Connect

8 clients · secrets stay placeholders

JSON (mcpServers)Claude CodeCodexOpenCodeCursorVS CodeGemini CLIGoose

{
  "mcpServers": {
    "brapi-mcp-server": {
      "type": "http",
      "url": "https://brapi.caseyjhand.com/mcp"
    }
  }
}

claude mcp add --transport http brapi-mcp-server https://brapi.caseyjhand.com/mcp

[mcp_servers.brapi-mcp-server]
url = "https://brapi.caseyjhand.com/mcp"

{
  "$schema": "https://opencode.ai/config.json",
  "mcp": {
    "brapi-mcp-server": {
      "type": "remote",
      "url": "https://brapi.caseyjhand.com/mcp",
      "enabled": true
    }
  }
}

{
  "mcpServers": {
    "brapi-mcp-server": {
      "type": "http",
      "url": "https://brapi.caseyjhand.com/mcp"
    }
  },
  "deeplink": "cursor://anysphere.cursor-deeplink/mcp/install?name=brapi-mcp-server&config=eyJ0eXBlIjoiaHR0cCIsInVybCI6Imh0dHBzOi8vYnJhcGkuY2FzZXlqaGFuZC5jb20vbWNwIn0%3D"
}

{
  "servers": {
    "brapi-mcp-server": {
      "type": "http",
      "url": "https://brapi.caseyjhand.com/mcp"
    }
  }
}

{
  "mcpServers": {
    "brapi-mcp-server": {
      "httpUrl": "https://brapi.caseyjhand.com/mcp"
    }
  }
}

extensions:
  "brapi-mcp-server":
    enabled: true
    name: "brapi-mcp-server"
    type: streamable_http
    uri: "https://brapi.caseyjhand.com/mcp"
    timeout: 300

Quality 67 / 100needs work

protocol88 · weight 25

pass
protocol.modernsupports 2026-07-28 (server/discover)
pass
protocol.statelessanswers without a session
pass
protocol.transportstreamable HTTP
warn
protocol.list_ttltools/list declares ttlMs 0, so clients re-fetch it on every use

authorizationn/a · weight 15

n/a
auth.prm, auth.as_metadata, auth.cimdno remote uses OAuth
n/a
auth.secret_in_urlno templated URL

tool hygiene71 · weight 30

pass
tools.descriptionsevery tool has a description
warn
tools.description_length1 tools have descriptions over 1,024 characters, which crowds the context
pass
tools.schemasevery tool has an object input schema
pass
tools.annotations22 of 22 tools declare readOnlyHint or destructiveHint
fail
tools.directory_hintsno tool declares all four of readOnlyHint, destructiveHint, idempotentHint and openWorldHint; missing: brapi_connect (destructiveHint); brapi_build_phenotype_matrix (destructiveHint, idempotentHint); brapi_get_germplasm (destructiveHint, openWorldHint); …
warn
tools.token_costabout 12,524 tokens to load every tool
pass
tools.api_dumptools are not a one-to-one API dump

stability25 · weight 15

warn
stability.changes49 tool changes in 30 days
fail
stability.rug_pull7 tools kept their name but changed most of their description in 30 days; review before trusting them

dependenciesn/a · weight 15

n/a
deps.known_vulns, deps.mcp_sdk_version, deps.resolvabledeps.dev does not know @cyanheads/[email protected], @cyanheads/[email protected]

22 tools, about 12,524 tokens to load them all · tool set 62aeb8aba4f3 · tools last changed 2026-10-19 · checked 2026-10-20 13:17 UTC

