@cyanheads/gbif-biodiversity-mcp-server 0.2.0

package/dist/services/gbif/types.d.ts

@@ -0,0 +1,254 @@
+/**
+ * @fileoverview Domain types for the GBIF API service.
+ * @module services/gbif/types
+ */
+export type TaxonomicRank = 'KINGDOM' | 'PHYLUM' | 'CLASS' | 'ORDER' | 'FAMILY' | 'GENUS' | 'SPECIES' | 'SUBSPECIES' | 'VARIETY' | 'FORM' | 'UNRANKED';
+export type TaxonomicStatus = 'ACCEPTED' | 'SYNONYM' | 'HOMOTYPIC_SYNONYM' | 'HETEROTYPIC_SYNONYM' | 'DOUBTFUL' | 'MISAPPLIED' | 'PROPARTE_SYNONYM';
+export type MatchType = 'EXACT' | 'FUZZY' | 'HIGHERORDER' | 'NONE';
+/** Raw response from /species/match */
+export type RawSpeciesMatch = {
+    usageKey?: number;
+    scientificName?: string;
+    canonicalName?: string;
+    rank?: string;
+    status?: string;
+    confidence?: number;
+    matchType?: string;
+    note?: string;
+    synonym?: boolean;
+    kingdom?: string;
+    phylum?: string;
+    class?: string;
+    order?: string;
+    family?: string;
+    genus?: string;
+    species?: string;
+    kingdomKey?: number;
+    phylumKey?: number;
+    classKey?: number;
+    orderKey?: number;
+    familyKey?: number;
+    genusKey?: number;
+    speciesKey?: number;
+};
+/** Raw response from /species/{key} */
+export type RawSpeciesRecord = {
+    key?: number;
+    nubKey?: number;
+    nameKey?: number;
+    scientificName?: string;
+    canonicalName?: string;
+    vernacularName?: string;
+    authorship?: string;
+    nameType?: string;
+    rank?: string;
+    origin?: string;
+    taxonomicStatus?: string;
+    nomenclaturalStatus?: string[];
+    numDescendants?: number;
+    numOccurrences?: number;
+    publishedIn?: string;
+    kingdom?: string;
+    phylum?: string;
+    clazz?: string;
+    order?: string;
+    family?: string;
+    genus?: string;
+    species?: string;
+    kingdomKey?: number;
+    phylumKey?: number;
+    classKey?: number;
+    orderKey?: number;
+    familyKey?: number;
+    genusKey?: number;
+    speciesKey?: number;
+    acceptedKey?: number;
+    accepted?: string;
+    parentKey?: number;
+    parent?: string;
+    basionymKey?: number;
+    basionym?: string;
+    extinct?: boolean;
+    marine?: boolean;
+    freshwater?: boolean;
+    terrestrial?: boolean;
+};
+/** Raw paginated response from /species/search */
+export type RawSpeciesSearchResponse = {
+    offset?: number;
+    limit?: number;
+    endOfRecords?: boolean;
+    count?: number;
+    results?: RawSpeciesRecord[];
+};
+/** Raw parent node from /species/{key}/parents */
+export type RawParentNode = {
+    key?: number;
+    rank?: string;
+    canonicalName?: string;
+    scientificName?: string;
+    nameKey?: number;
+};
+/** Raw children response from /species/{key}/children */
+export type RawChildrenResponse = {
+    offset?: number;
+    limit?: number;
+    endOfRecords?: boolean;
+    count?: number;
+    results?: RawSpeciesRecord[];
+};
+export type BasisOfRecord = 'HUMAN_OBSERVATION' | 'MACHINE_OBSERVATION' | 'PRESERVED_SPECIMEN' | 'LIVING_SPECIMEN' | 'MATERIAL_SAMPLE' | 'MATERIAL_CITATION' | 'OCCURRENCE' | 'LITERATURE';
+/** Raw occurrence record from /occurrence/search or /occurrence/{key} */
+export type RawOccurrenceRecord = {
+    key?: number;
+    datasetKey?: string;
+    occurrenceID?: string;
+    kingdomKey?: number;
+    phylumKey?: number;
+    classKey?: number;
+    orderKey?: number;
+    familyKey?: number;
+    genusKey?: number;
+    speciesKey?: number;
+    taxonKey?: number;
+    scientificName?: string;
+    canonicalName?: string;
+    kingdom?: string;
+    phylum?: string;
