Brapi Mcp Server

Overview

Plant-breeding data from any BrAPI (Breeding API) v2 server, including Breedbase instances such as Cassavabase and Sweetpotatobase and the Triticeae Toolbox (T3), with several servers connected at once under named aliases. Search studies, germplasm, observations, genotype calls, images, locations, and variants, walk pedigrees, and build phenotype and genotype matrices; results past the per-call cap spill into a DuckDB dataframe workspace that agents in the same session query with SQL. Runs as a stdio process, a local Streamable HTTP server, or the public hosted endpoint above.

Tools

Resources

Every resource reads the default connection and mirrors a tool; tool-only clients and multi-server workflows use the tools.

Prompts

Capability reference

brapi_connect _tool

• baseUrl and auth are optional: omitted values come from BRAPI_<ALIAS>_* env vars, the built-in aliases, then BRAPI_DEFAULT_* (see Per-alias credentials); alias (default default, pattern ^[a-zA-Z0-9_-]+$) keeps several servers registered at once; auth.mode is none, bearer, api_key, sgn (Breedbase /token exchange), or oauth2 (client credentials)
• Returns the orientation envelope: server identity, auth summary, capabilities (supported, notableGaps), active dialect, content counts, attribution for built-in servers, and nextToolSuggestions naming the entry-point finders this server can serve
• Typed errors: auth_session_required, auth_base_url_mismatch, alias_base_url_unset, auth_token_exchange_failed, auth_no_access_token, upstream_unauthorized, upstream_forbidden; a failed connect leaves any earlier registration under the alias intact

brapi_server_info _tool

• alias optional; forceRefresh (default false) refetches the capability profile instead of reading the cache
• Returns the same orientation envelope as brapi_connect

brapi_describe_filters _tool

• endpoint is one of studies, germplasm, observations, variables, images, variants, locations; unknown_endpoint carries availableEndpoints
• Each filter has name, type, description, and example; the catalog follows the v2.1 spec, and individual servers may honor a subset

brapi_find_studies _tool

• Filters: crop, trialTypes, seasons, locations, programs, trials, studyNames, active
• distributions over programName, studyType, seasons, locationName, commonCropName

brapi_get_study _tool

• studyDbId required; resolves program, trial, and location inline; study_not_found when the upstream has no such study
• Companion counts observationCount, observationUnitCount, variableCount; a count the server can't scope to the study is omitted with a warning, never reported as the server-wide total

brapi_find_germplasm _tool

• Filters: names, germplasmDbIds, germplasmPUIs, accessionNumbers, crops, synonyms, collections, genus, species; text is a client-side substring match on name, accession, display name, and synonyms that drops non-matching rows, so pair it with a server-side filter
• distributions over commonCropName, genus, species, collection, countryOfOriginCode

brapi_get_germplasm _tool

• germplasmDbId required; returns attributes and direct parents; germplasm_not_found when the upstream has no such germplasm
• Companion counts studyCount, directParentCount, directDescendantCount

brapi_walk_pedigree _tool

• 1–20 root germplasmDbIds; direction is ancestors (default), descendants, or both; maxDepth 1–10 (default 3); the walk stops at 1,000 nodes and sets truncated
• Deduplicated nodes and edges with depthReached, rootCount, leafCount, cycleCount, deadEndCount; past loadLimit, both sets spill to nodesDataframe and edgesDataframe

brapi_find_variables _tool

• Filters: variables, variableNames, variablePUIs, traitClasses, ontologies, studies, methods, scales, crop
• text ranks the full result set and moves matches to the top without dropping the rest; ontologyCandidates lists the ranked matches, each with source (puiMatch, nameMatch, synonymMatch, traitClassMatch)
• distributions over ontologyDbId, traitClass, scaleName

brapi_find_observations _tool

• Filters: studies, germplasm, variables, observationUnits, observations, seasons, programs, trials, observationLevels, timestampFrom / timestampTo
• distributions over observationVariableName, studyName, germplasmName, observationLevel, season

brapi_find_images _tool

• Filters: images, observationUnits, observations, studies, imageFileNames, mimeTypes, descriptiveOntologyTerms; returns metadata only, with bytes via brapi_get_image
• distributions over mimeType, studyName, observationUnitName, descriptiveOntologyTerms