Tool changes

2026-10-19brapi_raw_searchchangedoutput schema
2026-10-19brapi_raw_getchangedoutput schema
2026-10-19brapi_export_genotype_matrixchangeddescription, output schema
before
Pull genotype calls for a germplasm × variant set and pivot them into a matrix. `format` controls the output: `matrix-json` registers a wide germplasm × variant canvas dataframe for SQL analysis; `vcf-lite` returns VCF-subset text (in the `vcf` field) and also registers the dataframe; `plink` returns .ped/.map text (in the `ped`/`map` fields) and also registers the dataframe. vcf-lite/plink pull /variants metadata for CHROM/POS/REF/ALT (`.`/`0` when the server lacks them). Read the dataframe with brapi_dataframe_describe and brapi_dataframe_query (SQL). Column names are SQL-safe identifiers; `variantColumnLegend` maps them back to original variant IDs.
after · 57% of words in common
Pull genotype calls for a germplasm × variant set and pivot them into a matrix. `matrix-json` registers a wide canvas dataframe; `vcf-lite` adds VCF-subset text in `vcf`; `plink` adds .ped/.map text in `ped`/`map`. Text formats pull /variants metadata and convert zero-based BrAPI start to one-based positions; missing/invalid positions use `.`/`0`. Read the dataframe with brapi_dataframe_describe and brapi_dataframe_query (SQL). `variantColumnLegend` maps SQL-safe columns to original variant IDs.
2026-10-19brapi_find_genotype_callschangedoutput schema
2026-10-19brapi_find_variantschangedoutput schema
2026-10-19brapi_find_locationschangedoutput schema
2026-10-19brapi_find_imageschangedoutput schema
2026-10-19brapi_find_observationschangedoutput schema
2026-10-19brapi_find_variableschangedinput schema, output schema
2026-10-19brapi_germplasm_performancechangedoutput schema

Showing the latest 10. Full history: list_changes · trend: quality JSON.

Checks run on what our credential-free, read-only probes observe; tools are never called and no code audit is performed. How it is computed.

Trust 94 / 100

provenance80

liveness100

freshness100

hygiene100

+repository +namespace-matches-repo +reachable +uptime-99% +updated-1d-ago

Derived from observable signals (official registry feed and our own credential-free probes); no code audit performed. How it is computed.

Dependencies

@cyanheads/[email protected] npmthis version is not known to the dependency resolver

Dependency graphs from deps.dev; advisories from OSV.dev, including the GitHub Advisory Database and the PyPI Advisory Database; all CC BY 4.0. The graph is what a clean install of this version resolves today; nothing was installed or run. How it is checked.

Endpoints

remote	auth	reachable	uptime 30d	p50	protocol	last ok
`https://brapi.caseyjhand.com/mcp` streamable-http	none	yes	99%	206 ms	2026-07-28	2026-10-20

package	registry	version	runtime	secrets
`@cyanheads/brapi-mcp-server`	npm	0.10.1	npx
`@cyanheads/brapi-mcp-server`	npm	0.10.1	npx

Tools (22)

