@cyanheads/brapi-mcp-server 0.4.13 → 0.4.14

package/CLAUDE.md

@@ -188,6 +188,8 @@ async handler(input, ctx) {
 }
 ```
 
+**Declare contracts inline on each tool, even when similar across tools.** The contract is part of the tool's documented public surface — reading one tool definition file should give the full picture (input, output, errors, handler, format). Don't extract a shared `errors[]` constant or contract module to deduplicate near-identical entries; per-tool repetition is the intended cost of locality, and dynamic `recovery` hints often need tool-specific runtime context anyway.
+
 **Fallback (no contract entry fits, services, prototype tools):** throw via factories or plain `Error`.
 
 ```ts

package/README.md

@@ -7,7 +7,7 @@
 
 <div align="center">
 
-[![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/)
+[![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-0.4.14-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/)
 
 [![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)
 

package/changelog/0.4.x/0.4.13.md

@@ -40,3 +40,18 @@ Operators who attached per-alias credentials to a built-in via env vars need to
 | `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/mcp-server/tools/definitions/brapi-find-germplasm.tool.d.ts.map

@@ -1 +1 @@
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+{"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,

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

@@ -1 +1 @@
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package/dist/mcp-server/tools/shared/find-helpers.d.ts

@@ -153,6 +153,14 @@ export interface SpillInput<T> {
      * headers can still report the true upstream size.
      */
     rowFilter?: (row: T) => boolean;
+    /**
+     * Optional client-side transform applied to every row (first-page + spilled)
+     * before any predicate filter runs. Used to normalize sparse / duplicated
+     * upstream payloads (e.g. dedup'ing CassavaBase's 11×-repeated synonym
+     * arrays) so the in-context view, the persisted dataset, and the canvas
+     * dataframe all see the same cleaned shape. Runs before `rowFilter`.
+     */
+    rowMapper?: (row: T) => T;
     source: string;
     store: DatasetStore;
     /** Total reported by the server on the first page. */
@@ -211,6 +219,11 @@ export interface MaybeSpillInput<T> {
      * first-page rows are also filtered before being returned.
      */
     rowFilter?: (row: T) => boolean;
+    /**
+     * Optional client-side transform applied to every row (first-page + spilled)
+     * before persistence and before any `rowFilter`. See {@link SpillInput.rowMapper}.
+     */
+    rowMapper?: (row: T) => T;
     source: string;
     /**
      * Optional request overrides for spillover page pulls. Useful when a tool
@@ -248,6 +261,22 @@ export interface BrapiListResult<T> {
 export declare function extractRows<T>(result: BrapiListResult<T> | T[]): T[];
 /** Return the input as a non-empty string, or undefined. Used in distribution accessors. */
 export declare function asString(value: unknown): string | undefined;
+/**
+ * Drop entries from a `synonyms` array that are structurally identical to an
+ * entry already kept. Some Breedbase deployments (notably CassavaBase) return
+ * each registered synonym repeated 11× per germplasm record — the bloat is
+ * purely upstream and carries no information beyond the unique set.
+ *
+ * Identity is taken via a stable serialization (keys sorted recursively) so
+ * that two entries with the same fields but different property insertion
+ * order are recognized as duplicates — observed live: CassavaBase emits two
+ * key orderings on the same record. Two entries that genuinely differ on
+ * any field (e.g. same `synonym` text but different `type`) still hash to
+ * distinct keys and are both kept. When no duplicates are present the
+ * input row is returned by reference — the helper is allocation-free on
+ * the common case.
+ */
+export declare function dedupSynonymsByIdentity<T extends Record<string, unknown>>(row: T): T;
 /** Return the input as a non-empty string array, or undefined. */
 export declare function asStringArray(value: unknown): string[] | undefined;
 /**

