@cyanheads/brapi-mcp-server 0.4.12 → 0.4.13

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Files changed (11) hide show
  1. package/CLAUDE.md +1 -1
  2. package/README.md +147 -518
  3. package/changelog/0.4.x/0.4.13.md +42 -0
  4. package/dist/config/alias-credentials.d.ts.map +1 -1
  5. package/dist/config/alias-credentials.js +9 -2
  6. package/dist/config/alias-credentials.js.map +1 -1
  7. package/dist/config/builtin-aliases.d.ts.map +1 -1
  8. package/dist/config/builtin-aliases.js +22 -4
  9. package/dist/config/builtin-aliases.js.map +1 -1
  10. package/package.json +1 -1
  11. package/server.json +3 -3
package/CLAUDE.md CHANGED
@@ -1,7 +1,7 @@
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  # Agent Protocol
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  **Server:** brapi-mcp-server
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- **Version:** 0.4.11
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+ **Version:** 0.4.13
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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  > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
package/README.md CHANGED
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  <div align="center">
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- [![npm](https://img.shields.io/npm/v/@cyanheads/brapi-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/brapi-mcp-server) [![Version](https://img.shields.io/badge/Version-0.4.12-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
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+ [![npm](https://img.shields.io/npm/v/@cyanheads/brapi-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/brapi-mcp-server) [![Version](https://img.shields.io/badge/Version-0.4.13-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
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  [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![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-v1.3.11-blueviolet.svg?style=flat-square)](https://bun.sh/) [![Status](https://img.shields.io/badge/Status-Beta-yellow.svg?style=flat-square)](./CHANGELOG.md)
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  ## Tools
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- Twenty-two tools grouped by shape — connection tools bootstrap a session, `find_*` tools return a summarized page plus distributions and spill overflow rows into the DatasetStore, `get_*` tools fetch a single record with companion counts, plus pedigree walking, dataset lifecycle, an opt-in SQL/analytical workspace over spilled rows, an additive write surface for observations, and raw passthrough escape hatches.
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+ Twenty-two tools grouped by shape — connection tools bootstrap a session, `find_*` tools return a summarized page plus distributions and spill overflow rows into the DatasetStore, `get_*` tools fetch a single record with companion counts, plus pedigree walking, dataset lifecycle, an opt-in SQL workspace over spilled rows, an additive write surface for observations, and raw passthrough escape hatches.
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  ### Orient
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- | Tool Name | Description |
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- |:----------|:------------|
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- | `brapi_connect` | Connect to a BrAPI v2 server, authenticate, cache the capability profile, and return the full orientation envelope inline. |
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- | `brapi_server_info` | Return the full orientation envelope for a registered BrAPI connection — identity, capabilities, content counts, notes. |
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- | `brapi_describe_filters` | List valid filter names for a BrAPI endpoint — powers dynamic discovery for `extraFilters` on any `find_*` tool. |
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+ | Tool | Description |
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+ |:-----|:------------|
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+ | `brapi_connect` | Authenticate, register the connection under an alias, cache the capability profile, and return the orientation envelope inline. One call fully orients the agent. |
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+ | `brapi_server_info` | Re-fetch the orientation envelope for a registered alias — identity, auth, capabilities, content counts, attribution, notes. |
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+ | `brapi_describe_filters` | Static BrAPI v2.1 filter catalog for any endpoint — powers `extraFilters` discovery on every `find_*` tool. |
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  ### Retrieve
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- | Tool Name | Description |
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- |:----------|:------------|
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- | `brapi_find_studies` | Locate studies matching crop / trial type / season / location / program filters, with per-field distributions and dataset spillover. |
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- | `brapi_get_study` | Fetch a single study with program / trial / location FKs resolved and companion counts for observations, units, and variables. |
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- | `brapi_find_germplasm` | Find germplasm by name, synonym, accession, crop, or free-text query, with distributions and dataset spillover. |
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- | `brapi_get_germplasm` | Fetch a single germplasm with attributes, direct parents, and companion counts (studies, parents, direct descendants). |
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- | `brapi_walk_pedigree` | Walk germplasm ancestry or descendancy as a deduplicated DAG (BFS) with cycle detection, depth limits, and traversal stats. |
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- | `brapi_find_variables` | Find observation variables (traits) by name, class, ontology, or free-text; ranked client-side via `OntologyResolver` when `text` is supplied. |
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- | `brapi_find_observations` | Pull observation records filtered by study, germplasm, variable, season, or observation unit. Dataset spillover. |
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- | `brapi_find_images` | Filter images by observation unit / study / ontology term / MIME type — metadata only, bytes via `brapi_get_image`. |
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- | `brapi_get_image` | Fetch image bytes for up to 5 imageDbIds inline as `type: image` content blocks. Prefers `/images/{id}/imagecontent`, falls back to `imageURL`. |
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- | `brapi_find_locations` | Find research stations / field sites by country / type / abbreviation, with optional client-side bounding-box filter. |
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+ | Tool | Description |
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+ |:-----|:------------|
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+ | `brapi_find_studies` | Find studies by crop / trial type / season / location / program. Distributions + dataset spillover. |
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+ | `brapi_get_study` | Fetch a study with program / trial / location FKs resolved and companion counts (observations, units, variables). |
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+ | `brapi_find_germplasm` | Find germplasm by name, synonym, accession, PUI, crop, or free-text. Distributions + dataset spillover. |
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+ | `brapi_get_germplasm` | Fetch a germplasm with attributes, direct parents, and companion counts (studies, parents, descendants). |
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+ | `brapi_walk_pedigree` | BFS-walk ancestry / descendancy as a deduplicated DAG with cycle detection, depth limits, and traversal stats. |
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+ | `brapi_find_variables` | Find observation variables by name / class / ontology / free-text; ranked client-side via `OntologyResolver` when `text` is supplied. |
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+ | `brapi_find_observations` | Pull observation records by study / germplasm / variable / season / unit / timestamp. Dataset spillover. |
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+ | `brapi_find_images` | Filter image metadata by unit / study / ontology / MIME type. Bytes via `brapi_get_image`. |
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+ | `brapi_get_image` | Fetch image bytes for up to 5 imageDbIds inline as `type: image` blocks. Prefers `/imagecontent`, falls back to `imageURL`. |
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+ | `brapi_find_locations` | Find research stations by country / type / abbreviation, with optional client-side bbox filter. |
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  | `brapi_find_variants` | Find variant records by variant set, reference, or genomic region (1-based inclusive / exclusive). |
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- | `brapi_find_genotype_calls` | Pull genotype calls across a germplasm × variant set via async-search polling. Upstream pull bounded by deployment policy (`BRAPI_GENOTYPE_CALLS_MAX_PULL`, default 100k, max 500k); rows beyond `loadLimit` spill to DatasetStore. |
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+ | `brapi_find_genotype_calls` | Pull genotype calls via async-search polling. Upstream pull bounded by `BRAPI_GENOTYPE_CALLS_MAX_PULL` (default 100k, max 500k). |
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  ### Orchestrate
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- | Tool Name | Description |
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- |:----------|:------------|
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- | `brapi_manage_dataset` | Lifecycle for `find_*` spillover datasets — list, summary, load (paged rows with column projection), delete. |
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+ | Tool | Description |
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+ |:-----|:------------|
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+ | `brapi_manage_dataset` | Lifecycle for `find_*` spillover datasets — list / summary / load (paged + projected) / delete. |
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- ### Analyze
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+ ### Analyze (opt-in: `CANVAS_PROVIDER_TYPE=duckdb` + `BRAPI_CANVAS_ENABLED=true`)
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- | Tool Name | Description |
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- |:----------|:------------|
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- | `brapi_dataframe_query` | Run SELECT SQL across in-memory dataframes (DuckDB-backed). Spilled `find_*` datasets auto-register as `ds_<datasetId>` dataframes. Use `registerAs` to chain. Read-only — multi-statement, non-SELECT, file-reads, and exports are rejected. **Opt-in via `CANVAS_PROVIDER_TYPE=duckdb` + `BRAPI_CANVAS_ENABLED=true`** — omitted from `tools/list` otherwise. |
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- | `brapi_dataframe_describe` | List dataframes with column schema, row counts, and originating-dataset provenance for `ds_*` entries. |
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- | `brapi_dataframe_drop` | Drop a dataframe by name. Idempotent — `dropped: false` for unknown names. Underlying DatasetStore dataset is unaffected. |
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+ | Tool | Description |
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+ |:-----|:------------|
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+ | `brapi_dataframe_query` | SELECT SQL across in-memory dataframes (DuckDB-backed). Spilled `find_*` datasets auto-register as `ds_<datasetId>`. Read-only — multi-statement, non-SELECT, file-reads, and exports rejected. |
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+ | `brapi_dataframe_describe` | List dataframes with column schema, row counts, and dataset provenance. |
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+ | `brapi_dataframe_drop` | Drop a dataframe by name. Idempotent. Underlying dataset is unaffected. |
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- ### Write
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+ ### Write (opt-in: `BRAPI_ENABLE_WRITES=true`)
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- | Tool Name | Description |
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- |:----------|:------------|
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- | `brapi_submit_observations` | Submit new (POST) or updated (PUT) observation rows for a study. Default `mode: preview` validates only; `mode: apply` elicits confirmation, fans POST + PUT in parallel, and reports the post-write count. Additive — no observation is destroyed. **Opt-in via `BRAPI_ENABLE_WRITES=true`** — omitted from `tools/list` otherwise. |
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+ | Tool | Description |
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+ |:-----|:------------|
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+ | `brapi_submit_observations` | Two-phase observation write — `mode: preview` validates; `mode: apply` elicits confirmation, then fans POST + PUT in parallel. Additive only — no destructive deletion. |
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  ### Escape hatches
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- | Tool Name | Description |
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- |:----------|:------------|
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- | `brapi_raw_get` | Passthrough to any BrAPI `GET /{path}` the curated tools don't cover. Emits a routing nudge when a goal-shaped tool exists for the target. |
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- | `brapi_raw_search` | Passthrough to any BrAPI `POST /search/{noun}` with async polling handled transparently. Same routing nudge pattern. |
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+ | Tool | Description |
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+ |:-----|:------------|
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+ | `brapi_raw_get` | Passthrough to any BrAPI `GET /{path}` not covered by curated tools. Emits a routing nudge when one applies. |
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+ | `brapi_raw_search` | Passthrough to any `POST /search/{noun}` with async polling handled transparently. Same nudge pattern. |
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- ---
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-
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- ### `brapi_connect`
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- Session bootstrap. Authenticates to a BrAPI v2 server, registers the connection under a named alias, loads the capability profile via `CapabilityRegistry`, and inlines the full orientation envelope in the response. One call fully orients the agent.
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-
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- - `baseUrl` and `auth` are optional — when omitted they fall back to `BRAPI_<ALIAS>_*`, then a built-in registry of public BrAPI servers (`cassava`, `sweetpotato`, `wheat`, `breedbase`), then `BRAPI_DEFAULT_*` (see [Per-alias credentials](#per-alias-credentials) and [Built-in aliases](#built-in-aliases)). Agents can call `brapi_connect({ alias: 'cassava' })` with nothing else and credentials never enter the LLM context
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- - Tagged-union auth input: `none`, `sgn` (session-token exchange), `oauth2` (client-credentials exchange), `bearer`, `api_key`
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- - Multiple concurrent connections per session via distinct aliases
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- - Forces a fresh capability load on every connect — the agent expects current state
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- - Returns the same envelope as `brapi_server_info` — server identity, auth status, capability profile (supported/missing calls), content summary, server-specific notes
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-
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- > **Alias discovery.** Configured aliases are appended to this tool's description at server startup, so agents see the inventory on `tools/list` without anyone having to spell them out in the prompt. Restart the server after changing `BRAPI_<ALIAS>_*` env vars to refresh. Pre-configured aliases are shortcuts only — any other BrAPI v2 server is reachable by passing `baseUrl` directly.
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-
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- ---
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- ### `brapi_server_info`
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- On-demand orientation envelope for any registered alias. Useful for refreshing capability data after a long session or switching between aliases.
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- - Defaults to the most recent `brapi_connect` alias when `alias` is omitted
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- - `forceRefresh: true` bypasses the cached capability profile