`brapi_build_phenotype_matrix`read-only	Pull observations across one or more studies and pivot them into a germplasm × trait matrix materialized as a canvas dataframe. Returns a dataframe handle (read it with brapi_dataframe_describe and brapi_dataframe_query) plus a summary of dimensions and aggregate method. Long-form output is suitable for downstream GROUP BY analysis by study, germplasm, or variable. A study whose pull fails is named in warnings and the rest still build the matrix; the call fails only when every study failed.
`brapi_connect`	Open a connection to a BrAPI v2 server, authenticate, and return the full orientation envelope (server identity, capability profile, content summary, suggested next tools). Other BrAPI tools connect an alias the server has a URL configured for (a built-in or operator-configured alias, or `default` on a deployment with a default server) on first use; call this to connect any other server by `baseUrl`, to pass `auth`, or to re-point an alias. Supports multiple concurrent connections via named aliases. Credentials can be configured server-side and omitted from this call. When a request carries no MCP session on a deployment without per-user auth, aliases live in one namespace shared by every such caller: re-registering an alias re-points their later calls to it. Built-in known servers (callable with no `baseUrl` or `auth` — public BrAPI v2 endpoints): `bti-breedbase-demo`, `bti-cassava`, `bti-sweetpotato`. Operator-configured aliases on this deployment (credentials and/or baseUrl read from server env vars): `default`, `cassava`. Aliases are shortcuts only; any other BrAPI v2 server is reachable by passing `baseUrl` directly.
`brapi_dataframe_describe`read-only	Start here after a spillover. Lists dataframes (or describes one) with columns, row counts, and originating-source provenance. The dataframe name appears inline on every find_* response that spilled (`result.dataframe.tableName`) — pass it as `dataframe` to inspect schema and provenance before writing the first brapi_dataframe_query. On a shared HTTP endpoint without per-caller auth, listing without a name is available only where each MCP session has its own workspace, and never to a request without a session; pass a known name instead.
`brapi_dataframe_query`	Run SQL across in-memory dataframes. Dataframes auto-populate when find_* tools spill (named `df_<uuid>`) — the dataframe name appears inline on every find_* response that spilled (`result.dataframe.tableName`), so the typical flow is find_* → read the name → query here. Use brapi_dataframe_describe to inspect schema and provenance for a known name. SELECT only — writes/DDL/COPY/PRAGMA/ATTACH/file-reads are rejected. Use SQL as the paging idiom: `LIMIT/OFFSET` to walk results, projection to trim columns, aggregation to summarize. Use `registerAs` to chain — the result lands as a new dataframe.
`brapi_describe_filters`read-only	List the valid filter names for a BrAPI endpoint (studies, germplasm, observations, variables, images, variants, locations) — companion lookup for the `extraFilters` passthrough on any `find_*` tool. Entries reflect the BrAPI v2.1 spec; individual servers may implement subsets.
`brapi_export_genotype_matrix`read-only	Pull genotype calls for a germplasm × variant set and pivot them into a matrix. `matrix-json` registers a wide canvas dataframe; `vcf-lite` adds VCF-subset text in `vcf`; `plink` adds .ped/.map text in `ped`/`map`. Text formats pull /variants metadata and convert zero-based BrAPI start to one-based positions; missing/invalid positions use `.`/`0`. Read the dataframe with brapi_dataframe_describe and brapi_dataframe_query (SQL). `variantColumnLegend` maps SQL-safe columns to original variant IDs.
`brapi_find_genotype_calls`read-only	Pull genotype calls for a germplasm × variant set. Filter to bound cost — at minimum, set `variantSetDbId` or `germplasmDbIds`. The upstream pull is capped by deployment policy; when the pull is truncated, narrow the filters. results[] holds the leading calls up to `loadLimit` and a 24,000-byte budget; when it holds fewer than were collected, every collected call is materialized as a dataframe — read it with brapi_dataframe_describe and brapi_dataframe_query (SQL) instead of paging row-by-row.
`brapi_find_germplasm`read-only	Find germplasm by name, synonym, accession number, PUI, crop, or free-text query. Matches across registered synonyms. results[] holds the leading matches up to loadLimit and a 24,000-byte budget; when it holds fewer rows than matched, the matched set is materialized as a dataframe — read it with brapi_dataframe_describe and brapi_dataframe_query (SQL) instead of paging row-by-row.
`brapi_find_images`read-only	Filter images by observation unit, observation, study, descriptive ontology term, file name, or MIME type. Returns metadata only — use brapi_get_image to fetch bytes inline. results[] holds the leading matches up to loadLimit and a 24,000-byte budget; when it holds fewer rows than matched, the matched set is materialized as a dataframe — read it with brapi_dataframe_describe and brapi_dataframe_query (SQL).
`brapi_find_locations`read-only	Find research stations / field sites by country, abbreviation, type, location ID, or free-text. Countries filter by ISO 3166-1 alpha-3 code via countryCodes, or by free-form English country name via countryNames (resolved client-side to alpha-3 — "Uganda" → "UGA"). Optional bbox parameter restricts rows to a latitude/longitude window. When no first-page row falls inside it under the spec GeoJSON [lon, lat, alt] reading and a row carries a Point geometry, bbox is retried with axes swapped; if that matches, the swapped reading is used (non-conformant servers store [lat, lon, alt]) with a warning and `coordinateAxisOrder: "swapped"`. results[] holds the leading matches up to loadLimit and a 24,000-byte budget; when it holds fewer rows than matched, the matched set is materialized as a dataframe — read it with brapi_dataframe_describe and brapi_dataframe_query (SQL).