brapi_get_image _tool

• 1–5 imageDbIds per call, up to 20 MB each; images_unsupported when the server doesn't advertise /images
• Each image's source is imagecontent or the imageURL fallback; failed fetches land in per-image errors[] and suspect payloads (a non-image MIME type) in warnings[], so a partial batch still returns

brapi_find_locations _tool

• Filters: locations, locationNames, countryCodes (ISO 3166-1 alpha-3), countryNames (English names resolved to alpha-3), locationTypes, abbreviations; optional bbox needs all four of minLat, maxLat, minLon, maxLon and applies after the fetch
• distributions over countryCode, locationType; coordinateAxisOrder: "swapped" reports a server that stores coordinates as [lat, lon]

brapi_find_variants _tool

• Filters: variantSets, variants, references, and a genomic region of referenceName + start (inclusive) / end (exclusive), 1-based
• distributions over variantType, referenceName, variantSetDbId

brapi_find_genotype_calls _tool

• Needs at least one of variantSetDbId, variantSetDbIds, germplasmDbIds, callSetDbIds, variantDbIds (no_filters otherwise); optional callFormat (VCF, FLAPJACK, DARTSEQ, JSON)
• distributions over callSetName, variantName, variantSetDbId, plus the server's callFormatting; search_endpoint_disabled when the active dialect marks POST /search/calls as dead
• The upstream pull stops at BRAPI_GENOTYPE_CALLS_MAX_PULL (default 100,000) and sets truncated; loadLimit bounds only the inline preview

brapi_dataframe_describe _tool

• dataframe optional: omit to list every dataframe, or name one for columns, row count, and provenance (originating tool, baseUrl, query, expiry), which only auto-registered df_* tables carry
• Listing without a name fails with list_all_disabled_on_shared_http on an HTTP deployment where every caller shares the default tenant

brapi_dataframe_query _tool

• sql is a single SELECT; writes, DDL, COPY, PRAGMA, ATTACH, file reads, and system-catalog reads fail as sql_rejected, with the specific reason in data.gateReason
• Returns rowCount, typed columns, and rows bounded by preview (≤1,000), rowLimit, and BRAPI_CANVAS_MAX_ROWS; truncated, shown, cap, and notice disclose the cut
• registerAs (identifier, ≤63 characters) saves the full result as a new dataframe for chaining

brapi_dataframe_drop _tool

• dataframe required; returns dropped: false, not an error, for an unknown name
• Registered only when BRAPI_CANVAS_DROP_ENABLED=true

brapi_dataframe_export _tool

• format is csv, parquet, or json; optional columns or sql (mutually exclusive) and filename (no path separators or ..; omit for a timestamp-suffixed default); returns the absolute path, sizeBytes, and rowCount
• Typed errors: export_dir_unset, dataframe_not_found, invalid_filename, mutually_exclusive_projection
• Registered only over stdio with BRAPI_EXPORT_DIR set

brapi_build_phenotype_matrix _tool

• studies required (≥1), optional variables / germplasm subsets; shape wide (default) or long; aggregate mean (default), median, first, or all (always long form); loadLimit caps observations per study
• Returns the matrix as a dataframe plus observationCount, germplasmCount, variableCount, and variableLegend mapping SQL-safe column names to variable names; truncated / cap flag a study that hit loadLimit; no_observation_path when neither /observations nor /observationunits returns data

brapi_germplasm_performance _tool

• germplasmDbId required; discovers its studies (up to 200) unless studyDbIds is supplied; optional variables subset; germplasm_not_found when the upstream has no such germplasm
• perVariable rows carry n, mean, median, sd (omitted when n < 2 or non-numeric), min, max, studyCount, studyDbIds, and seasons

brapi_export_genotype_matrix _tool

• variantSetDbId required (no_filters otherwise), optional germplasmDbIds; format is matrix-json, vcf-lite (adds vcf text), or plink (adds ped / map text), and every format registers the germplasm × variant dataframe
• variantColumnLegend maps SQL-safe column names back to variant IDs; search_endpoint_disabled when the active dialect marks POST /search/calls as dead
• maxCalls / maxColumns can lower BRAPI_GENOTYPE_CALLS_MAX_PULL / BRAPI_GENOTYPE_MATRIX_MAX_COLUMNS but never raise them; truncated means a ceiling fired, and warnings names which

