@cyanheads/brapi-mcp-server 0.4.12 → 0.4.14

package/changelog/0.4.x/0.4.13.md

@@ -0,0 +1,57 @@
+---
+summary: "Built-in alias rename — source-prefixed handles (`bti-*`, `t3-*`); adds T3/Oat and T3/Barley; fixes hyphenated-builtin env shadow."
+breaking: false
+---
+
+# 0.4.13 — 2026-05-04
+
+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.
+
+## Added
+
+- **`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.
+
+## Changed
+
+- **Built-in aliases renamed to source-prefixed handles** so the hosting source is visible at the call site:
+
+  | Before | After |
+  |:-------|:------|
+  | `cassava` | `bti-cassava` |
+  | `sweetpotato` | `bti-sweetpotato` |
+  | `wheat` | `t3-wheat` |
+  | `breedbase` | `bti-breedbase-demo` |
+
+  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.
+
+## Fixed
+
+- **`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.
+
+## Migration
+
+Operators who attached per-alias credentials to a built-in via env vars need to rename:
+
+| Old env var | New env var |
+|:------------|:------------|
+| `BRAPI_CASSAVA_*` | `BRAPI_BTI_CASSAVA_*` |
+| `BRAPI_SWEETPOTATO_*` | `BRAPI_BTI_SWEETPOTATO_*` |
+| `BRAPI_WHEAT_*` | `BRAPI_T3_WHEAT_*` |
+| `BRAPI_BREEDBASE_*` | `BRAPI_BTI_BREEDBASE_DEMO_*` |
+
+`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.
+
+## Built-in registry snapshot
+
+Six public BrAPI v2 servers now resolve out-of-the-box from `brapi_connect`. All ship CC-BY attribution metadata via the orientation envelope; live totals probed 2026-05-04:
+
+| Alias | Upstream | Hosted by | Crop | Studies | Germplasm | Variables |
+|:------|:---------|:----------|:-----|--------:|----------:|----------:|
+| `bti-cassava` | [cassavabase.org](https://cassavabase.org/) | Boyce Thompson Institute | Cassava | 8,340 | 842,464 | 968 |
+| `bti-sweetpotato` | [sweetpotatobase.org](https://sweetpotatobase.org/) | Boyce Thompson Institute | Sweet potato | 2,020 | 182,175 | 486 |
+| `bti-breedbase-demo` | [breedbase.org](https://breedbase.org/) | Boyce Thompson Institute | _Demo_ | 26 | 880 | 572 |
+| `t3-wheat` | [wheat.triticeaetoolbox.org](https://wheat.triticeaetoolbox.org/) | Triticeae Toolbox (T3) | Wheat | 9,006 | 87,740 | 11,296 |
+| `t3-oat` | [oat.triticeaetoolbox.org](https://oat.triticeaetoolbox.org/) | Triticeae Toolbox (T3) | Oat | 2,564 | 59,780 | 288 |
+| `t3-barley` | [barley.triticeaetoolbox.org](https://barley.triticeaetoolbox.org/) | Triticeae Toolbox (T3) | Barley | 1,574 | 63,859 | 208 |
+
+Servers brapi.org/servers lists as no-auth that actually require login on every endpoint (`musabase.org`, `solgenomics.net`, `yambase.org`, `mgis5`, `gigwa-CIAT`) are intentionally absent. Citation: 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).