`brapi_find_observations`read-only	Pull observation records filtered by study, germplasm, variable, season, or observation unit. Without a studies, trials, observationUnits, or observations anchor, a GET query first runs a one-row count probe and skips the bulk pull (warnings says so) when the probe fails or reports more than 5,000 matches. results[] holds the leading matches up to loadLimit and a 24,000-byte budget; when those bounds cut it short, the matched set is materialized as a dataframe — read it with brapi_dataframe_describe and brapi_dataframe_query (SQL).
`brapi_find_studies`read-only	Locate studies matching crop, trial type, season, location, or program. Enriches results with program/trial/location context in one call. results[] holds the leading matches up to loadLimit and a 24,000-byte budget; when it holds fewer rows than matched, the matched set is materialized as a dataframe — read it with brapi_dataframe_describe and brapi_dataframe_query (SQL).
`brapi_find_variables`read-only	Find observation variables (traits) by name, trait class, ontology term, or free-text query. Free-text queries are ranked against every fetched row by PUI, name, synonym, and trait text; a candidate carries the ontology PUI of its row as termId when the row has one. results[] holds the leading rows up to loadLimit and a 24,000-byte budget; when it holds fewer rows than matched, the matched set is materialized as a dataframe — read it with brapi_dataframe_describe and brapi_dataframe_query (SQL).
`brapi_find_variants`read-only	Find variant records by variant set, reference sequence, or genomic region (start/end, 0-based inclusive / exclusive per the BrAPI spec; servers may differ). results[] holds the leading matches up to loadLimit and a 24,000-byte budget; when it holds fewer rows than matched, the matched set is materialized as a dataframe — read it with brapi_dataframe_describe and brapi_dataframe_query (SQL).
`brapi_germplasm_performance`read-only	Aggregate a single germplasm's observations across studies, returning per-variable statistics (n, mean, median, sd, min, max), contributing studies, seasons, and collection coverage. SGN/Breedbase uses advertised germplasm-scoped observation units with embedded measurements, including zeros. Other servers discover up to 200 studies before pulling per study. Pass studyDbIds to skip discovery and restrict collection to known studies. Per-study observation limits, page limits, failures, and incomplete scans appear in coverage and warnings. For the underlying matrix, use brapi_build_phenotype_matrix.
`brapi_get_germplasm`read-only	Fetch a single germplasm by DbId with attributes and direct parents. Response companions report study count, direct parent count, and direct descendant count — signals for pedigree depth and observation coverage.
`brapi_get_image`read-only	Fetch image bytes for up to 5 imageDbIds and return them inline as `type: image` content blocks. Falls back to the metadata `imageURL` when the server lacks dedicated image-content delivery or that request fails. No filesystem side-effects.
`brapi_get_study`read-only	Fetch a single study by DbId with its program, trial, and location records resolved where those lookups succeed. Response includes cheap observation/observation-unit/variable counts as drill-down signals.
`brapi_raw_get`read-only	Passthrough to BrAPI GET /{path} without foreign-key resolution. List results (result array or result.data) return a leading preview within loadLimit and a 24,000-byte budget on each serialized row representation; an oversized first row returns no inline rows. Omitted fetched rows remain in a dataframe readable with brapi_dataframe_describe and brapi_dataframe_query. Explicit params.page/pageSize fetches only that upstream page, staging it if trimmed. Non-list results and envelope siblings are preserved. Emits a suggestion when a curated tool covers the endpoint.
`brapi_raw_search`read-only	Passthrough to BrAPI POST /search/{noun}, polling async search IDs. Sends loadLimit as the initial pageSize unless body.page/pageSize drives explicit paging. List previews fit loadLimit and a 24,000-byte budget on each serialized row representation; an oversized first row returns no inline rows. Every fetched row omitted inline stays in a dataframe readable with brapi_dataframe_describe and brapi_dataframe_query. Explicit paging fetches only the requested page, staging it if trimmed. Non-list results and envelope siblings are preserved; no distributions or foreign-key resolution.
`brapi_server_info`read-only	Return the full orientation envelope for a BrAPI connection — server identity, capabilities, content counts, suggested finders, and notes. Pass forceRefresh to refetch the cached capability scan; pass an alias to read a non-default connection.
`brapi_walk_pedigree`read-only	Walk germplasm ancestry or descendancy as a deduplicated DAG with cycle detection and depth limits. leafCount counts graph terminals, confirmedLeafCount counts successfully verified leaves, and frontier records unresolved directions. Nodes and edges each fit loadLimit and a 24,000-byte preview budget; trimmed discovered graphs and already-fetched omitted relatives are staged for brapi_dataframe_describe and brapi_dataframe_query (SQL). Diagrams describe only the discovered graph, never unvisited relatives.