brapi_submit_observations _tool

• studyDbId plus 1–5,000 observations; a row with observationDbId updates via PUT, one without creates via POST, and nothing is deleted
• mode: "preview" (default) returns valid, invalid, routing counts, and perRowWarnings without writing; mode: "apply" asks the caller to confirm (force: true skips it) and writes only on the round that redeems the server's record of that prompt, for the same caller, server, study, and rows — a pre-supplied or replayed answer is asked again — and returns posted, updated, and studyObservationCount; failures are observations_unsupported, study_not_found, post_unsupported, put_unsupported, and user_declined
• Registered only when BRAPI_ENABLE_WRITES=true; requires the brapi:write:observations scope

brapi_raw_get _tool

• path is a relative route such as /samples (a full URL fails as cross_origin_path); optional params and loadLimit
• Returns the raw envelope (url, metadata, result) plus a suggestion when a curated tool covers the endpoint; list results past loadLimit spill to a dataframe unless params.page / params.pageSize drive paging

brapi_raw_search _tool

• noun (e.g. observations, calls, germplasm) and a body posted verbatim to POST /search/{noun}; async searches are polled to completion
• Returns kind (sync or async), searchResultsDbId, result, and a suggestion; spills like brapi_raw_get unless body.page / body.pageSize is set; search_endpoint_disabled when the active dialect marks the route as dead

brapi://server/info _resource

• Orientation envelope for the default connection as application/json
• Same payload as brapi_server_info called with no arguments

brapi://calls _resource

• Capability profile for the default connection: supported services with their HTTP methods and versions, plus crops
• Reflects what /serverinfo + /calls returned at the last load

brapi://study/{studyDbId} _resource

• Same payload as brapi_get_study on the default connection
• study_not_found when the upstream has no such study

brapi://germplasm/{germplasmDbId} _resource

• Same payload as brapi_get_germplasm on the default connection
• germplasm_not_found when the upstream has no such germplasm

brapi://filters/{endpoint} _resource

• Same payload as brapi_describe_filters; unknown_endpoint for an endpoint outside the catalog
• Listing brapi://filters returns one resource per endpoint

brapi://variable/{observationVariableDbId} _resource

• The /variables/{id} record (trait, scale, method, ontology) on the default connection
• variable_not_found when the upstream has no such variable

brapi_eda_study _prompt

• Arguments: studyDbId required; alias optional
• Returns one user message: a six-step playbook (orient, variables, coverage, missing data, IQR outliers, optional pedigree walk) ending in a markdown report with recommended next steps

brapi_meta_analysis _prompt

• Arguments: germplasmDbIds (comma-separated) and traitName required; alias optional, run once per alias for multi-server analyses
• Returns one user message: a seven-step playbook (resolve the trait, discover studies, build the observation table, harmonize scales, summarize per study and across studies, optional pedigree walk) ending in a report that cites every dataframe handle or filter map used

Features

Built on @cyanheads/mcp-ts-core: stdio and Streamable HTTP transports, pluggable auth (none / jwt / oauth), swappable storage (in-memory, filesystem, Supabase, Cloudflare KV/R2/D1), structured logging with optional OpenTelemetry tracing.

BrAPI-specific:

• Shared finder contract: the seven filter finders (studies, germplasm, variables, observations, images, locations, variants) take alias, loadLimit, and extraFilters (keys from brapi_describe_filters), and return results, hasMore, distributions, and an optional dataframe handle
• Dataframe spillover: past loadLimit, finders page the rest of the result (up to 50 pages and 50,000 rows) into a DuckDB df_<uuid> table and return its handle
• Dialect adapters (spec, brapi-test, breedbase, cassavabase, bms), detected per connection, translate v2.1 plural filters into the form each server family honors, drop filters it ignores, and switch to POST /search/{noun} when a GET would narrow a multi-value filter; BRAPI_<ALIAS>_DIALECT pins one
• Several connections at once under named aliases, with three public Breedbase servers built in and credentials resolved per alias from env vars, so they stay out of the LLM context
• Capability-aware calls: each connection's /serverinfo + /calls profile is cached and checked before a tool calls an endpoint; a per-connection concurrency cap and exponential-backoff retries cover 429/5xx

Agent-friendly output:

• Typed failures: every connection-scoped tool and resource fails with unknown_alias until brapi_connect registers the alias, and a filter finder or brapi_build_phenotype_matrix fails with all_filters_dropped instead of widening to an unfiltered pull when the dialect drops every filter supplied
• Query echo on every finder: totalCount, returnedCount, the exact appliedFilters sent upstream, a refinementHint on broad results, an empty-result notice, and warnings
• Graceful partial failure: brapi_get_image returns per-image errors[] and warnings[] rows instead of failing the batch
• Discriminated outputs: brapi_submit_observations returns a mode-discriminated result (preview / apply), brapi_raw_search reports kind, and brapi_get_image reports each image's source

Working with dataframes

When a finder's upstream total exceeds loadLimit, the response carries a dataframe handle: tableName, rowCount, columns, createdAt, expiresAt, plus truncated, maxRows, and totalCount when a cap fired. Columns renamed to pass the SQL identifier check map back to their upstream keys in columnLegend.