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- ---
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- ### `brapi_describe_filters`
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- Static filter catalog drawn from the BrAPI v2.1 spec — name, type, description, and example per filter. Use it before constructing `extraFilters` on any `find_*` tool.
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- - Covers `studies`, `germplasm`, `variables`, `observations`, `images`, `variants`, `locations`
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- - Catalog entries reflect the v2.1 spec; individual servers may implement subsets (the capability profile from `brapi_connect` tells you which)
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- - Response includes `specReference` link and the full list of available endpoints for discovery
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- ---
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- ### `brapi_find_studies`
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- Locate studies with filters on crop, trial type, season, location, program, free text. Pulls an initial page (capped at `loadLimit`) and, when the upstream total exceeds `loadLimit`, spills the full union into `DatasetStore` and returns a dataset handle.
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- - Distributions computed across the full row set (`programName`, `studyType`, `seasons`, `locationName`, `commonCropName`)
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- - Refinement hint suggests which field to narrow when results exceed `loadLimit`
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- - `extraFilters` escape hatch for server-specific filter keys (discover via `brapi_describe_filters`)
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- - Warnings surface when `extraFilters` collides with named inputs
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- ---
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- ### `brapi_get_study`
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- Fetch a single study by `studyDbId` with FKs resolved via `ReferenceDataCache` and cheap `pageSize=0` probes for observation / observation-unit / variable counts.
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- - Resolves `programDbId`, `trialDbId`, `locationDbId` into full records in one call
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- - Companion counts signal where to drill next without a full page pull
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- - Warnings when the upstream server doesn't support count probes
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- ---
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- ### `brapi_find_germplasm`
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- Find germplasm by name, synonym, accession number, PUI, crop, or free-text. Matches across registered synonyms per BrAPI semantics.
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- - Distributions across `commonCropName`, `genus`, `species`, `collection`, `countryOfOriginCode`
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- - Dataset spillover identical to `brapi_find_studies`
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- - Refinement hint identifies the highest-cardinality dimension for narrowing
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- ---
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- ### `brapi_get_germplasm`
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- Fetch a single germplasm with attributes, direct parents, and three companion counts (studies the germplasm appeared in, direct parents, direct descendants) — the counts signal where pedigree traversal could go next.
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- - Pulls `/germplasm/{id}`, `/germplasm/{id}/attributes`, `/germplasm/{id}/pedigree`, and `/germplasm/{id}/progeny` in one call
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- - Warnings when the upstream server omits any of those sub-endpoints
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- ---
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- ### `brapi_walk_pedigree`
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- Walk germplasm ancestry or descendancy as a deduplicated DAG. BrAPI only exposes one generation per call, so this tool BFS-expands from each root, breaks cycles, and enforces a 1000-node safety cap.
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- - `direction`: `ancestors` (parents), `descendants` (progeny), or `both`
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- - Up to 20 roots per call, depth capped at 10 (default 3)
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- - Returns nodes + edges plus traversal stats (`depthReached`, `leafCount`, `cycleCount`, `deadEndCount`, `truncated`)
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- - Warnings when the server doesn't expose `/germplasm/{id}/pedigree` or `/progeny`
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- ---
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- ### `brapi_find_variables`
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- Find observation variables (traits) by name, trait class, ontology term, or free-text. When `text` is supplied, results are re-ranked client-side via `OntologyResolver`; otherwise falls back to upstream order.
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- - Distributions across `ontologyDbId`, `traitClass`, `scaleName`
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- - Ontology candidates (top 10) surfaced separately when `text` is supplied, with source attribution (`puiMatch` / `nameMatch` / `synonymMatch` / `traitClassMatch`)
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- - Dataset spillover and `extraFilters` passthrough identical to other `find_*` tools
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- ---
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- ### `brapi_find_observations`
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- Pull observation records filtered by study, germplasm, variable, season, observation unit, observation level, or timestamp range.
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- - Distributions across `observationVariableName`, `studyName`, `germplasmName`, `observationLevel`, `season`
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- - Dataset spillover when the upstream total exceeds `loadLimit` — handle passes to `brapi_manage_dataset`
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- ---
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- ### `brapi_find_images`
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- Filter images by observation unit, observation, study, descriptive ontology term, file name, or MIME type. Returns metadata only — use `brapi_get_image` for bytes.
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- - Distributions across `mimeType`, `studyName`, `observationUnitName`, `descriptiveOntologyTerms`
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- - Dataset spillover for large result sets
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- ---
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- ### `brapi_get_image`
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- Fetch image bytes for up to 5 `imageDbIds` and return them inline as `type: image` content blocks. Hard cap of 20 MB per image.
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- - Prefers BrAPI `/images/{id}/imagecontent`; falls back to the `imageURL` field when the server doesn't implement imagecontent
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- - Relative `imageURL`s resolve against the registered base URL; absolute URLs pass through (no auth attached to the fallback)
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- - Per-image error reporting — partial success is surfaced cleanly
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- ---
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- ### `brapi_find_locations`
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- Find research stations / field sites by country, abbreviation, type, or location ID.
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- - Optional client-side bounding-box filter (`bbox: {minLat, maxLat, minLon, maxLon}`) applied after the upstream fetch (BrAPI has no spec-level bbox filter)
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- - Distributions across `countryCode` and `locationType`
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- - All four corners required to activate `bbox`; mismatched values produce a warning and the filter is skipped
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- ---
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- ### `brapi_find_variants`
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- Find variant records by variant set, reference sequence, or genomic region.
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- - Genomic region uses 1-based inclusive `start` / exclusive `end` per the BrAPI spec
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- - Distributions across `variantType`, `referenceName`, `variantSetDbId`
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- - Warns when `start >= end`
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- ---
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- ### `brapi_find_genotype_calls`
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- Pull genotype calls for a germplasm × variant set. Handles BrAPI's async-search pattern (`POST /search/calls` → `GET /search/calls/{id}`) transparently.
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- - Requires at least one filter (`variantSetDbId`, `germplasmDbIds`, `callSetDbIds`, `variantDbIds`) — unfiltered pulls are rejected
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- - Upstream pull bounded by deployment policy (`BRAPI_GENOTYPE_CALLS_MAX_PULL`, default 100,000, hard ceiling 500,000) — protects upstream from unbounded sequential paginated GETs. `truncated: true` flags when the cap was hit; agents narrow the filters and re-pull, or query the spilled dataframe
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- - Rows beyond `loadLimit` (default 200) spill to `DatasetStore` for paged follow-up via `brapi_manage_dataset`, or SQL-queryable access via `brapi_dataframe_query`
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- - Echoes server-reported genotype-encoding (`expandHomozygotes`, `unknownString`, `sepPhased`, `sepUnphased`) so the agent can interpret the values
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- ---
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- ### `brapi_manage_dataset`
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- Consolidated lifecycle tool for datasets produced by `find_*` spillovers.
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- - `mode: list` — enumerate datasets with source / query / rowCount / expiration
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- - `mode: summary` — per-dataset metadata and provenance
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- - `mode: load` — paged rows (up to 1000 per page) with optional column projection
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- - `mode: delete` — drop metadata and payload
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- - Export (CSV / Parquet) is deferred until the write surface lands
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- ---
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- ### `brapi_dataframe_query`
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- Run SQL across in-memory dataframes — a SQL/analytical workspace backed by the framework's DuckDB-powered DataCanvas. Spilled `find_*` datasets auto-register as `ds_<datasetId>` dataframes; describe them via `brapi_dataframe_describe` before composing a query.
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- > **Off by default.** Both gates must be on: `CANVAS_PROVIDER_TYPE=duckdb` (framework-side) and `BRAPI_CANVAS_ENABLED=true` (server-side, default true). Requires the optional `@duckdb/node-api` peer dep. Not available on Cloudflare Workers — DuckDB has no V8-isolate build.
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- - Read-only enforcement via the framework's three-layer SQL gate (single statement → SELECT only → plan-walk allowlist), plus a server-side deny-list for `read_json*` / `read_parquet*` / `iceberg_scan` / `delta_scan` that bypass the canvas
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- - `registerAs` materializes the result as a new dataframe — full result lives in the workspace, response carries a bounded `preview` slice plus the full `rowCount`
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- - `BRAPI_CANVAS_MAX_ROWS` (default 10,000) caps response materialization; raising `rowLimit` past this is silently capped — use `registerAs` instead
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- - `BRAPI_CANVAS_QUERY_TIMEOUT_MS` (default 30,000) wraps the query in a wall-clock cap on top of `ctx.signal`
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- - Per-tenant default workspace cached in `ctx.state` — agents never see the underlying canvasId
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- - SQL-gate rejections translate to a typed `sql_rejected` reason, preserving the granular gate code on `data.gateReason`
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- ---
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- ### `brapi_dataframe_describe`
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- List the dataframes available in the current workspace (or describe one by name) with column schema, row counts, and originating-dataset provenance.
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- - `ds_*`-prefixed dataframes carry full provenance: originating tool (`source`), `baseUrl`, original `query`, `createdAt`, `expiresAt`
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- - User-derived dataframes (created via `brapi_dataframe_query({ registerAs })`) show structural info only
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- - Pass `tableName` to scope to one entry; omit to list all
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- ---
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- ### `brapi_dataframe_drop`
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- Release a dataframe by name. Idempotent — returns `dropped: false` rather than failing when the name is unknown.
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-
270
- - Drops the dataframe and its provenance metadata; the underlying DatasetStore dataset is untouched
271
- - Use `brapi_manage_dataset mode=delete` to drop both the dataset and its dataframe in one call
272
-
273
- ---
274
-
275
- ### `brapi_raw_get`
276
-
277
- Last-resort passthrough to any BrAPI `GET /{path}` the curated tools don't cover (e.g. `/samples`, `/methods`, `/scales`, `/crosses`). Returns the raw upstream envelope plus pagination metadata.
278
-
279
- - Rejects absolute URLs in `path` — cross-origin smuggling via the registered base URL is blocked
280
- - Emits a `suggestion` field when a goal-shaped tool covers the target endpoint (e.g. calling `raw_get /studies` nudges you to `brapi_find_studies`)
281
- - Does not enrich results, resolve foreign keys, or compute distributions — prefer curated tools when they apply
282
-
283
- ---
284
-
285
- ### `brapi_raw_search`
286
-
287
- Last-resort passthrough to any BrAPI `POST /search/{noun}`. Handles the 202 / async-poll pattern transparently.
288
-
289
- - Same routing-nudge behavior as `brapi_raw_get`
290
- - Returns `kind: sync | async` and the `searchResultsDbId` when the server took the async path
291
-
292
- ---
293
-
294
- ### `brapi_submit_observations`
295
-
296
- Two-phase write for observation rows. Default `mode: preview` validates rows against the study's variables and returns a routing breakdown; `mode: apply` elicits user confirmation when the client supports it, then POSTs new rows and PUTs rows carrying `observationDbId` in parallel.
297
-
298
- > **Off by default.** Registered only when the operator sets `BRAPI_ENABLE_WRITES=true`; omitted from the surface otherwise. Operator-level deploy-time consent for the only mutation tool — the in-tool preview default, `ctx.elicit` confirmation, `force: true` bypass, and `brapi:write:observations` auth scope all continue to apply when registration is on.
299
-
300
- - POST/PUT routing keyed on per-row `observationDbId` presence — mixed batches in one call
301
- - Pre-flight pulls `/studies/{id}/observationvariables` to flag rows whose variable isn't exposed by the study (warning, not rejection — the upstream is the source of truth)
302
- - Apply mode requires `ctx.elicit` confirmation OR an explicit `force: true` flag (rejected with `Forbidden` otherwise)
303
- - Post-write probe re-fetches `/studies/{id}/observations?pageSize=0` to surface the new total in the response
304
- - `latestObservationTimestamp` echoes the most recent `observationTimeStamp` across the accepted rows
305
- - Additive only — destructive deletion is not exposed; corrections route through PUT
306
- - Auth scope: `brapi:write:observations` (HTTP deployments only)
74
+ > **Alias discovery.** Built-in and operator-configured aliases are appended to the `brapi_connect` description at server startup, so agents see the inventory on `tools/list`. Restart after env-var changes to refresh.
307
75
 