package/changelog/0.4.x/0.4.14.md

@@ -0,0 +1,22 @@
+---
+summary: "Live-fire fixes against Cassavabase: canvas dataframes survive null columns; deduplicates 11×-repeated synonyms; find_variables actually re-ranks against the spilled union; truthful truncated-dataset metadata; trims empty nested containers."
+breaking: false
+---
+
+# 0.4.14 — 2026-05-04
+
+Five bugs surfaced when probing the live Cassavabase surface. Each one was a quiet failure mode — wrong row counts, missing reranks, phantom duplicates — that didn't trip tests but shaped what an agent saw at the call site. Fixes verified against the upstream JSON. Internal `applyRowTransforms` refactor consolidates the spillover map-then-filter pattern. Framework bumped to 0.8.14.
+
+## Fixed
+
+- **Canvas auto-register no longer rolls back on null-bearing columns.** The framework's `schemaSniffer` infers `nullable: false` for any column that happened to be non-null in the first sniff sample, and DuckDB's appender rolls back the entire batch the first time a later row carries `null` for that column — surfaced live as `rowCount: 0` on a 348-row spillover. `CanvasBridge.registerDataset` now walks every row, classifies types, and emits an explicit all-nullable `ColumnSchema[]` so the dataframe accepts the full row set. The framework's sniffer bug is unaddressed upstream as of `@cyanheads/mcp-ts-core` 0.8.14; the workaround stays in place until the sniffer either widens to all-nullable by default or exposes an opt-in.
+- **`brapi_find_germplasm` / `brapi_get_germplasm` deduplicate `synonyms` arrays by structural identity.** Cassavabase emits each registered synonym repeated 11× per germplasm record — observed 66 entries collapse to 6 unique. Identity is taken via a stable JSON serialization (recursive key sort) because the upstream emits two different key orderings (`{synonym, type}` and `{type, synonym}`) on the same record, so insertion-order-dependent `JSON.stringify` was missing dupes. Persisted dataset, in-context view, and canvas dataframe all see the cleaned shape consistently.
+- **`brapi_find_variables` free-text rerank now walks the full upstream union, not the first page.** The ontology resolver matches against the spilled `fullRows` (e.g. all 750 variables on Cassavabase), but the rerank loop only iterated `firstPage.rows` (15 rows under the default `loadLimit`) — so matched dbIds that sat past the in-context window produced an empty `matched` set and a no-op rerank. "Dry matter content" now lands in `results[]` instead of orphaned in `ontologyCandidates[]`. Result is sliced back to `loadLimit` after the merge so the response stays bounded.
+- **Truncated dataset handles no longer report a misleading `maxRows: 50000` when the page cap fired first.** `MAX_SPILLOVER_PAGES = 50` × a small `loadLimit` (e.g. 15) caps the spillover at 750 rows, well below the 50,000-row cap — but `spillToDataset` was unconditionally tagging `maxRows = MAX_SPILLOVER_ROWS` whenever truncation occurred. `maxRows` now appears only when the row cap actually fired; page-cap events log a structured warning for operators and surface to the agent as `truncated: true` without the false 50k bound, signalling that raising `loadLimit` will push past it.
+
+## Changed
+
+- **`brapi_find_variables` strips top-level keys whose value is an empty container** (`method: {}`, etc.) from the in-context rows. Cassavabase attaches these to every variable record and the bloat is pure noise. Conservative: a nested object is dropped only when every leaf is null/undefined/empty-string; objects with any non-empty field are kept untouched, including their null siblings. Applied to in-context rows only — the spilled dataset and canvas dataframe keep the raw upstream shape for research traceability.
+- **`brapi_find_variables.text` description rewritten** to match what the code now does — "Ranks the full upstream union (the spilled dataset when one is produced, otherwise the first page) via the ontology resolver, then fills the in-context window up to loadLimit with matches first and unmatched rows for context." The old wording said "Re-ranks (does not subset) the returned rows," which understated where the rerank actually pulls from.
+- **Internal: `applyRowTransforms` consolidates the spillover map-then-filter pattern.** Three sites in `find-helpers.ts` (`maybeSpill` early-exit, `maybeSpill` error fallback, `spillToDataset`) had been duplicating the same two-line "apply mapper before filter" sequence. Centralizing it removes the drift risk that any one call site silently skips the new `rowMapper` hook.
+- **`@cyanheads/mcp-ts-core` ^0.8.13 → ^0.8.14.** Polish release upstream — adds `tool-defs-analysis` skill (read-only LLM-language audit across a server's definitions) and re-exports `disabledTool` from the package root. AGENTS.md / CLAUDE.md sync picks up the "Declare contracts inline on each tool" guidance.