1. brapi_find_observations { studies: ["s-422"] }   → first-page rows inline + dataframe.tableName = "df_<uuid>" (when totalCount > loadLimit)2. brapi_dataframe_describe { dataframe: "df_<uuid>" }   → schema + provenance (originating tool, baseUrl, query, expiry)3. brapi_dataframe_query { sql: "SELECT germplasmName, value FROM df_<uuid> WHERE observationVariableDbId = 'V1' LIMIT 100" }   → typed columns + bounded rows

Dataframe names are capability tokens, not row-level ACLs: anyone holding a name in the same session or tenant bucket (see Deployment shapes) can read its rows. Provenance lasts BRAPI_DATASET_TTL_SECONDS (default 24h); set BRAPI_CANVAS_DROP_ENABLED=true to expose brapi_dataframe_drop for explicit cleanup.

Getting started

Public Hosted Instance

A public instance is available at https://brapi.caseyjhand.com/mcp — no installation required. Point any MCP client at it via Streamable HTTP:

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

Self-Hosted / Local

Add the following to your MCP client configuration file.

{  "mcpServers": {    "brapi-mcp-server": {      "type": "stdio",      "command": "bunx",      "args": ["@cyanheads/brapi-mcp-server@latest"],      "env": {        "MCP_TRANSPORT_TYPE": "stdio",        "MCP_LOG_LEVEL": "info"      }    }  }}

Or with npx (no Bun required):

{  "mcpServers": {    "brapi-mcp-server": {      "type": "stdio",      "command": "npx",      "args": ["-y", "@cyanheads/brapi-mcp-server@latest"],      "env": {        "MCP_TRANSPORT_TYPE": "stdio",        "MCP_LOG_LEVEL": "info"      }    }  }}

Or with Docker:

{  "mcpServers": {    "brapi-mcp-server": {      "type": "stdio",      "command": "docker",      "args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/brapi-mcp-server:latest"]    }  }}

For Streamable HTTP, set the transport and start the server:

MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http# Server listens at http://localhost:3010/mcp

No env vars are required: the built-in aliases (bti-cassava, bti-sweetpotato, bti-breedbase-demo) connect as-is, and brapi_connect accepts any other BrAPI v2 URL at runtime. For servers that need a login, set credentials as env vars so passwords, tokens, and keys stay out of the LLM context (see Per-alias credentials).

Prerequisites

• Bun v1.4.0 or higher (or Node.js v24+).
• @duckdb/node-api, installed as a regular dependency, with prebuilt native bindings for macOS, Linux (glibc and musl), and Windows on x64 and arm64. Cloudflare Workers is not supported.

Installation

1. Clone the repository:

git clone https://github.com/cyanheads/brapi-mcp-server.git

2. Navigate into the directory:

cd brapi-mcp-server

3. Install dependencies:

bun install

4. Configure environment:

cp .env.example .env# edit .env if you need credentials or non-default settings

Configuration

Every variable is optional.

See .env.example for the full list of optional overrides.

Per-alias credentials

brapi_connect fills baseUrl and auth from env vars when the agent omits them, in this order:

1. Agent input, within the pairing rules below.
2. Per-alias env vars: BRAPI_<ALIAS>_*, uppercased with hyphens as underscores (my-server → BRAPI_MY_SERVER_*).
3. Built-in aliases: see Built-in aliases.
4. BRAPI_DEFAULT_BASE_URL, for an alias with no URL or credentials of its own.

Env credentials go only to the server configured with them:

• An alias's credentials pair with its BRAPI_<ALIAS>_BASE_URL, else its enabled built-in URL. A caller baseUrl that points elsewhere fails with auth_base_url_mismatch. Credentials with no URL of their own, including those left behind by a built-in disabled via BRAPI_BUILTIN_ALIASES_DISABLED, fail with alias_base_url_unset and are never sent to BRAPI_DEFAULT_BASE_URL.
• BRAPI_DEFAULT_* credentials attach only when the resolved URL is BRAPI_DEFAULT_BASE_URL; an alias pointed anywhere else connects without auth unless it has credentials of its own. With no BRAPI_DEFAULT_BASE_URL set, default credentials fail with alias_base_url_unset.