308
76
  ---
309
77
 
310
78
  ## Resources
311
79
 
312
- Six MCP resources mirror the curated tool surface for clients that prefer URI-addressable access. Tool-only clients lose nothing — every resource has a corresponding tool path.
313
-
314
- | URI template | Description |
315
- |:-------------|:------------|
316
- | `brapi://server/info` | Orientation envelope for the default connection (mirror of `brapi_server_info`). |
317
- | `brapi://calls` | Raw capability profile — supported services, their methods/versions, declared crops. |
318
- | `brapi://study/{studyDbId}` | Single study with FKs resolved (mirror of `brapi_get_study`). |
319
- | `brapi://germplasm/{germplasmDbId}` | Single germplasm with attributes and parents (mirror of `brapi_get_germplasm`). |
320
- | `brapi://dataset/{datasetId}` | Metadata + provenance for a persisted dataset (paged rows via `brapi_manage_dataset` mode `load`). |
321
- | `brapi://filters/{endpoint}` | Filter catalog for a BrAPI endpoint (mirror of `brapi_describe_filters`). |
80
+ URI-addressable mirrors of the curated tool surface for clients that prefer resources. All resources use the default connection — multi-server workflows route through tools.
322
81
 
323
- All resources use the default connection. Multi-server workflows route through the tool surface where alias is an explicit input.
82
+ | URI template | Mirrors |
83
+ |:-------------|:--------|
84
+ | `brapi://server/info` | `brapi_server_info` (default connection) |
85
+ | `brapi://calls` | Raw capability profile |
86
+ | `brapi://study/{studyDbId}` | `brapi_get_study` |
87
+ | `brapi://germplasm/{germplasmDbId}` | `brapi_get_germplasm` |
88
+ | `brapi://dataset/{datasetId}` | Dataset metadata + provenance |
89
+ | `brapi://filters/{endpoint}` | `brapi_describe_filters` |
324
90
 
325
91
  ---
326
92
 
327
93
  ## Prompts
328
94
 
329
- Two prompt templates package multi-step BrAPI workflows so the agent can pick them off the shelf.
95
+ Multi-step BrAPI workflow templates — pure user-message generators, no side effects.
330
96
 
331
97
  | Name | Args | Purpose |
332
98
  |:-----|:-----|:--------|
333
- | `brapi_eda_study` | `studyDbId`, `alias?` | Exploratory-data-analysis playbook for a single study — orient, variables, coverage, missing data, outliers, pedigree side-quest, structured report. |
334
- | `brapi_meta_analysis` | `germplasmDbIds` (CSV), `traitName`, `alias?` | Cross-study meta-analysis playbook — trait resolution, study discovery, harmonization, per-germplasm × per-study summary, across-study summary, pedigree context. |
335
-
336
- Pure templates — they generate the user message a downstream LLM consumes. No side effects.
99
+ | `brapi_eda_study` | `studyDbId`, `alias?` | EDA playbook for one study — orient, variables, coverage, missing data, outliers, pedigree, structured report. |
100
+ | `brapi_meta_analysis` | `germplasmDbIds` (CSV), `traitName`, `alias?` | Cross-study meta-analysis — trait resolution, study discovery, harmonization, per-germplasm × per-study and across-study summaries. |
337
101
 