package/dist/mcp-server/tools/shared/find-helpers.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"find-helpers.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/find-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,KAAK,OAAO,EAAE,KAAK,cAAc,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE9E,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAC9D,OAAO,KAAK,EACV,WAAW,EACX,aAAa,EACb,eAAe,EACf,mBAAmB,EACnB,YAAY,EACb,MAAM,kCAAkC,CAAC;AAC1C,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,mCAAmC,CAAC;AACtE,OAAO,KAAK,EAAE,iBAAiB,EAAE,MAAM,yCAAyC,CAAC;AACjF,OAAO,KAAK,EAEV,eAAe,EACf,YAAY,EACb,MAAM,mCAAmC,CAAC;AAC3C,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,qCAAqC,CAAC;AAE5E,kFAAkF;AAClF,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,OAAO,GAAG,OAAO,CAExD;AAED,iFAAiF;AACjF,eAAO,MAAM,kBAAkB,QAAS,CAAC;AAEzC,+EAA+E;AAC/E,eAAO,MAAM,mBAAmB,KAAK,CAAC;AAEtC,eAAO,MAAM,UAAU,4BAI0E,CAAC;AAElG,eAAO,MAAM,cAAc,4BAOxB,CAAC;AAEJ,eAAO,MAAM,iBAAiB,uDAK3B,CAAC;AAEJ;;;GAGG;AACH,wBAAgB,YAAY,CAC1B,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC9B,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,SAAS,EAC1C,QAAQ,EAAE,MAAM,EAAE,GACjB,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAiBzB;AAED;;;;;;;;;GASG;AACH,wBAAgB,yBAAyB,CACvC,GAAG,EAAE,cAAc,CAAC,qBAAqB,CAAC,EAC1C,OAAO,EAAE,YAAY,EACrB,QAAQ,EAAE,MAAM,EAChB,OAAO,EAAE,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,EAC1C,QAAQ,EAAE,MAAM,EAAE,GACjB,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAezB;AAED,MAAM,MAAM,SAAS,GACjB;IACE,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACjC,IAAI,EAAE,KAAK,CAAC;IACZ,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;CACjB,GACD;IACE,IAAI,EAAE,QAAQ,CAAC;IACf,IAAI,EAAE,MAAM,CAAC;IACb,UAAU,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACpC,OAAO,EAAE,MAAM,CAAC;CACjB,CAAC;AAEN,MAAM,WAAW,qBAAqB;IACpC,OAAO,EAAE,YAAY,CAAC;IACtB,QAAQ,EAAE,MAAM,CAAC;IACjB,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACjC,OAAO,EAAE,iBAAiB,CAAC;IAC3B,UAAU,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACpC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED;;;;;;GAMG;AACH,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,qBAAqB,GAAG,SAAS,CAgDxE;AA6BD,gDAAgD;AAChD,wBAAgB,mBAAmB,CACjC,UAAU,EAAE,gBAAgB,EAC5B,MAAM,CAAC,EAAE,mBAAmB,CAAC,QAAQ,CAAC,EACtC,SAAS,GAAE,mBAAwB,GAClC,mBAAmB,CAKrB;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,uBAAuB,CACrC,UAAU,EAAE,gBAAgB,EAC5B,OAAO,EAAE,YAAY,EACrB,MAAM,EAAE,YAAY,EACpB,QAAQ,EAAE,MAAM,EAAE,EAClB,MAAM,CAAC,EAAE,mBAAmB,CAAC,QAAQ,CAAC,GACrC,mBAAmB,CAUrB;AAED;;;;GAIG;AACH,wBAAgB,mBAAmB,CAAC,CAAC,EACnC,IAAI,EAAE,SAAS,CAAC,EAAE,EAClB,QAAQ,EAAE,CAAC,GAAG,EAAE,CAAC,KAAK,MAAM,GAAG,SAAS,MAAM,EAAE,GAAG,SAAS,GAAG,IAAI,GAClE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAYxB;AAED;;;;;;GAMG;AACH,wBAAgB,gBAAgB,CAAC,IAAI,EAAE;IACrC,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;IACd,aAAa,EAAE,MAAM,CAAC;IACtB,UAAU,EAAE,MAAM,CAAC;IACnB,OAAO,CAAC,EAAE;QAAE,QAAQ,EAAE,MAAM,CAAC;QAAC,SAAS,CAAC,EAAE,MAAM,CAAA;KAAE,GAAG,SAAS,CAAC;CAChE,GAAG,MAAM,CAMT;AAED;;;;;GAKG;AACH,wBAAgB,oBAAoB,CAClC,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAChC,YAAY,GAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAM,GACxC,MAAM,CAUR;AAED,iEAAiE;AACjE,wBAAgB,mBAAmB,CAAC,aAAa,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC,GAAG,MAAM,CAajG;AAED,MAAM,WAAW,UAAU,CAAC,CAAC;IAC3B,iEAAiE;IACjE,OAAO,EAAE,OAAO,CAAC;IACjB,sDAAsD;IACtD,YAAY,EAAE,MAAM,CAAC;IACrB,IAAI,EAAE,CAAC,EAAE,CAAC;IACV,8EAA8E;IAC9E,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED;;;;GAIG;AACH,wBAAsB,eAAe,CAAC,CAAC,EACrC,MAAM,EAAE,WAAW,EACnB,UAAU,EAAE,gBAAgB,EAC5B,IAAI,EAAE,MAAM,EACZ,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAChC,SAAS,EAAE,MAAM,EACjB,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAQxB;AAED,gFAAgF;AAChF,wBAAsB,mBAAmB,CAAC,CAAC,EACzC,MAAM,EAAE,WAAW,EACnB,UAAU,EAAE,gBAAgB,EAC5B,KAAK,EAAE,SAAS,EAChB,SAAS,EAAE,MAAM,EACjB,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CASxB;AA8CD,MAAM,WAAW,UAAU,CAAC,CAAC;IAC3B,MAAM,EAAE,WAAW,CAAC;IACpB,UAAU,EAAE,gBAAgB,CAAC;IAC7B,GAAG,EAAE,OAAO,CAAC;IACb,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACjC,yDAAyD;IACzD,SAAS,EAAE,CAAC,EAAE,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;IAClB,2DAA2D;IAC3D,kBAAkB,CAAC,EAAE,mBAAmB,CAAC;IACzC,IAAI,EAAE,MAAM,CAAC;IACb,mFAAmF;IACnF,KAAK,CAAC,EAAE,SAAS,CAAC;IAClB;;;;;;OAMG;IACH,SAAS,CAAC,EAAE,CAAC,GAAG,EAAE,CAAC,KAAK,OAAO,CAAC;IAChC;;;;;;OAMG;IACH,SAAS,CAAC,EAAE,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,CAAC;IAC1B,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,YAAY,CAAC;IACpB,sDAAsD;IACtD,UAAU,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,WAAW,CAAC,CAAC;IAC5B,OAAO,EAAE,eAAe,CAAC;IACzB,4EAA4E;IAC5E,QAAQ,EAAE,CAAC,EAAE,CAAC;IACd,YAAY,EAAE,MAAM,CAAC;CACtB;AAED;;;;GAIG;AACH,eAAO,MAAM,mBAAmB;;;;;;;;;;iBAyB9B,CAAC;AAEH,MAAM,MAAM,aAAa,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,mBAAmB,CAAC,CAAC;AAEhE;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,MAAM,EAAE,aAAa,GAAG,MAAM,EAAE,CAenE;AAED;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,SAAS,EAAE,MAAM,EAAE,GAAG,GAAE,IAAiB,GAAG,MAAM,CAcjF;AAED,kEAAkE;AAClE,wBAAgB,eAAe,CAAC,QAAQ,EAAE,eAAe,GAAG,aAAa,CAaxE;AAED,MAAM,WAAW,eAAe,CAAC,CAAC;IAChC,MAAM,EAAE,WAAW,CAAC;IACpB,UAAU,EAAE,gBAAgB,CAAC;IAC7B,GAAG,EAAE,OAAO,CAAC;IACb,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACjC,SAAS,EAAE,UAAU,CAAC,CAAC,CAAC,CAAC;IACzB,SAAS,EAAE,MAAM,CAAC;IAClB,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,CAAC,EAAE,SAAS,CAAC;I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package/dist/mcp-server/tools/shared/find-helpers.js