+    order?: string;
+    family?: string;
+    genus?: string;
+    species?: string;
+    genericName?: string;
+    specificEpithet?: string;
+    taxonRank?: string;
+    taxonomicStatus?: string;
+    decimalLatitude?: number;
+    decimalLongitude?: number;
+    coordinateUncertaintyInMeters?: number;
+    coordinatePrecision?: number;
+    continent?: string;
+    stateProvince?: string;
+    country?: string;
+    countryCode?: string;
+    locality?: string;
+    publishingCountry?: string;
+    elevation?: number;
+    elevationAccuracy?: number;
+    depth?: number;
+    eventDate?: string;
+    eventTime?: string;
+    year?: number;
+    month?: number;
+    day?: number;
+    basisOfRecord?: string;
+    institutionCode?: string;
+    collectionCode?: string;
+    catalogNumber?: string;
+    recordNumber?: string;
+    identifiedBy?: string;
+    recordedBy?: string;
+    individualCount?: number;
+    sex?: string;
+    lifeStage?: string;
+    establishmentMeans?: string;
+    iucnRedListCategory?: string;
+    datasetName?: string;
+    issues?: string[];
+    media?: RawMedia[];
+    identifiers?: RawIdentifier[];
+    gadm?: unknown;
+};
+export type RawMedia = {
+    type?: string;
+    format?: string;
+    identifier?: string;
+    title?: string;
+    description?: string;
+    license?: string;
+    rightsHolder?: string;
+    publisher?: string;
+    references?: string;
+    created?: string;
+};
+export type RawIdentifier = {
+    type?: string;
+    identifier?: string;
+};
+/** Raw search response from /occurrence/search */
+export type RawOccurrenceSearchResponse = {
+    offset?: number;
+    limit?: number;
+    endOfRecords?: boolean;
+    count?: number;
+    results?: RawOccurrenceRecord[];
+    facets?: RawFacet[];
+};
+export type RawFacet = {
+    field?: string;
+    counts?: Array<{
+        name?: string;
+        count?: number;
+    }>;
+};
+export type RawDatasetRecord = {
+    key?: string;
+    doi?: string;
+    type?: string;
+    title?: string;
+    description?: string;
+    citation?: {
+        text?: string;
+        identifier?: string;
+    };
+    license?: string;
+    publishingOrganizationKey?: string;
+    publishingCountry?: string;
+    hostingOrganizationKey?: string;
+    installationKey?: string;
+    numConstituents?: number;
+    numRecords?: number;
+    recordCount?: number;
+    createdBy?: string;
+    modifiedBy?: string;
+    created?: string;
+    modified?: string;
+    deleted?: string;
+    contacts?: RawContact[];
+    temporalCoverages?: unknown[];
+    geographicCoverages?: unknown[];
+};
+export type RawContact = {
+    type?: string;
+    firstName?: string;
+    lastName?: string;
+    email?: string[];
+    organization?: string;
+};
+export type RawDatasetSearchResponse = {
+    offset?: number;
+    limit?: number;
+    endOfRecords?: boolean;
+    count?: number;
+    results?: RawDatasetRecord[];
+};
+export type RawOrganizationRecord = {
+    key?: string;
+    title?: string;
+    description?: string;
+    country?: string;
+    city?: string;
+    latitude?: number;
+    longitude?: number;
+    endorsingNodeKey?: string;
+    endorsementApproved?: boolean;
+    contacts?: RawContact[];
+};
+export type RawOrganizationSearchResponse = {
+    offset?: number;
+    limit?: number;
+    endOfRecords?: boolean;
+    count?: number;
+    results?: RawOrganizationRecord[];
+};
+//# sourceMappingURL=types.d.ts.map

package/dist/services/gbif/types.d.ts.map

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package/dist/services/gbif/types.js