338
102
  ---
339
103
 
340
- ## Features
341
-
342
- Built on [`@cyanheads/mcp-ts-core`](https://www.npmjs.com/package/@cyanheads/mcp-ts-core):
343
-
344
- - Declarative tool, resource, and prompt definitions — single file per primitive, framework handles registration and validation
345
- - Unified error handling — handlers throw, framework catches, classifies, and formats
346
- - Pluggable auth: `none`, `jwt`, `oauth`
347
- - Swappable storage backends: `in-memory`, `filesystem`, `Supabase`, `Cloudflare KV/R2/D1`
348
- - Structured logging with optional OpenTelemetry tracing
349
- - STDIO and Streamable HTTP transports
350
-
351
- BrAPI-specific:
352
-
353
- - **Multi-server session** — `ServerRegistry` maps aliases to live BrAPI connections, so one agent session can span Breedbase, T3, and Sweetpotatobase in parallel
354
- - **Capability-aware calls** — `CapabilityRegistry` caches the `/serverinfo` profile per connection and guards every tool call against unsupported endpoints before they hit the wire
355
- - **Tolerant capability discovery** — if `/serverinfo` is unavailable or sparse, discovery falls back to `/calls` and returns a partial orientation envelope with explicit notes
356
- - **Find-route planning** — curated `find_*` tools prefer GET list endpoints, then fall back to POST `/search/{noun}` when only search is advertised
357
- - **Dataset spillover** — `find_*` tools cap in-context rows at `loadLimit` and transparently persist larger unions (up to 50k rows / 50 pages) as handles in `DatasetStore`; `brapi_manage_dataset` pages / projects / deletes them
358
- - **Dataframes (Tier 3, opt-in)** — spilled `find_*` rows auto-register as DuckDB-backed dataframes named `ds_<datasetId>`; agents run SELECT SQL across them via `brapi_dataframe_query`, with read-only enforcement and a per-tenant workspace. Gated by `CANVAS_PROVIDER_TYPE=duckdb` + `BRAPI_CANVAS_ENABLED=true`; requires the optional `@duckdb/node-api` peer dep. Not available on Cloudflare Workers.
359
- - **Async-search transparency** — `brapi_find_genotype_calls` and `brapi_raw_search` handle the `POST /search/{noun}` → `GET /search/{noun}/{id}` 202-retry pattern without the agent needing to know
360
- - **Pedigree DAG walks** — `brapi_walk_pedigree` BFS-traverses ancestry or descendancy with cycle detection, depth limits, and traversal stats — BrAPI only exposes one generation per call
361
- - **Image content** — `brapi_get_image` fetches image bytes inline as MCP `type: image` blocks, preferring `/images/{id}/imagecontent` and falling back to the metadata `imageURL` field
362
- - **Free-text variable ranking** — `OntologyResolver` scores variable records against a query (PUI / name / synonym / trait-class) so `find_variables text:"..."` returns ranked candidates even when the server has no `/ontologies` endpoint
363
- - **Dynamic filter discovery** — static v2.1 filter catalog plus an `extraFilters` passthrough lets agents drive any server-specific filter without schema churn
364
- - **Auth variants in one schema** — tagged-union connection auth covers none / bearer / api-key / SGN session-token exchange / OAuth2 client-credentials exchange in a single input shape
365
- - **Compatibility matrix** — live server probes are tracked in [docs/compatibility.md](./docs/compatibility.md)
366
- - **Typed error contracts** — every declared failure mode carries a stable `data.reason`, an HTTP-style `code`, and a `recovery.hint` mirrored onto the wire, so agent clients can route errors deterministically (e.g. `unknown_alias` → re-run `brapi_connect`, `dataset_not_found` → drop the stale handle)
367
- - **Last-resort escape hatches** — `brapi_raw_get` and `brapi_raw_search` pass through to any endpoint with routing nudges pointing at the curated tool when one exists
104
+ ## BrAPI-specific features
105
+
106
+ - **Multi-server session** — `ServerRegistry` maps aliases to live BrAPI connections; one session can span Breedbase, T3, and Sweetpotatobase in parallel.
107
+ - **Capability-aware calls** — `CapabilityRegistry` caches `/serverinfo` per connection and guards every tool call against unsupported endpoints. Falls back to `/calls` when `/serverinfo` is sparse.
108
+ - **Built-in known-server registry** — `bti-cassava`, `bti-sweetpotato`, `bti-breedbase-demo`, `t3-wheat`, `t3-oat`, `t3-barley` resolve out-of-the-box without env vars; orientation envelope carries CC-BY attribution.
109
+ - **Dataset spillover** — `find_*` tools cap in-context rows at `loadLimit` and persist larger unions (up to 50k rows / 50 pages) as handles in `DatasetStore`. `brapi_manage_dataset` pages / projects / deletes them.
110
+ - **Dataframes (Tier 3, opt-in)** — spilled rows auto-register as DuckDB-backed `ds_<datasetId>` dataframes; agents run SELECT SQL via `brapi_dataframe_query` with read-only enforcement and a per-tenant workspace. Requires the optional `@duckdb/node-api` peer dep. Not on Cloudflare Workers.
111
+ - **Async-search transparency** — `brapi_find_genotype_calls` and `brapi_raw_search` handle the `POST /search/{noun}` → `GET /search/{noun}/{id}` 202-retry pattern automatically.
112
+ - **Pedigree DAG walks** — `brapi_walk_pedigree` BFS-traverses ancestry / descendancy with cycle detection (BrAPI only exposes one generation per call).
113
+ - **Image content** — `brapi_get_image` fetches bytes inline as MCP `type: image` blocks, preferring `/images/{id}/imagecontent` with `imageURL` fallback.
114
+ - **Free-text variable ranking** — `OntologyResolver` scores variables against a query (PUI / name / synonym / trait-class) so `find_variables text:"..."` returns ranked candidates even without `/ontologies`.
115
+ - **Auth variants in one schema** — tagged-union covers `none` / `bearer` / `api_key` / `sgn` (session-token exchange) / `oauth2` (client-credentials).
116
+ - **Typed error contracts** — every declared failure mode carries a stable `data.reason`, an HTTP-style `code`, and a `recovery.hint` so clients can route deterministically.
117
+ - **Compatibility matrix** — live server probes tracked in [docs/compatibility.md](./docs/compatibility.md).
118
+
119
+ Built on [`@cyanheads/mcp-ts-core`](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) — declarative definitions, unified error handling, pluggable auth (`none` / `jwt` / `oauth`), swappable storage, structured logging with optional OTel, STDIO + Streamable HTTP transports.
368
120
 
369
121
  ---
370
122
 
371
123
  ## Getting started
372
124
 
373
- Add the following to your MCP client configuration file.
125
+ Add to your MCP client config — pick one runner:
374
126
 
375
127
  ```json
376
128
  {
@@ -379,146 +131,63 @@ Add the following to your MCP client configuration file.
379
131
  "type": "stdio",
380
132
  "command": "bunx",
381
133
  "args": ["@cyanheads/brapi-mcp-server@latest"],
382
- "env": {
383
- "MCP_TRANSPORT_TYPE": "stdio",
384
- "MCP_LOG_LEVEL": "info"
385
- }
134
+ "env": { "MCP_TRANSPORT_TYPE": "stdio", "MCP_LOG_LEVEL": "info" }
386
135
  }
387
136
  }
388
137
  }
389
138
  ```
390
139
 
391
- Or with npx (no Bun required):
140
+ Swap `command`/`args` for `npx -y @cyanheads/brapi-mcp-server@latest` (no Bun) or `docker run -i --rm -e MCP_TRANSPORT_TYPE=stdio ghcr.io/cyanheads/brapi-mcp-server:latest`.
392
141
 
393
- ```json
394
- {
395
- "mcpServers": {
396
- "brapi": {
397
- "type": "stdio",
398
- "command": "npx",
399
- "args": ["-y", "@cyanheads/brapi-mcp-server@latest"],
400
- "env": {
401
- "MCP_TRANSPORT_TYPE": "stdio",
402
- "MCP_LOG_LEVEL": "info"
403
- }
404
- }
405
- }
406
- }
407
- ```
408
-
409
- Or with Docker:
410
-
411
- ```json
412
- {
413
- "mcpServers": {
414
- "brapi": {
415
- "type": "stdio",
416
- "command": "docker",
417
- "args": [
418
- "run", "-i", "--rm",
419
- "-e", "MCP_TRANSPORT_TYPE=stdio",
420
- "ghcr.io/cyanheads/brapi-mcp-server:latest"
421
- ]
422
- }
423
- }
424
- }
425
- ```
426
-
427
- For Streamable HTTP, set the transport and start the server:
142
+ For Streamable HTTP:
428
143
 
429
144
  ```sh
430
145
  MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
431
146
  # Server listens at http://localhost:3010/mcp
432
147
  ```
433
148
 
434
- No environment variables are required for the public BrAPI test server — agents can open connections at runtime via `brapi_connect`. **For credentialed servers, prefer env vars over agent input**: set `BRAPI_DEFAULT_*` for a default connection, or `BRAPI_<ALIAS>_*` per registered alias, so passwords / tokens / API keys stay out of the LLM context. See [Per-alias credentials](#per-alias-credentials).
435
-
436
- ### Prerequisites
437
-
438
- - [Bun v1.3.11](https://bun.sh/) or higher (or Node.js v22+).
439
- - A BrAPI v2 endpoint to point at — the public [test server](https://test-server.brapi.org/brapi/v2) works out of the box; production servers typically need credentials.
440
- - *(Optional)* [`@duckdb/node-api`](https://www.npmjs.com/package/@duckdb/node-api) — required only to enable the dataframe surface (`CANVAS_PROVIDER_TYPE=duckdb`). Listed as an optional peer dep so the bare install stays light. Linux/macOS/Windows × x64 plus Linux/macOS arm64 supported (Windows arm64 is unsupported by DuckDB upstream). Not available on Cloudflare Workers.
441
-
442
- ### Installation
443
-
444
- 1. **Clone the repository:**
445
-
446
- ```sh
447
- git clone https://github.com/cyanheads/brapi-mcp-server.git
448
- ```
449
-
450
- 2. **Navigate into the directory:**
451
-
452
- ```sh
453
- cd brapi-mcp-server
454
- ```
455
-
456
- 3. **Install dependencies:**
457
-
458
- ```sh
459
- bun install
460
- ```
149
+ No env vars are required — the six built-in aliases (`bti-cassava`, `bti-sweetpotato`, `bti-breedbase-demo`, `t3-wheat`, `t3-oat`, `t3-barley`) resolve out-of-the-box, and agents can connect to any other BrAPI v2 URL at runtime via `brapi_connect`. **For credentialed servers, prefer env vars over agent input** so passwords / tokens / API keys stay out of the LLM context — see [Per-alias credentials](#per-alias-credentials).
461
150
 
462
- 4. **Configure environment:**
463
-
464
- ```sh
465
- cp .env.example .env
466
- # edit .env and set required vars
467
- ```
151
+ **Prerequisites:** [Bun v1.3.11+](https://bun.sh/) or Node.js v22+. *(Optional)* [`@duckdb/node-api`](https://www.npmjs.com/package/@duckdb/node-api) for the dataframe surface — Linux/macOS/Windows × x64 plus Linux/macOS arm64 (no Windows arm64; no Cloudflare Workers).
468
152
 
469
153
  ---
470
154
 
471
155
  ## Configuration
472
156
 
473
- Every variable is optional — agents can configure connections entirely at runtime via `brapi_connect`. Set the `BRAPI_DEFAULT_*` variables if you want a default connection without an explicit `brapi_connect` call.
157
+ Every variable is optional.
474
158
 