package/dist/config/alias-credentials.d.ts.map

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package/dist/config/alias-credentials.js

@@ -130,12 +130,19 @@ const ALIAS_BASE_URL_PATTERN = /^BRAPI_([A-Z0-9_]+)_BASE_URL$/;
 export function discoverConfiguredAliases(env = process.env) {
     const result = [];
     const seen = new Set();
+    const builtins = listBuiltinAliases(env);
+    // Reverse-map for hyphen → underscore env-var translation: a builtin named
+    // `bti-cassava` exposes BRAPI_BTI_CASSAVA_*, but the regex below only sees
+    // the underscored form. Without this map, an env var that shadows a
+    // hyphenated builtin would be reported as a separate `bti_cassava` alias.
+    const builtinByUnderscoredName = new Map(builtins.map((b) => [b.alias.replace(/-/g, '_'), b]));
     for (const [key, value] of Object.entries(env)) {
         const match = key.match(ALIAS_BASE_URL_PATTERN);
         const captured = match?.[1];
         if (!captured || !value)
             continue;
-        const alias = captured.toLowerCase();
+        const lowerCaptured = captured.toLowerCase();
+        const alias = builtinByUnderscoredName.get(lowerCaptured)?.alias ?? lowerCaptured;
         const creds = readAliasCredentials(alias, env);
         result.push({
             alias,
@@ -145,7 +152,7 @@ export function discoverConfiguredAliases(env = process.env) {
         });
         seen.add(alias);
     }
-    for (const builtin of listBuiltinAliases(env)) {
+    for (const builtin of builtins) {
         if (seen.has(builtin.alias))
             continue;
         const creds = readAliasCredentials(builtin.alias, env);

package/dist/config/alias-credentials.js.map

@@ -1 +1 @@
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package/dist/config/builtin-aliases.d.ts.map

@@ -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"}
+{"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

@@ -27,7 +27,7 @@ const BREEDBASE_CITATION = 'Morales et al. 2022. "Breedbase: a digital ecosystem
  */
 export const BUILTIN_ALIASES = Object.freeze([
     Object.freeze({
-        alias: 'cassava',
+        alias: 'bti-cassava',
         baseUrl: 'https://cassavabase.org/brapi/v2',
         homepage: 'https://cassavabase.org/',
         organizationName: 'Boyce Thompson Institute',
@@ -36,7 +36,7 @@ export const BUILTIN_ALIASES = Object.freeze([
         citation: BREEDBASE_CITATION,
     }),
     Object.freeze({
-        alias: 'sweetpotato',
+        alias: 'bti-sweetpotato',
         baseUrl: 'https://sweetpotatobase.org/brapi/v2',
         homepage: 'https://sweetpotatobase.org/',
         organizationName: 'Boyce Thompson Institute',
@@ -45,7 +45,7 @@ export const BUILTIN_ALIASES = Object.freeze([
         citation: BREEDBASE_CITATION,
     }),
     Object.freeze({
-        alias: 'wheat',
+        alias: 't3-wheat',
         baseUrl: 'https://wheat.triticeaetoolbox.org/brapi/v2',
         homepage: 'https://wheat.triticeaetoolbox.org/',
         organizationName: 'Triticeae Toolbox (T3)',
@@ -54,7 +54,25 @@ export const BUILTIN_ALIASES = Object.freeze([
         citation: BREEDBASE_CITATION,
     }),
     Object.freeze({
-        alias: 'breedbase',
+        alias: 't3-oat',
+        baseUrl: 'https://oat.triticeaetoolbox.org/brapi/v2',
+        homepage: 'https://oat.triticeaetoolbox.org/',
+        organizationName: 'Triticeae Toolbox (T3)',
+        cropFocus: 'Oat',
+        license: 'CC-BY',
+        citation: BREEDBASE_CITATION,
+    }),
+    Object.freeze({
+        alias: 't3-barley',
+        baseUrl: 'https://barley.triticeaetoolbox.org/brapi/v2',
+        homepage: 'https://barley.triticeaetoolbox.org/',
+        organizationName: 'Triticeae Toolbox (T3)',
+        cropFocus: 'Barley',
+        license: 'CC-BY',
+        citation: BREEDBASE_CITATION,
+    }),
+    Object.freeze({
+        alias: 'bti-breedbase-demo',
         baseUrl: 'https://breedbase.org/brapi/v2',
         homepage: 'https://breedbase.org/',
         organizationName: 'Boyce Thompson Institute',

