBAAwB,CAAC,GAAsC;IAC7E,MAAM,MAAM,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC;SACvB,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,GAAG,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;SAC5C,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC;IACnC,OAAO,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,SAAS,CAAC;AAC5C,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,0BAA0B,CAAC,GAAwC;IACjF,MAAM,OAAO,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC;SACxB,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,WAAW,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC;SAC5C,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC;IAChC,OAAO,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC;AAC9C,CAAC;AAED,kDAAkD;AAClD,MAAM,UAAU,SAAS,CAAC,IAAY;IACpC,OAAO,IAAI;SACR,OAAO,CAAC,UAAU,EAAE,GAAG,CAAC;SACxB,OAAO,CAAC,QAAQ,EAAE,GAAG,CAAC;SACtB,OAAO,CAAC,OAAO,EAAE,GAAG,CAAC;SACrB,OAAO,CAAC,OAAO,EAAE,GAAG,CAAC;SACrB,OAAO,CAAC,SAAS,EAAE,GAAG,CAAC;SACvB,OAAO,CAAC,QAAQ,EAAE,GAAG,CAAC;SACtB,OAAO,CAAC,QAAQ,EAAE,GAAG,CAAC;SACtB,OAAO,CAAC,QAAQ,EAAE,GAAG,CAAC;SACtB,OAAO,CAAC,QAAQ,EAAE,GAAG,CAAC;SACtB,OAAO,CAAC,MAAM,EAAE,GAAG,CAAC;SACpB,IAAI,EAAE,CAAC;AACZ,CAAC"}
package/dist/services/gbif/types.d.ts CHANGED
@@ -50,7 +50,7 @@ export type RawSpeciesRecord = {
50
50
  publishedIn?: string;
51
51
  kingdom?: string;
52
52
  phylum?: string;
53
- clazz?: string;
53
+ class?: string;
54
54
  order?: string;
55
55
  family?: string;
56
56
  genus?: string;
@@ -118,6 +118,7 @@ export type RawOccurrenceRecord = {
118
118
  canonicalName?: string;
119
119
  kingdom?: string;
120
120
  phylum?: string;
121
+ class?: string;
121
122
  order?: string;
122
123
  family?: string;
123
124
  genus?: string;
@@ -160,7 +161,18 @@ export type RawOccurrenceRecord = {
160
161
  issues?: string[];
161
162
  media?: RawMedia[];
162
163
  identifiers?: RawIdentifier[];
163
- gadm?: unknown;
164
+ gadm?: RawGadm;
165
+ };
166
+ /** A single GADM administrative level — stable GID plus the area name. */
167
+ export type RawGadmLevel = {
168
+ gid?: string;
169
+ name?: string;
170
+ };
171
+ /** GADM administrative geography nested on an occurrence (levels 0–2 used). */
172
+ export type RawGadm = {
173
+ level0?: RawGadmLevel;
174
+ level1?: RawGadmLevel;
175
+ level2?: RawGadmLevel;
164
176
  };
165
177
  export type RawMedia = {
166
178
  type?: string;
@@ -218,8 +230,8 @@ export type RawDatasetRecord = {
218
230
  modified?: string;
219
231
  deleted?: string;
220
232
  contacts?: RawContact[];
221
- temporalCoverages?: unknown[];
222
- geographicCoverages?: unknown[];
233
+ temporalCoverages?: RawTemporalCoverage[];
234
+ geographicCoverages?: RawGeographicCoverage[];
223
235
  };
224
236
  export type RawContact = {
225
237
  type?: string;
@@ -228,6 +240,15 @@ export type RawContact = {
228
240
  email?: string[];
229
241
  organization?: string;
230
242
  };
243
+ /** A temporal coverage range on a dataset (GBIF's `range`-shaped entry). */
244
+ export type RawTemporalCoverage = {
245
+ start?: string;
246
+ end?: string;
247
+ };
248
+ /** A geographic coverage entry on a dataset. */
249
+ export type RawGeographicCoverage = {
250
+ description?: string;
251
+ };
231
252
  export type RawDatasetSearchResponse = {
232
253
  offset?: number;
233
254
  limit?: number;
package/dist/services/gbif/types.d.ts.map CHANGED
@@ -1 +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": "0.5.0",
3
+ "version": "0.5.1",
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",
@@ -54,7 +54,7 @@
54
54
  "url": "https://github.com/cyanheads/gbif-biodiversity-mcp-server/issues"
55
55
  },
56
56
  "homepage": "https://github.com/cyanheads/gbif-biodiversity-mcp-server#readme",
57
- "author": "cyanheads <casey@caseyjhand.com> (https://github.com/cyanheads/gbif-biodiversity-mcp-server#readme)",
57
+ "author": "Casey Hand <casey@caseyjhand.com> (https://caseyjhand.com)",
58
58
  "funding": [
59
59
  {
60
60
  "type": "github",
@@ -66,21 +66,22 @@
66
66
  }
67
67
  ],
68
68
  "license": "Apache-2.0",
69
- "packageManager": "bun@1.3.2",
69
+ "packageManager": "bun@1.3.14",
70
70
  "engines": {
71
- "bun": ">=1.3.2",
71
+ "bun": ">=1.3.0",
72
72
  "node": ">=24.0.0"
73
73
  },
74
74
  "publishConfig": {
75
75
  "access": "public"
76
76
  },
77
77
  "dependencies": {
78
- "@cyanheads/mcp-ts-core": "^0.10.10",
78
+ "@cyanheads/mcp-ts-core": "^0.10.14",
79
79
  "pino-pretty": "^13.1.3",
80
80
  "zod": "^4.4.3"
81
81
  },
82
82
  "devDependencies": {
83
83
  "@biomejs/biome": "^2.5.0",
84
+ "@socketsecurity/bun-security-scanner": "^1.1.2",
84
85
  "@types/node": "^26.0.0",
85
86
  "depcheck": "^1.4.7",
86
87
  "ignore": "^7.0.5",
package/server.json CHANGED
@@ -12,14 +12,14 @@
12
12
  "url": "https://gbif-biodiversity.caseyjhand.com/mcp"
13
13
  }
14
14
  ],
15
- "version": "0.5.0",
15
+ "version": "0.5.1",
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": "0.5.0",
22
+ "version": "0.5.1",
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": "0.5.0",
51
+ "version": "0.5.1",
52
52
  "packageArguments": [
53
53
  {
54
54
  "type": "positional",