475
159
  | Variable | Description | Default |
476
160
  |:---------|:------------|:--------|
477
- | `BRAPI_DEFAULT_BASE_URL` | Default BrAPI v2 base URL including path prefix (e.g. `https://test-server.brapi.org/brapi/v2`). | — |
478
- | `BRAPI_DEFAULT_USERNAME` | Default SGN-family username for session-token auth. | — |
479
- | `BRAPI_DEFAULT_PASSWORD` | Default SGN-family password. | — |
480
- | `BRAPI_DEFAULT_OAUTH_CLIENT_ID` | Default OAuth2 client ID (e.g. CGIAR-family servers). | — |
481
- | `BRAPI_DEFAULT_OAUTH_CLIENT_SECRET` | Default OAuth2 client secret. | — |
482
- | `BRAPI_DEFAULT_API_KEY` | Default static API key. | — |
483
- | `BRAPI_DEFAULT_API_KEY_HEADER` | Header name carrying the static API key. | `Authorization` |
484
- | `BRAPI_LOAD_LIMIT` | In-context row cap before `find_*` tools spill to `DatasetStore`. | `200` |
485
- | `BRAPI_MAX_CONCURRENT_REQUESTS` | Per-connection concurrency cap for parallel upstream fan-out. | `4` |
486
- | `BRAPI_RETRY_MAX_ATTEMPTS` | Max retries on 429/5xx before surfacing the error. | `3` |
487
- | `BRAPI_RETRY_BASE_DELAY_MS` | Base delay for exponential backoff between retries. | `500` |
161
+ | `BRAPI_DEFAULT_BASE_URL` | Default BrAPI v2 base URL (e.g. `https://test-server.brapi.org/brapi/v2`). | — |
162
+ | `BRAPI_DEFAULT_USERNAME` / `_PASSWORD` | SGN session-token auth for the default connection. | — |
163
+ | `BRAPI_DEFAULT_OAUTH_CLIENT_ID` / `_OAUTH_CLIENT_SECRET` | OAuth2 client-credentials for the default connection. | — |
164
+ | `BRAPI_DEFAULT_API_KEY` / `_API_KEY_HEADER` | Static API key for the default connection. | header `Authorization` |
165
+ | `BRAPI_BUILTIN_ALIASES_DISABLED` | Comma-separated alias names (case-insensitive) to remove from the built-in registry. | — |
166
+ | `BRAPI_LOAD_LIMIT` | In-context row cap before `find_*` spills to `DatasetStore`. | `200` |
167
+ | `BRAPI_MAX_CONCURRENT_REQUESTS` | Per-connection concurrency cap. | `4` |
168
+ | `BRAPI_RETRY_MAX_ATTEMPTS` / `BRAPI_RETRY_BASE_DELAY_MS` | Retry policy for 429/5xx with exponential backoff. | `3` / `500` |
488
169
  | `BRAPI_REQUEST_TIMEOUT_MS` | Per-request HTTP timeout. | `30000` |
489
- | `BRAPI_SEARCH_POLL_TIMEOUT_MS` | Total budget for async `/search/{noun}/{id}` polling. | `60000` |
490
- | `BRAPI_SEARCH_POLL_INTERVAL_MS` | Interval between async-search status checks. | `1000` |
491
- | `BRAPI_DATASET_TTL_SECONDS` | TTL for spilled datasets. | `86400` |
492
- | `BRAPI_DATASET_STORE_DIR` | Filesystem path for `DatasetStore` payloads when filesystem storage is active. | — |
493
- | `BRAPI_REFERENCE_CACHE_TTL_SECONDS` | TTL for reference-data cache entries (programs, trials, locations, crops). | `3600` |
494
- | `BRAPI_ALLOW_PRIVATE_IPS` | Allow connecting to RFC 1918 / loopback targets. Dev-only. | `false` |
495
- | `BRAPI_ENABLE_WRITES` | 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 for this deployment. | `false` |
496
- | `BRAPI_GENOTYPE_CALLS_MAX_PULL` | Hard ceiling on rows pulled from the upstream BrAPI server in a single `brapi_find_genotype_calls` invocation. Bounds total page count per query — protects upstream from unbounded pagination loops. Maximum 500,000. | `100000` |
497
- | `CANVAS_PROVIDER_TYPE` | Framework-side switch for the `DataCanvas` primitive. Set to `duckdb` to enable the dataframe surface. Fails closed on Cloudflare Workers. | `none` |
498
- | `BRAPI_CANVAS_ENABLED` | Server-side gate for `brapi_dataframe_*` tools. Effective only when `CANVAS_PROVIDER_TYPE=duckdb`. | `true` |
499
- | `BRAPI_CANVAS_MAX_ROWS` | Hard cap on rows materialized into a `brapi_dataframe_query` response. Use `registerAs` to keep larger result sets in the workspace. | `10000` |
500
- | `BRAPI_CANVAS_QUERY_TIMEOUT_MS` | Per-query wall-clock timeout for `brapi_dataframe_query`. | `30000` |
501
- | `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` |
502
- | `MCP_HTTP_PORT` | Port for HTTP server. | `3010` |
503
- | `MCP_AUTH_MODE` | Auth mode: `none`, `jwt`, or `oauth`. | `none` |
504
- | `MCP_LOG_LEVEL` | Log level (RFC 5424). | `info` |
505
- | `STORAGE_PROVIDER_TYPE` | Storage backend. | `in-memory` |
506
- | `OTEL_ENABLED` | Enable OpenTelemetry. | `false` |
507
-
508
- Per-alias overrides follow the `BRAPI_<ALIAS>_*` pattern — see [Per-alias credentials](#per-alias-credentials).
509
-
510
- See [`.env.example`](./.env.example) for the full list of optional overrides.
170
+ | `BRAPI_SEARCH_POLL_TIMEOUT_MS` / `_INTERVAL_MS` | Async `/search` polling budget + interval. | `60000` / `1000` |
171
+ | `BRAPI_DATASET_TTL_SECONDS` / `BRAPI_DATASET_STORE_DIR` | TTL for spilled datasets + filesystem path when filesystem storage is active. | `86400` / — |
172
+ | `BRAPI_REFERENCE_CACHE_TTL_SECONDS` | TTL for programs / trials / locations / crops cache. | `3600` |
173
+ | `BRAPI_ALLOW_PRIVATE_IPS` | Allow RFC 1918 / loopback targets. Dev-only. | `false` |
174
+ | `BRAPI_ENABLE_WRITES` | Opt-in for `brapi_submit_observations` registration. | `false` |
175
+ | `BRAPI_GENOTYPE_CALLS_MAX_PULL` | Upstream row ceiling per `brapi_find_genotype_calls` invocation. Max 500,000. | `100000` |
176
+ | `CANVAS_PROVIDER_TYPE` | Framework `DataCanvas` switch — set to `duckdb` to enable the dataframe surface. | `none` |
177
+ | `BRAPI_CANVAS_ENABLED` / `BRAPI_CANVAS_MAX_ROWS` / `BRAPI_CANVAS_QUERY_TIMEOUT_MS` | Dataframe surface gate, response row cap, per-query timeout. | `true` / `10000` / `30000` |
178
+ | `MCP_TRANSPORT_TYPE` / `MCP_HTTP_PORT` | Transport (`stdio` \| `http`) + HTTP port. | `stdio` / `3010` |
179
+ | `MCP_AUTH_MODE` / `MCP_LOG_LEVEL` / `STORAGE_PROVIDER_TYPE` / `OTEL_ENABLED` | Auth mode (`none` \| `jwt` \| `oauth`), log level, storage backend, OpenTelemetry. | `none` / `info` / `in-memory` / `false` |
180
+
181
+ Per-alias overrides follow the `BRAPI_<ALIAS>_*` pattern — see [`.env.example`](./.env.example) for every override and inline comments.
511
182
 
512
183
  ### Per-alias credentials
513
184
 
514
- `brapi_connect` resolves `baseUrl` and `auth` from env vars when the agent omits them, so credentials never enter the LLM context. Four layers of precedence:
185
+ `brapi_connect` resolves `baseUrl` and `auth` from env vars when the agent omits them — credentials never enter the LLM context. Four layers of precedence:
515
186
 
516
187
  1. **Explicit agent input** — always wins.
517
- 2. **Per-alias env vars** — `BRAPI_<ALIAS>_*` where the alias name is uppercased and hyphens become underscores (`my-server` → `BRAPI_MY_SERVER_*`).
518
- 3. **Built-in known-server registry** — see [Built-in aliases](#built-in-aliases) below.
519
- 4. **Default env vars** — `BRAPI_DEFAULT_*`, only consulted when the alias differs from `default`.
520
-
521
- When the baseUrl is satisfied by a builtin, `BRAPI_DEFAULT_*` credentials are **not** layered on top — those belong to the default server, not whatever upstream the builtin happens to point at. Per-alias credentials still apply, since those were explicitly set for this alias.
188
+ 2. **Per-alias env vars** — `BRAPI_<ALIAS>_*` (uppercased, hyphens → underscores: `my-server` → `BRAPI_MY_SERVER_*`).
189
+ 3. **Built-in known-server registry** — see [Built-in aliases](#built-in-aliases).
190
+ 4. **Default env vars** — `BRAPI_DEFAULT_*`, only when the alias differs from `default`. Not layered on top of a built-in URL — defaults belong to the default server.
522
191
 
523
192
  Each alias carries **one** credential family — auth mode is derived from which fields are set:
524
193
 
@@ -530,75 +199,58 @@ Each alias carries **one** credential family — auth mode is derived from which
530
199
  | `_OAUTH_CLIENT_ID` + `_OAUTH_CLIENT_SECRET` (+ optional `_OAUTH_TOKEN_URL`) | `oauth2` |
531
200
  | _(none set)_ | `none` |
532
201
 
533
- Mixing families within a single alias raises a `ValidationError` naming the conflict.
202
+ Mixing families within an alias raises a `ValidationError`.
534
203
 