package/dist/config/builtin-aliases.js.map

@@ -1 +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,SAAS;QAChB,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,aAAa;QACpB,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,OAAO;QACd,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,WAAW;QAClB,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"}
+{"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/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-find-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6IjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiT7B,CAAC"}
+{"version":3,"file":"brapi-find-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8IjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAqT7B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.js

@@ -14,7 +14,7 @@ import { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
 import { getDatasetStore } from '../../../services/dataset-store/index.js';
 import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, applyDialectFiltersOrFail, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFiltersOrFail, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, dedupSynonymsByIdentity, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
 const GermplasmRowSchema = z
     .object({
     germplasmDbId: z.string().describe('Server-side identifier for the germplasm.'),
@@ -210,6 +210,10 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             loadLimit,
             ctx,
             store: datasetStore,
+            // CassavaBase repeats every synonym entry 11× per record. Dedup at the
+            // spillover layer so the in-context view, the persisted dataset, and
+            // the canvas dataframe all see the cleaned shape consistently.
+            rowMapper: dedupSynonymsByIdentity,
         };
         if (text)
             spillInput.rowFilter = (row) => rowMatchesText(row, text);

package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-find-variables.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variables.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiLjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAgS7B,CAAC"}
+{"version":3,"file":"brapi-find-variables.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variables.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiLjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiT7B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.js