URLs compare after normalizing host case, default ports, and trailing slashes. Caller-supplied auth is never mixed with env credentials.

Each alias carries one credential family, and the auth mode follows from which fields are set. Mixing families within an alias raises a ValidationError.

BRAPI_<ALIAS>_DIALECT pins the dialect adapter (spec, brapi-test, breedbase, cassavabase, bms) when detection picks the wrong one; auto or unset detects it.

# .env — attach write credentials to the built-in 'bti-cassava' aliasBRAPI_BTI_CASSAVA_USERNAME=aliceBRAPI_BTI_CASSAVA_PASSWORD=...# (BASE_URL omitted — the built-in registry covers it)
# Static API key as alias 'prod'BRAPI_PROD_BASE_URL=https://my-brapi.example.com/brapi/v2BRAPI_PROD_API_KEY=...BRAPI_PROD_API_KEY_HEADER=X-API-Key

The agent then calls brapi_connect({ alias: 'bti-cassava' }) with no baseUrl, no auth, and no secrets in the prompt.

Built-in aliases

These public BrAPI v2 endpoints connect with no configuration. Their orientation envelope carries license, citation, and homepage in an attribution block (Creative Commons Attribution).

The registry holds only servers verified for anonymous reads. Servers that require login, including the Triticeae Toolbox (T3) wheat, oat, and barley hosts, connect through BRAPI_<ALIAS>_BASE_URL plus credentials (see .env.example).

BRAPI_<ALIAS>_BASE_URL overrides a built-in URL, e.g. to point bti-sweetpotato at a staging mirror via BRAPI_BTI_SWEETPOTATO_BASE_URL. BRAPI_<ALIAS>_USERNAME and friends attach credentials on top of the built-in URL; each Breedbase instance has its own user table, so write access needs a separate account on each. BRAPI_BUILTIN_ALIASES_DISABLED=bti-cassava,bti-breedbase-demo removes entries.

Citation: all three built-ins reference Morales et al. 2022, "Breedbase: a digital ecosystem for modern plant breeding." G3 12(7): jkac078. doi:10.1093/g3journal/jkac078.

Running the server

Local development

• Build and run the production version:

  sh

  # One-time buildbun run rebuild
  # Run the built serverbun run start            # transport from MCP_TRANSPORT_TYPE (stdio default)bun run start:stdiobun run start:http
  # Or run from source with hot reloadbun --watch src/index.ts

• Run checks and tests:

  sh

  bun run devcheck         # Lint, format, typecheck, security, changelog syncbun run test             # Vitest suitebun run lint:mcp         # Validate MCP definitions

Docker

docker build -t brapi-mcp-server .docker run --rm -p 3010:3010 brapi-mcp-server

The image defaults to HTTP transport, stateful session mode, and logs to /var/log/brapi-mcp-server. OpenTelemetry peer dependencies are installed by default; build with --build-arg OTEL_ENABLED=false to omit them.

Deployment shapes

Two kinds of state scope by tenant and, by default, by MCP session: connection state (registered aliases and exchanged upstream tokens) and dataframes (df_<uuid> tables, usable by anyone who holds the name within its bucket). Three configurations set where those buckets end:

Stdio is always a single session. Clients on MCP protocol revision 2026-07-28 carry no session on any transport, so outside the per-user-credentials shape they land in the shared tenant workspace, where re-registering an alias re-points every such caller's later calls to it.

On HTTP without per-user auth, brapi_dataframe_describe won't list dataframes without a name, and brapi_dataframe_query rejects system-catalog reads in every shape, so a caller without a known df_<uuid> name can't enumerate other callers' tables.

Project structure

Development guide

See 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 tenant-scoped storage — no console, no direct persistence access
• Add new tools to the matching group in src/mcp-server/tools/definitions/index.ts; src/index.ts composes the groups behind their feature flags
• Wrap upstream calls: validate raw → normalize → return output schema; never fabricate missing fields

Contributing

Issues are welcome. Run checks and tests before submitting:

bun run devcheckbun run test

License

Apache-2.0 — see LICENSE for details.