535
204
  ```sh
536
- # .env — register Cassavabase as alias 'cassava'
537
- BRAPI_CASSAVA_BASE_URL=https://cassavabase.org/brapi/v2
538
- BRAPI_CASSAVA_USERNAME=alice
539
- BRAPI_CASSAVA_PASSWORD=...
205
+ # .env — attach write credentials to the built-in 'bti-cassava' alias
206
+ BRAPI_BTI_CASSAVA_USERNAME=alice
207
+ BRAPI_BTI_CASSAVA_PASSWORD=...
208
+ # (BASE_URL omitted — built-in registry covers it)
540
209
 
541
- # Register a static-API-key server as alias 'prod'
210
+ # Static API key as alias 'prod'
542
211
  BRAPI_PROD_BASE_URL=https://my-brapi.example.com/brapi/v2
543
212
  BRAPI_PROD_API_KEY=...
544
213
  BRAPI_PROD_API_KEY_HEADER=X-API-Key
545
-
546
- # Register an OAuth2 client-credentials server as alias 'secure'
547
- BRAPI_SECURE_BASE_URL=https://my-oauth-brapi.example.com/brapi/v2
548
- BRAPI_SECURE_OAUTH_CLIENT_ID=...
549
- BRAPI_SECURE_OAUTH_CLIENT_SECRET=...
550
- BRAPI_SECURE_OAUTH_TOKEN_URL=https://auth.example.com/oauth/token
551
214
  ```
552
215
 
553
- Then the agent calls `brapi_connect({ alias: 'cassava' })` — no `baseUrl`, no `auth`, no secrets in the prompt.
216
+ Then the agent calls `brapi_connect({ alias: 'bti-cassava' })` — no `baseUrl`, no `auth`, no secrets in the prompt.
554
217
 
555
218
  ### Built-in aliases
556
219
 
557
- The server ships with a curated registry of public BrAPI v2 endpoints. Each alias resolves out-of-the-box without any env vars — call `brapi_connect({ alias: 'cassava' })` and the resolver fills in the URL. Each entry is published under [Creative Commons Attribution](https://creativecommons.org/licenses/by/4.0/); the orientation envelope surfaces license, citation, and homepage in its `attribution` block so agents can satisfy reuse terms automatically.
220
+ The server ships with a curated registry of public BrAPI v2 endpoints. Each resolves out-of-the-box; the orientation envelope surfaces license, citation, and homepage in its `attribution` block under [Creative Commons Attribution](https://creativecommons.org/licenses/by/4.0/).
558
221
 
559
222
  | Alias | Upstream | Hosted by | Crop | Notes |
560
223
  |:------|:---------|:----------|:-----|:------|
561
- | `cassava` | [cassavabase.org](https://cassavabase.org/) | Boyce Thompson Institute | Cassava | NextGen Cassava project |
562
- | `sweetpotato` | [sweetpotatobase.org](https://sweetpotatobase.org/) | Boyce Thompson Institute | Sweet potato | |
563
- | `wheat` | [wheat.triticeaetoolbox.org](https://wheat.triticeaetoolbox.org/) | Triticeae Toolbox (T3) | Wheat | |
564
- | `breedbase` | [breedbase.org](https://breedbase.org/) | Boyce Thompson Institute | _Demo_ | Sample data only — not production records. Useful for onboarding and tests. |
224
+ | `bti-cassava` | [cassavabase.org](https://cassavabase.org/) | Boyce Thompson Institute | Cassava | NextGen Cassava |
225
+ | `bti-sweetpotato` | [sweetpotatobase.org](https://sweetpotatobase.org/) | Boyce Thompson Institute | Sweet potato | |
226
+ | `bti-breedbase-demo` | [breedbase.org](https://breedbase.org/) | Boyce Thompson Institute | _Demo_ | Sample data only — onboarding + tests. |
227
+ | `t3-wheat` | [wheat.triticeaetoolbox.org](https://wheat.triticeaetoolbox.org/) | Triticeae Toolbox (T3) | Wheat | Wheat CAP / IWYP. |
228
+ | `t3-oat` | [oat.triticeaetoolbox.org](https://oat.triticeaetoolbox.org/) | Triticeae Toolbox (T3) | Oat | Global Oat Genetics Database. |
229
+ | `t3-barley` | [barley.triticeaetoolbox.org](https://barley.triticeaetoolbox.org/) | Triticeae Toolbox (T3) | Barley | T-CAP / US Wheat & Barley Scab Initiative. |
565
230
 
566
- **Override:** set `BRAPI_<ALIAS>_BASE_URL=...` to repoint an alias at a staging mirror or a fork — env always wins over the builtin URL. Set `BRAPI_<ALIAS>_USERNAME=...` etc. to attach credentials on top of the builtin URL when you need write access (each Breedbase instance has its own user table — separate registration on each upstream).
231
+ Set `BRAPI_<ALIAS>_BASE_URL` to repoint at a staging mirror or fork (env wins over the built-in URL — hyphens in the alias become underscores in the env var, so `t3-wheat` → `BRAPI_T3_WHEAT_BASE_URL`). Set `BRAPI_<ALIAS>_USERNAME` etc. to attach credentials on top of the built-in URL — each Breedbase instance has its own user table, so write access requires separate registration on each upstream. Use `BRAPI_BUILTIN_ALIASES_DISABLED=bti-cassava,t3-wheat` to strip specific entries.
567
232
 
568
- **Opt-out:** `BRAPI_BUILTIN_ALIASES_DISABLED=cassava,wheat` (comma-separated, case-insensitive) removes specific aliases from resolution and discovery for deployments that prefer a stripped surface.
569
-
570
- **Citation:** all four shipped builtins reference the same foundational paper — Morales et al. 2022, _"Breedbase: a digital ecosystem for modern plant breeding."_ G3 12(7): jkac078. [doi:10.1093/g3journal/jkac078](https://doi.org/10.1093/g3journal/jkac078).
233
+ **Citation:** all six built-ins reference Morales et al. 2022, _"Breedbase: a digital ecosystem for modern plant breeding."_ G3 12(7): jkac078. [doi:10.1093/g3journal/jkac078](https://doi.org/10.1093/g3journal/jkac078).
571
234
 
572
235
  ---
573
236
 
574
237
  ## Running the server
575
238
 
576
- ### Local development
577
-
578
- - **Hot-reload dev mode** (Bun runs TypeScript directly):
579
-
580
- ```sh
581
- MCP_TRANSPORT_TYPE=stdio bun --watch src/index.ts
582
- MCP_TRANSPORT_TYPE=http bun --watch src/index.ts
583
- ```
584
-
585
- - **Build and run the production version:**
586
-
587
- ```sh
588
- bun run rebuild
589
- bun run start # transport selected via MCP_TRANSPORT_TYPE (stdio default)
590
- # or pin the transport explicitly:
591
- bun run start:stdio
592
- bun run start:http
593
- ```
594
-
595
- - **Run checks and tests:**
596
-
597
- ```sh
598
- bun run devcheck # Lint, format, typecheck, security, changelog sync
599
- bun run test # Vitest suite
600
- bun run lint:mcp # Validate MCP definitions against spec
601
- ```
239
+ ```sh
240
+ # Hot-reload dev (Bun runs TS directly)
241
+ bun --watch src/index.ts
242
+
243
+ # Production
244
+ bun run rebuild
245
+ bun run start # transport via MCP_TRANSPORT_TYPE (stdio default)
246
+ bun run start:stdio # or pin explicitly
247
+ bun run start:http
248
+
249
+ # Checks
250
+ bun run devcheck # lint + format + typecheck + security + changelog sync
251
+ bun run test # Vitest
252
+ bun run lint:mcp # validate MCP definitions
253
+ ```
602
254
 