@@ -0,0 +1,6 @@
+/**
+ * @fileoverview Domain types for the GBIF API service.
+ * @module services/gbif/types
+ */
+export {};
+//# sourceMappingURL=types.js.map

package/dist/services/gbif/types.js.map

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package/package.json

@@ -0,0 +1,91 @@
+{
+  "name": "@cyanheads/gbif-biodiversity-mcp-server",
+  "version": "0.2.0",
+  "mcpName": "io.github.cyanheads/gbif-biodiversity-mcp-server",
+  "description": "Search GBIF species taxonomy, occurrence records, datasets, and publishers via MCP. STDIO or Streamable HTTP.",
+  "type": "module",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "bin": {
+    "gbif-biodiversity-mcp-server": "dist/index.js"
+  },
+  "files": ["dist/", "README.md", "LICENSE", "CLAUDE.md", "Dockerfile", "server.json"],
+  "scripts": {
+    "build": "bun run scripts/build.ts",
+    "rebuild": "bun run scripts/clean.ts && bun run build",
+    "clean": "bun run scripts/clean.ts",
+    "devcheck": "bun run scripts/devcheck.ts",
+    "tree": "bun run scripts/tree.ts",
+    "format": "biome check --write --unsafe",
+    "test": "bunx vitest run",
+    "audit:refresh": "rm -f bun.lock && bun install && bun audit",
+    "list-skills": "bun run scripts/list-skills.ts",
+    "lint:mcp": "bun run scripts/lint-mcp.ts",
+    "lint:packaging": "bun run scripts/lint-packaging.ts",
+    "bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/gbif-biodiversity-mcp-server.mcpb",
+    "changelog:build": "bun run scripts/build-changelog.ts",
+    "changelog:check": "bun run scripts/build-changelog.ts --check",
+    "publish-mcp": "mcp-publisher login github -token \"$(security find-generic-password -a \"$USER\" -s mcp-publisher-github-pat -w)\" && mcp-publisher publish",
+    "publish:compat": "cd dist && jq '.name = \"@cyanheads/gbif-mcp-server\"' package.json > tmp.json && mv tmp.json package.json && npm publish --access public && jq '.name = \"@cyanheads/gbif-biodiversity-mcp-server\"' package.json > tmp.json && mv tmp.json package.json",
+    "start:stdio": "MCP_TRANSPORT_TYPE=stdio bun ./dist/index.js",
+    "start:http": "MCP_TRANSPORT_TYPE=http bun ./dist/index.js"
+  },
+  "keywords": [
+    "mcp",
+    "mcp-server",
+    "model-context-protocol",
+    "typescript",
+    "bun",
+    "stdio",
+    "streamable-http",
+    "gbif",
+    "biodiversity",
+    "species",
+    "taxonomy",
+    "occurrences",
+    "darwin-core",
+    "natural-history"
+  ],
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/cyanheads/gbif-biodiversity-mcp-server.git"
+  },
+  "bugs": {
+    "url": "https://github.com/cyanheads/gbif-biodiversity-mcp-server/issues"
+  },
+  "homepage": "https://github.com/cyanheads/gbif-biodiversity-mcp-server#readme",
+  "author": "cyanheads <casey@caseyjhand.com> (https://github.com/cyanheads/gbif-biodiversity-mcp-server#readme)",
+  "funding": [
+    {
+      "type": "github",
+      "url": "https://github.com/sponsors/cyanheads"
+    },
+    {
+      "type": "buy_me_a_coffee",
+      "url": "https://www.buymeacoffee.com/cyanheads"
+    }
+  ],
+  "license": "Apache-2.0",
+  "packageManager": "bun@1.3.2",
+  "engines": {
+    "bun": ">=1.3.2",
+    "node": ">=24.0.0"
+  },
+  "publishConfig": {
+    "access": "public"
+  },
+  "dependencies": {
+    "@cyanheads/mcp-ts-core": "^0.9.9",
+    "pino-pretty": "^13.1.3",
+    "zod": "^4.4.3"
+  },
+  "devDependencies": {
+    "@biomejs/biome": "^2.4.15",
+    "@types/node": "^25.9.1",
+    "depcheck": "^1.4.7",
+    "ignore": "^7.0.5",
+    "tsc-alias": "^1.8.17",
+    "typescript": "^6.0.3",
+    "vitest": "^4.1.7"
+  }
+}