@@ -177,7 +177,7 @@ export const brapiFindVariables = tool('brapi_find_variables', {
         text: z
             .string()
             .optional()
-            .describe('Free-text query. **Re-ranks (does not subset)** the returned rows client-side — matched rows are promoted to the top, unmatched rows still appear below. Use exact filters (`variables`, `variableNames`, `variablePUIs`, `traitClasses`, `ontologies`) to actually narrow the result set. Differs from `brapi_find_germplasm.text`, which subsets client-side.'),
+            .describe('Free-text query. Ranks the **full upstream union** (the spilled dataset when one is produced, otherwise the first page) via the ontology resolver, then fills the in-context window up to loadLimit with matches first and unmatched rows for context. Use exact filters (`variables`, `variableNames`, `variablePUIs`, `traitClasses`, `ontologies`) to actually narrow the upstream pull. Differs from `brapi_find_germplasm.text`, which drops unmatched rows.'),
         loadLimit: LoadLimitInput,
         extraFilters: ExtraFiltersInput,
     }),
@@ -247,9 +247,16 @@ export const brapiFindVariables = tool('brapi_find_variables', {
                 // and fall back to PUI for any candidate that lacked the dbId.
                 const matchedDbIds = new Set(candidates.map((c) => c.observationVariableDbId).filter((v) => Boolean(v)));
                 const matchedPuis = new Set(candidates.map((c) => c.termId).filter((v) => Boolean(v)));
+                // Iterate the full spilled union, not just firstPage.rows. The
+                // ontology resolver matches against fullRows, so matched dbIds
+                // routinely sit past the in-context window (e.g. "dry matter
+                // content" hits CO_334:0002058, which is row ~700 of 750 in
+                // alphabetical order). Walking firstPage.rows alone produced an
+                // empty `matched` set and a no-op rerank. After the merge, slice
+                // back to loadLimit so the response stays bounded.
                 const matched = [];
                 const rest = [];
-                for (const row of firstPage.rows) {
+                for (const row of fullRows) {
                     const dbId = row.observationVariableDbId;
                     const pui = row.observationVariablePUI;
                     const isMatch = (typeof dbId === 'string' && matchedDbIds.has(dbId)) ||
@@ -259,7 +266,7 @@ export const brapiFindVariables = tool('brapi_find_variables', {
                     else
                         rest.push(row);
                 }
-                rankedResults = [...matched, ...rest];
+                rankedResults = [...matched, ...rest].slice(0, loadLimit);
             }
         }
         const distributions = {
@@ -305,10 +312,19 @@ export const brapiFindVariables = tool('brapi_find_variables', {
                 'text',
             ],
         });
+        // Strip top-level keys whose value is a non-array object with no
+        // meaningful fields (every leaf null/undefined/empty). CassavaBase
+        // emits `method: {}` and similar empty containers on every variable,
+        // and the bloat is pure noise in the in-context view. Objects that
+        // carry any non-empty field are kept untouched — including their null
+        // siblings — so no information is dropped, only empty containers.
+        // Applied to in-context rows only; the spilled dataset and canvas
+        // dataframe keep the raw upstream shape for research traceability.
+        const inContextRows = rankedResults.map(pruneEmptyNestedObjects);
         const result = {
             alias: connection.alias,
-            results: rankedResults,
-            returnedCount: rankedResults.length,
+            results: inContextRows,
+            returnedCount: inContextRows.length,
             totalCount,
             hasMore: firstPage.hasMore,
             distributions,
@@ -417,4 +433,29 @@ export const brapiFindVariables = tool('brapi_find_variables', {
         return [{ type: 'text', text: lines.join('\n') }];
     },
 });
+/**
+ * Drop top-level keys whose value is a non-array object with no meaningful
+ * content. Used to suppress bloat-only containers like `method: {}` that
+ * some Breedbase deployments attach to every variable record. An object is
+ * considered meaningful iff at least one of its values is non-null,
+ * non-undefined, and non-empty-string. Arrays (including empty arrays) are
+ * always preserved — `[]` carries the semantic "no entries" rather than
+ * "container exists but empty".
+ */
+function pruneEmptyNestedObjects(row) {
+    let changed = false;
+    const out = {};
+    for (const [key, value] of Object.entries(row)) {
+        if (value && typeof value === 'object' && !Array.isArray(value)) {
+            const inner = value;
+            const meaningful = Object.values(inner).some((v) => v !== null && v !== undefined && v !== '');
+            if (!meaningful) {
+                changed = true;
+                continue;
+            }
+        }
+        out[key] = value;
+    }
+    return changed ? out : row;
+}
 //# sourceMappingURL=brapi-find-variables.tool.js.map

package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.js.map

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package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-get-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA6O5B,CAAC"}
+{"version":3,"file":"brapi-get-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0GjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiP5B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.js

@@ -12,7 +12,7 @@ import { getBrapiClient } from '../../../services/brapi-client/index.js';
 import { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
 import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, appendPassthroughLines, buildRequestOptions, collectPassthroughParts, isUpstreamNotFound, } from '../shared/find-helpers.js';
+import { AliasInput, appendPassthroughLines, buildRequestOptions, collectPassthroughParts, dedupSynonymsByIdentity, isUpstreamNotFound, } from '../shared/find-helpers.js';
 const GermplasmSchema = z
     .object({
     germplasmDbId: z.string().describe('Server-side identifier for the germplasm.'),
@@ -173,9 +173,13 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
         ]);
         const parents = pedigree?.parents ?? [];
         const attrList = attributes ?? [];
+        // Some Breedbase deployments (CassavaBase) repeat each synonym entry 11×.
+        // Dedup structurally so the in-context view matches what `find_germplasm`
+        // returns and the agent isn't asked to reason about phantom duplicates.
+        const cleanedGermplasm = dedupSynonymsByIdentity(germplasm);
         const result = {
             alias: connection.alias,
-            germplasm: germplasm,
+            germplasm: cleanedGermplasm,
             parents,
             attributes: attrList,
             directParentCount: parents.length,