603
255
  ### Docker
604
256
 
@@ -607,66 +259,43 @@ docker build -t brapi-mcp-server .
607
259
  docker run --rm -p 3010:3010 brapi-mcp-server
608
260
  ```
609
261
 
610
- The Dockerfile defaults to HTTP transport, stateless 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.
262
+ Defaults to HTTP transport, stateless session mode, logs to `/var/log/brapi-mcp-server`. OTel peer deps are installed by default — `--build-arg OTEL_ENABLED=false` to omit.
611
263
 
612
264
  ### Multi-user HTTP deployments
613
265
 
614
- `ctx.state` — where `ServerRegistry` (connection aliases + resolved bearer tokens), `DatasetStore` (spilled `find_*` rows), and `CapabilityRegistry` (cached `/serverinfo` profiles) live — is **scoped by `tenantId`, not by MCP session id**. Tenant resolution:
266
+ `ctx.state` (where `ServerRegistry`, `DatasetStore`, and `CapabilityRegistry` live) is **scoped by `tenantId`, not session id**:
615
267
 
616
- | Mode | Resolved `tenantId` |
617
- |:-----|:--------------------|
268
+ | Mode | `tenantId` |
269
+ |:-----|:-----------|
618
270
  | `MCP_TRANSPORT_TYPE=stdio` (any auth) | `default` |
619
- | `MCP_TRANSPORT_TYPE=http` + `MCP_AUTH_MODE=none` (default) | `default` for every connected client |
620
- | `MCP_TRANSPORT_TYPE=http` + `MCP_AUTH_MODE=jwt` or `oauth` | JWT `tid` claim, fail-closed if absent |
621
-
622
- In HTTP + `none`, every client shares one bucket: connection aliases registered by one user (including the access token resolved from an SGN `/token` exchange) are reachable to any other connected user. For shared HTTP deployments, set `MCP_AUTH_MODE=jwt` (HS256, `MCP_AUTH_SECRET_KEY`) or `oauth` (JWKS, `OAUTH_ISSUER_URL` + `OAUTH_AUDIENCE`) so each caller's `tid` carves its own state.
623
-
624
- ---
271
+ | `http` + `MCP_AUTH_MODE=none` | `default` for every client — **shared bucket** |
272
+ | `http` + `jwt` or `oauth` | JWT `tid` claim, fail-closed if absent |
625
273
 
626
- ## Project structure
627
-
628
- | Directory | Purpose |
629
- |:----------|:--------|
630
- | `src/index.ts` | `createApp()` entry point — registers 22 tools, 6 resources, 2 prompts, and inits the eight services. |
631
- | `src/config` | Server-specific environment variable parsing with Zod. |
632
- | `src/mcp-server/tools` | Tool definitions (`*.tool.ts`) and shared helpers (`orientation-envelope`, `find-helpers`, `connect-auth-schema`, `raw-routing-hints`). |
633
- | `src/mcp-server/resources` | Resource definitions (`*.resource.ts`) — URI-addressable mirrors of curated tool data. |
634
- | `src/mcp-server/prompts` | Prompt definitions (`*.prompt.ts`) — multi-step BrAPI workflow templates. |
635
- | `src/services/brapi-client` | HTTP client with retry, concurrency capping, async-search polling, private-IP guard, and binary fetch. |
636
- | `src/services/brapi-filters` | Static BrAPI v2.1 filter catalog. |
637
- | `src/services/canvas-bridge` | Bridge over the framework's `DataCanvas` primitive — per-tenant default-workspace resolution, dataframe naming, provenance tracking. |
638
- | `src/services/capability-registry` | Per-connection capability profile cache. |
639
- | `src/services/dataset-store` | Tenant-scoped dataset handles for spilled `find_*` results. Auto-registers rows as dataframes when the canvas-bridge is enabled. |
640
- | `src/services/ontology-resolver` | Free-text → ontology-candidate matcher powering `brapi_find_variables` ranking. |
641
- | `src/services/reference-data-cache` | Cache for programs, trials, locations, crops. |
642
- | `src/services/server-registry` | Alias → live BrAPI connection map with auth resolution. |
643
- | `tests/` | Unit and integration tests mirroring `src/`. |
644
- | `docs/design.md` | End-to-end surface design (current + planned tools). |
274
+ For shared HTTP deployments, set `MCP_AUTH_MODE=jwt` (HS256, `MCP_AUTH_SECRET_KEY`) or `oauth` (JWKS, `OAUTH_ISSUER_URL` + `OAUTH_AUDIENCE`) so each caller's `tid` carves its own state. Otherwise registered aliases — including SGN-exchanged bearer tokens — leak across users.
645
275
 
646
276
  ---
647
277
 
648
- ## Development guide
278
+ ## Development
649
279
 
650
- See [`CLAUDE.md`](./CLAUDE.md) for development guidelines and architectural rules. The short version:
280
+ See [`CLAUDE.md`](./CLAUDE.md) for full architectural rules. Short version:
651
281
 
652
282
  - Handlers throw, framework catches — no `try/catch` in tool logic
653
- - Use `ctx.log` for request-scoped logging, `ctx.state` for tenant-scoped storage
283
+ - Use `ctx.log` for logging, `ctx.state` for storage — no `console`, no direct persistence
654
284
  - Register new tools in the `tools` array of `createApp()` in `src/index.ts`
655
- - Wrap upstream calls: validate raw → normalize to domain type → return output schema; never fabricate missing fields
656
-
657
- ---
658
-
659
- ## Contributing
660
-
661
- Issues and pull requests are welcome. Run checks and tests before submitting:
285
+ - Wrap upstream calls: validate raw → normalize → return output schema; never fabricate missing fields
662
286
 
663
287
  ```sh
664
- bun run devcheck
665
- bun run test
288
+ git clone https://github.com/cyanheads/brapi-mcp-server.git
289
+ cd brapi-mcp-server
290
+ bun install
291
+ cp .env.example .env # edit if you need credentials
292
+ bun run devcheck && bun run test
666
293
  ```
667
294
 
295
+ PRs welcome.
296
+
668
297
  ---
669
298
 
670
299
  ## License
671
300
 
672
- Apache-2.0 — see [LICENSE](LICENSE) for details.
301
+ Apache-2.0 — see [LICENSE](LICENSE).
package/changelog/0.4.x/0.4.13.md ADDED
@@ -0,0 +1,42 @@
1
+ ---
2
+ summary: "Built-in alias rename — source-prefixed handles (`bti-*`, `t3-*`); adds T3/Oat and T3/Barley; fixes hyphenated-builtin env shadow."
3
+ breaking: false
4
+ ---
5
+
6
+ # 0.4.13 — 2026-05-04
7
+
8
+ Source-prefixed alias rename across the built-in registry, plus two new T3 small-grains servers. Tool schemas refresh on next connect, so agents reading the current connect tool description pick up the new handles automatically. Operators with per-alias credential env vars (e.g. `BRAPI_CASSAVA_USERNAME`) need to rename to the new prefix (`BRAPI_BTI_CASSAVA_USERNAME`) — see Migration below.
9
+
10
+ ## Added
11
+
12
+ - **`t3-oat` and `t3-barley` built-ins** — Triticeae Toolbox (T3) hosts three sibling Breedbase instances at `*.triticeaetoolbox.org`; only wheat shipped before. Live probes confirm anonymous reads return real data: T3/Oat advertises 2,564 studies / 59,780 germplasm / 288 variables, T3/Barley 1,574 / 63,859 / 208. Same Breedbase platform underneath, same CC-BY posture, same Morales et al. 2022 citation as the existing entries.
13
+
14
+ ## Changed
15
+
16
+ - **Built-in aliases renamed to source-prefixed handles** so the hosting source is visible at the call site:
17
+
18
+ | Before | After |
19
+ |:-------|:------|
20
+ | `cassava` | `bti-cassava` |
21
+ | `sweetpotato` | `bti-sweetpotato` |
22
+ | `wheat` | `t3-wheat` |
23
+ | `breedbase` | `bti-breedbase-demo` |
24
+
25
+ Tool input schema is unchanged (alias is still a free-form `z.string().regex(...)`), and the connect tool description lists current builtins dynamically — fresh agent sessions read the new handles and use them. Custom env-only aliases under the old short names (`cassava`, `sweetpotato`, `wheat`, `breedbase`) are now valid free-form names that resolve via `BRAPI_<ALIAS>_*` env vars only — they no longer shadow a built-in.
26
+
27
+ ## Fixed
28
+
29
+ - **`discoverConfiguredAliases` reverse-maps env var keys against hyphenated builtins.** The regex extracted alias names from `BRAPI_<X>_BASE_URL` keys but couldn't tell whether an underscore in the captured group should map back to a hyphen, so an env var like `BRAPI_BTI_CASSAVA_BASE_URL` was reported as a separate `bti_cassava` alias instead of shadowing the built-in `bti-cassava`. Discovery now consults the registry's underscored-name map and uses the canonical hyphenated alias when one matches. `resolveConnectInput` was unaffected — it derives the env prefix from the alias the agent passed.
30
+
31
+ ## Migration
32
+
33
+ Operators who attached per-alias credentials to a built-in via env vars need to rename:
34
+
35
+ | Old env var | New env var |
36
+ |:------------|:------------|
37
+ | `BRAPI_CASSAVA_*` | `BRAPI_BTI_CASSAVA_*` |
38
+ | `BRAPI_SWEETPOTATO_*` | `BRAPI_BTI_SWEETPOTATO_*` |
39
+ | `BRAPI_WHEAT_*` | `BRAPI_T3_WHEAT_*` |
40
+ | `BRAPI_BREEDBASE_*` | `BRAPI_BTI_BREEDBASE_DEMO_*` |
41
+
42
+ `BRAPI_BUILTIN_ALIASES_DISABLED` values follow the same rename. Hardcoded `alias: 'cassava'` (etc.) in agent system prompts or saved scripts also need updating to the new handles.
package/dist/config/alias-credentials.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
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package/dist/config/alias-credentials.js CHANGED
@@ -130,12 +130,19 @@ const ALIAS_BASE_URL_PATTERN = /^BRAPI_([A-Z0-9_]+)_BASE_URL$/;
130
130
  export function discoverConfiguredAliases(env = process.env) {
131
131
  const result = [];
132
132
  const seen = new Set();
133
+ const builtins = listBuiltinAliases(env);
134
+ // Reverse-map for hyphen → underscore env-var translation: a builtin named
135
+ // `bti-cassava` exposes BRAPI_BTI_CASSAVA_*, but the regex below only sees