package/server.json

@@ -0,0 +1,117 @@
+{
+  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
+  "name": "io.github.cyanheads/gbif-biodiversity-mcp-server",
+  "description": "Search GBIF species taxonomy, occurrence records, datasets, and publishers.",
+  "repository": {
+    "url": "https://github.com/cyanheads/gbif-biodiversity-mcp-server",
+    "source": "github"
+  },
+  "remotes": [
+    {
+      "type": "streamable-http",
+      "url": "https://gbif-biodiversity.caseyjhand.com/mcp"
+    }
+  ],
+  "version": "0.2.0",
+  "packages": [
+    {
+      "registryType": "npm",
+      "registryBaseUrl": "https://registry.npmjs.org",
+      "identifier": "@cyanheads/gbif-biodiversity-mcp-server",
+      "runtimeHint": "bun",
+      "version": "0.2.0",
+      "packageArguments": [
+        {
+          "type": "positional",
+          "value": "run"
+        },
+        {
+          "type": "positional",
+          "value": "start:stdio"
+        }
+      ],
+      "environmentVariables": [
+        {
+          "name": "GBIF_API_KEY",
+          "description": "GBIF API key for higher rate limits. Sent as HTTP Basic Auth username.",
+          "format": "string",
+          "isRequired": false
+        },
+        {
+          "name": "MCP_LOG_LEVEL",
+          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').",
+          "format": "string",
+          "isRequired": false,
+          "default": "info"
+        }
+      ],
+      "transport": {
+        "type": "stdio"
+      }
+    },
+    {
+      "registryType": "npm",
+      "registryBaseUrl": "https://registry.npmjs.org",
+      "identifier": "@cyanheads/gbif-biodiversity-mcp-server",
+      "runtimeHint": "bun",
+      "version": "0.2.0",
+      "packageArguments": [
+        {
+          "type": "positional",
+          "value": "run"
+        },
+        {
+          "type": "positional",
+          "value": "start:http"
+        }
+      ],
+      "environmentVariables": [
+        {
+          "name": "GBIF_API_KEY",
+          "description": "GBIF API key for higher rate limits. Sent as HTTP Basic Auth username.",
+          "format": "string",
+          "isRequired": false
+        },
+        {
+          "name": "MCP_HTTP_HOST",
+          "description": "The hostname for the HTTP server.",
+          "format": "string",
+          "isRequired": false,
+          "default": "127.0.0.1"
+        },
+        {
+          "name": "MCP_HTTP_PORT",
+          "description": "The port to run the HTTP server on.",
+          "format": "string",
+          "isRequired": false,
+          "default": "3010"
+        },
+        {
+          "name": "MCP_HTTP_ENDPOINT_PATH",
+          "description": "The endpoint path for the MCP server.",
+          "format": "string",
+          "isRequired": false,
+          "default": "/mcp"
+        },
+        {
+          "name": "MCP_AUTH_MODE",
+          "description": "Authentication mode to use: 'none', 'jwt', or 'oauth'.",
+          "format": "string",
+          "isRequired": false,
+          "default": "none"
+        },
+        {
+          "name": "MCP_LOG_LEVEL",
+          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').",
+          "format": "string",
+          "isRequired": false,
+          "default": "info"
+        }
+      ],
+      "transport": {
+        "type": "streamable-http",
+        "url": "http://localhost:3010/mcp"
+      }
+    }
+  ]
+}