Schemas: list_tools.

Similar MCP servers

More from io.github.cyanheads

And 140 more from this publisher.

Official server.json

{
  "name": "io.github.cyanheads/brapi-mcp-server",
  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
  "remotes": [
    {
      "url": "https://brapi.caseyjhand.com/mcp",
      "type": "streamable-http"
    }
  ],
  "version": "0.10.1",
  "packages": [
    {
      "version": "0.10.1",
      "transport": {
        "type": "stdio"
      },
      "identifier": "@cyanheads/brapi-mcp-server",
      "runtimeHint": "npx",
      "registryType": "npm",
      "registryBaseUrl": "https://registry.npmjs.org",
      "environmentVariables": [
        {
          "name": "BRAPI_DEFAULT_BASE_URL",
          "format": "string",
          "description": "Default BrAPI v2 base URL. Optional — connections can be opened at runtime via the brapi_connect tool instead."
        },
        {
          "name": "BRAPI_ENABLE_WRITES",
          "format": "string",
          "default": "false",
          "description": "Opt-in flag for the write surface (brapi_submit_observations). Off by default — the tool is omitted from tools/list unless the operator opts in."
        },
        {
          "name": "BRAPI_PAGE_SIZE",
          "format": "string",
          "default": "1000",
          "description": "Upstream pageSize used during canvas spillover walks (decoupled from BRAPI_LOAD_LIMIT). Dataframe ceiling = pageSize × 50 pages, capped at 50,000 rows."
        },
        {
          "name": "MCP_LOG_LEVEL",
          "format": "string",
          "default": "info",
          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn')."
        }
      ]
    },
    {
      "version": "0.10.1",
      "transport": {
        "url": "http://localhost:3010/mcp",
        "type": "streamable-http"
      },
      "identifier": "@cyanheads/brapi-mcp-server",
      "runtimeHint": "npx",
      "registryType": "npm",
      "registryBaseUrl": "https://registry.npmjs.org",
      "environmentVariables": [
        {
          "name": "MCP_TRANSPORT_TYPE",
          "value": "http",
          "format": "string",
          "description": "Selects the HTTP transport."
        },
        {
          "name": "BRAPI_DEFAULT_BASE_URL",
          "format": "string",
          "description": "Default BrAPI v2 base URL. Optional — connections can be opened at runtime via the brapi_connect tool instead."
        },
        {
          "name": "BRAPI_ENABLE_WRITES",
          "format": "string",
          "default": "false",
          "description": "Opt-in flag for the write surface (brapi_submit_observations). Off by default — the tool is omitted from tools/list unless the operator opts in."
        },
        {
          "name": "BRAPI_PAGE_SIZE",
          "format": "string",
          "default": "1000",
          "description": "Upstream pageSize used during canvas spillover walks (decoupled from BRAPI_LOAD_LIMIT). Dataframe ceiling = pageSize × 50 pages, capped at 50,000 rows."
        },
        {
          "name": "MCP_HTTP_HOST",
          "format": "string",
          "default": "127.0.0.1",
          "description": "The hostname for the HTTP server."
        },
        {
          "name": "MCP_HTTP_PORT",
          "format": "string",
          "default": "3010",
          "description": "The port to run the HTTP server on."
        },
        {
          "name": "MCP_HTTP_ENDPOINT_PATH",
          "format": "string",
          "default": "/mcp",
          "description": "The endpoint path for the MCP server."
        },
        {
          "name": "MCP_AUTH_MODE",
          "format": "string",
          "default": "none",
          "description": "Authentication mode to use: 'none', 'jwt', or 'oauth'."
        },
        {
          "name": "MCP_LOG_LEVEL",
          "format": "string",
          "default": "info",
          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn')."
        }
      ]
    }
  ],
  "repository": {
    "url": "https://github.com/cyanheads/brapi-mcp-server",
    "source": "github"
  },
  "description": "Collaborative BrAPI v2.1 MCP workspace: studies, germplasm, genotypes across Breedbase, T3, more."
}