136
+ // the underscored form. Without this map, an env var that shadows a
137
+ // hyphenated builtin would be reported as a separate `bti_cassava` alias.
138
+ const builtinByUnderscoredName = new Map(builtins.map((b) => [b.alias.replace(/-/g, '_'), b]));
133
139
  for (const [key, value] of Object.entries(env)) {
134
140
  const match = key.match(ALIAS_BASE_URL_PATTERN);
135
141
  const captured = match?.[1];
136
142
  if (!captured || !value)
137
143
  continue;
138
- const alias = captured.toLowerCase();
144
+ const lowerCaptured = captured.toLowerCase();
145
+ const alias = builtinByUnderscoredName.get(lowerCaptured)?.alias ?? lowerCaptured;
139
146
  const creds = readAliasCredentials(alias, env);
140
147
  result.push({
141
148
  alias,
@@ -145,7 +152,7 @@ export function discoverConfiguredAliases(env = process.env) {
145
152
  });
146
153
  seen.add(alias);
147
154
  }
148
- for (const builtin of listBuiltinAliases(env)) {
155
+ for (const builtin of builtins) {
149
156
  if (seen.has(builtin.alias))
150
157
  continue;
151
158
  const creds = readAliasCredentials(builtin.alias, env);
package/dist/config/alias-credentials.js.map CHANGED
@@ -1 +1 @@
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+ 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package/dist/config/builtin-aliases.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"builtin-aliases.d.ts","sourceRoot":"","sources":["../../src/config/builtin-aliases.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAKH,MAAM,WAAW,YAAY;IAC3B,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;IACvB,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC;IAC1B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC;IAC1B,QAAQ,CAAC,MAAM,CAAC,EAAE,OAAO,CAAC;IAC1B,QAAQ,CAAC,OAAO,EAAE,OAAO,CAAC;IAC1B,QAAQ,CAAC,gBAAgB,EAAE,MAAM,CAAC;CACnC;AAED;;;;;;GAMG;AACH,eAAO,MAAM,eAAe,EAAE,aAAa,CAAC,YAAY,CAsCtD,CAAC;AAmBH;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAC9B,KAAK,EAAE,MAAM,EACb,GAAG,GAAE,MAAM,CAAC,UAAwB,GACnC,YAAY,GAAG,SAAS,CAK1B;AAED;;;;GAIG;AACH,wBAAgB,kBAAkB,CAChC,GAAG,GAAE,MAAM,CAAC,UAAwB,GACnC,aAAa,CAAC,YAAY,CAAC,CAI7B"}
1
+ {"version":3,"file":"builtin-aliases.d.ts","sourceRoot":"","sources":["../../src/config/builtin-aliases.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAKH,MAAM,WAAW,YAAY;IAC3B,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;IACvB,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC;IAC1B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC;IAC1B,QAAQ,CAAC,MAAM,CAAC,EAAE,OAAO,CAAC;IAC1B,QAAQ,CAAC,OAAO,EAAE,OAAO,CAAC;IAC1B,QAAQ,CAAC,gBAAgB,EAAE,MAAM,CAAC;CACnC;AAED;;;;;;GAMG;AACH,eAAO,MAAM,eAAe,EAAE,aAAa,CAAC,YAAY,CAwDtD,CAAC;AAmBH;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAC9B,KAAK,EAAE,MAAM,EACb,GAAG,GAAE,MAAM,CAAC,UAAwB,GACnC,YAAY,GAAG,SAAS,CAK1B;AAED;;;;GAIG;AACH,wBAAgB,kBAAkB,CAChC,GAAG,GAAE,MAAM,CAAC,UAAwB,GACnC,aAAa,CAAC,YAAY,CAAC,CAI7B"}
package/dist/config/builtin-aliases.js CHANGED
@@ -27,7 +27,7 @@ const BREEDBASE_CITATION = 'Morales et al. 2022. "Breedbase: a digital ecosystem
27
27
  */
28
28
  export const BUILTIN_ALIASES = Object.freeze([
29
29
  Object.freeze({
30
- alias: 'cassava',
30
+ alias: 'bti-cassava',
31
31
  baseUrl: 'https://cassavabase.org/brapi/v2',
32
32
  homepage: 'https://cassavabase.org/',
33
33
  organizationName: 'Boyce Thompson Institute',
@@ -36,7 +36,7 @@ export const BUILTIN_ALIASES = Object.freeze([
36
36
  citation: BREEDBASE_CITATION,
37
37
  }),
38
38
  Object.freeze({
39
- alias: 'sweetpotato',
39
+ alias: 'bti-sweetpotato',
40
40
  baseUrl: 'https://sweetpotatobase.org/brapi/v2',
41
41
  homepage: 'https://sweetpotatobase.org/',
42
42
  organizationName: 'Boyce Thompson Institute',
@@ -45,7 +45,7 @@ export const BUILTIN_ALIASES = Object.freeze([
45
45
  citation: BREEDBASE_CITATION,
46
46
  }),
47
47
  Object.freeze({
48
- alias: 'wheat',
48
+ alias: 't3-wheat',
49
49
  baseUrl: 'https://wheat.triticeaetoolbox.org/brapi/v2',
50
50
  homepage: 'https://wheat.triticeaetoolbox.org/',
51
51
  organizationName: 'Triticeae Toolbox (T3)',
@@ -54,7 +54,25 @@ export const BUILTIN_ALIASES = Object.freeze([
54
54
  citation: BREEDBASE_CITATION,
55
55
  }),
56
56
  Object.freeze({
57
- alias: 'breedbase',
57
+ alias: 't3-oat',
58
+ baseUrl: 'https://oat.triticeaetoolbox.org/brapi/v2',
59
+ homepage: 'https://oat.triticeaetoolbox.org/',
60
+ organizationName: 'Triticeae Toolbox (T3)',
61
+ cropFocus: 'Oat',
62
+ license: 'CC-BY',
63
+ citation: BREEDBASE_CITATION,
64
+ }),
65
+ Object.freeze({
66
+ alias: 't3-barley',
67
+ baseUrl: 'https://barley.triticeaetoolbox.org/brapi/v2',
68
+ homepage: 'https://barley.triticeaetoolbox.org/',
69
+ organizationName: 'Triticeae Toolbox (T3)',
70
+ cropFocus: 'Barley',
71
+ license: 'CC-BY',
72
+ citation: BREEDBASE_CITATION,
73
+ }),
74
+ Object.freeze({
75
+ alias: 'bti-breedbase-demo',
58
76
  baseUrl: 'https://breedbase.org/brapi/v2',
59
77
  homepage: 'https://breedbase.org/',
60
78
  organizationName: 'Boyce Thompson Institute',
package/dist/config/builtin-aliases.js.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"builtin-aliases.js","sourceRoot":"","sources":["../../src/config/builtin-aliases.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAEH,MAAM,kBAAkB,GACtB,+IAA+I,CAAC;AAalJ;;;;;;GAMG;AACH,MAAM,CAAC,MAAM,eAAe,GAAgC,MAAM,CAAC,MAAM,CAAC;IACxE,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,aAAa;QACpB,OAAO,EAAE,kCAAkC;QAC3C,QAAQ,EAAE,0BAA0B;QACpC,gBAAgB,EAAE,0BAA0B;QAC5C,SAAS,EAAE,SAAS;QACpB,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;KAC7B,CAAC;IACF,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,iBAAiB;QACxB,OAAO,EAAE,sCAAsC;QAC/C,QAAQ,EAAE,8BAA8B;QACxC,gBAAgB,EAAE,0BAA0B;QAC5C,SAAS,EAAE,aAAa;QACxB,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;KAC7B,CAAC;IACF,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,UAAU;QACjB,OAAO,EAAE,6CAA6C;QACtD,QAAQ,EAAE,qCAAqC;QAC/C,gBAAgB,EAAE,wBAAwB;QAC1C,SAAS,EAAE,OAAO;QAClB,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;KAC7B,CAAC;IACF,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,QAAQ;QACf,OAAO,EAAE,2CAA2C;QACpD,QAAQ,EAAE,mCAAmC;QAC7C,gBAAgB,EAAE,wBAAwB;QAC1C,SAAS,EAAE,KAAK;QAChB,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;KAC7B,CAAC;IACF,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,WAAW;QAClB,OAAO,EAAE,8CAA8C;QACvD,QAAQ,EAAE,sCAAsC;QAChD,gBAAgB,EAAE,wBAAwB;QAC1C,SAAS,EAAE,QAAQ;QACnB,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;KAC7B,CAAC;IACF,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,oBAAoB;QAC3B,OAAO,EAAE,gCAAgC;QACzC,QAAQ,EAAE,wBAAwB;QAClC,gBAAgB,EAAE,0BAA0B;QAC5C,SAAS,EAAE,oBAAoB;QAC/B,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;QAC5B,MAAM,EAAE,IAAI;KACb,CAAC;CACH,CAAC,CAAC;AAEH,MAAM,gBAAgB,GAAG,gCAAgC,CAAC;AAE1D;;;GAGG;AACH,SAAS,eAAe,CAAC,GAAsB;IAC7C,MAAM,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAC,CAAC;IAClC,IAAI,CAAC,GAAG;QAAE,OAAO,IAAI,GAAG,EAAE,CAAC;IAC3B,MAAM,GAAG,GAAG,IAAI,GAAG,EAAU,CAAC;IAC9B,KAAK,MAAM,IAAI,IAAI,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;QAClC,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;QAC1C,IAAI,OAAO;YAAE,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;IAChC,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,gBAAgB,CAC9B,KAAa,EACb,MAAyB,OAAO,CAAC,GAAG;IAEpC,MAAM,GAAG,GAAG,KAAK,CAAC,WAAW,EAAE,CAAC;IAChC,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,CAAC;IACtC,IAAI,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC;QAAE,OAAO;IAC9B,OAAO,eAAe,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,KAAK,KAAK,GAAG,CAAC,CAAC;AAC9D,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,kBAAkB,CAChC,MAAyB,OAAO,CAAC,GAAG;IAEpC,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,CAAC;IACtC,IAAI,QAAQ,CAAC,IAAI,KAAK,CAAC;QAAE,OAAO,eAAe,CAAC;IAChD,OAAO,eAAe,CAAC,MAAM,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC;AACvE,CAAC"}
package/package.json CHANGED
@@ -1,7 +1,7 @@
1
1
  {
2
2
  "name": "@cyanheads/brapi-mcp-server",
3
3
  "mcpName": "io.github.cyanheads/brapi-mcp-server",
4
- "version": "0.4.12",
4
+ "version": "0.4.13",
5
5
  "description": "BrAPI v2.1 MCP server — studies, germplasm, observations, genotypes, images, and pedigrees.",
6
6
  "author": "Casey Hand @cyanheads (https://github.com/cyanheads/brapi-mcp-server#readme)",
7
7
  "type": "module",
package/server.json CHANGED
@@ -6,14 +6,14 @@
6
6
  "url": "https://github.com/cyanheads/brapi-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "0.4.12",
9
+ "version": "0.4.13",
10
10
  "packages": [
11
11
  {
12
12
  "registryType": "npm",
13
13
  "registryBaseUrl": "https://registry.npmjs.org",
14
14
  "identifier": "@cyanheads/brapi-mcp-server",
15
15
  "runtimeHint": "bun",
16
- "version": "0.4.12",
16
+ "version": "0.4.13",
17
17
  "packageArguments": [
18
18
  { "type": "positional", "value": "run" },
19
19
  { "type": "positional", "value": "start:stdio" }
@@ -49,7 +49,7 @@
49
49
  "registryBaseUrl": "https://registry.npmjs.org",
50
50
  "identifier": "@cyanheads/brapi-mcp-server",
51
51
  "runtimeHint": "bun",
52
- "version": "0.4.12",
52
+ "version": "0.4.13",
53
53
  "packageArguments": [
54
54
  { "type": "positional", "value": "run" },
55
55
  { "type": "positional", "value": "start:http" }