@@ -385,12 +385,11 @@ export function toDatasetHandle(metadata) {
  * union to DatasetStore and returns both the full set and the handle.
  */
 export async function maybeSpill(input) {
-    const { firstPage, rowFilter } = input;
+    const { firstPage, rowMapper, rowFilter } = input;
     if (!firstPage.hasMore ||
         firstPage.totalCount === undefined ||
         firstPage.totalCount <= input.loadLimit) {
-        const rows = rowFilter ? firstPage.rows.filter(rowFilter) : firstPage.rows;
-        return { fullRows: rows };
+        return { fullRows: applyRowTransforms(firstPage.rows, rowMapper, rowFilter) };
     }
     const spillInput = {
         store: input.store,
@@ -404,6 +403,8 @@ export async function maybeSpill(input) {
         firstPage: firstPage.rows,
         totalCount: firstPage.totalCount,
     };
+    if (rowMapper)
+        spillInput.rowMapper = rowMapper;
     if (rowFilter)
         spillInput.rowFilter = rowFilter;
     if (input.route)
@@ -421,10 +422,19 @@ export async function maybeSpill(input) {
         if (!input.warnings || !(err instanceof SpillPageFetchError))
             throw err;
         input.warnings.push(`Dataset spillover skipped after returning the first ${firstPage.rows.length} row(s): ${formatSpillError(err)}. Narrow filters, raise loadLimit enough to fit the result in one page, or retry when the upstream server is responsive.`);
-        const rows = rowFilter ? firstPage.rows.filter(rowFilter) : firstPage.rows;
-        return { fullRows: rows };
+        return { fullRows: applyRowTransforms(firstPage.rows, rowMapper, rowFilter) };
     }
 }
+/**
+ * Apply mapper before filter on a row set. Centralizes the order constraint
+ * across the three spillover sites — early-exit, error fallback, and persist
+ * — so they can't drift apart and accidentally filter raw rows the spilled
+ * dataset has already normalized.
+ */
+function applyRowTransforms(rows, mapper, filter) {
+    const mapped = mapper ? rows.map(mapper) : rows;
+    return filter ? mapped.filter(filter) : mapped;
+}
 /**
  * Pull every remaining page up to MAX_SPILLOVER_* caps, then persist the
  * union to DatasetStore. Returns the dataset metadata plus the full row set
@@ -459,7 +469,7 @@ export async function spillToDataset(input) {
     const reachedRowCap = rows.length >= remainingTarget && input.totalCount > rows.length;
     const reachedPageCap = pagesFetched >= MAX_SPILLOVER_PAGES && input.totalCount > rows.length;
     const truncated = reachedRowCap || reachedPageCap;
-    const persistedRows = input.rowFilter ? rows.filter(input.rowFilter) : rows;
+    const persistedRows = applyRowTransforms(rows, input.rowMapper, input.rowFilter);
     const createInput = {
         source: input.source,
         baseUrl: input.connection.baseUrl,
@@ -468,7 +478,25 @@ export async function spillToDataset(input) {
     };
     if (truncated) {
         createInput.truncated = true;
-        createInput.maxRows = MAX_SPILLOVER_ROWS;
+        // `maxRows` only carries meaning when the row cap fired — it's the upper
+        // bound the spillover honored. When the page cap fired first (small
+        // `loadLimit` × `MAX_SPILLOVER_PAGES` < upstream total), reporting
+        // `maxRows = MAX_SPILLOVER_ROWS` is misleading: the dataset stopped at
+        // `loadLimit × MAX_SPILLOVER_PAGES`, well below the row cap. Log the
+        // page-cap event for operators; the agent sees only `truncated: true`
+        // without the false 50k bound and can raise `loadLimit` to push past it.
+        if (reachedRowCap) {
+            createInput.maxRows = MAX_SPILLOVER_ROWS;
+        }
+        else if (reachedPageCap) {
+            input.ctx.log.warning('Spillover hit page cap before exhausting upstream', {
+                source: input.source,
+                pagesFetched,
+                maxPages: MAX_SPILLOVER_PAGES,
+                rowsFetched: rows.length,
+                totalCount: input.totalCount,
+            });
+        }
     }
     const dataset = await input.store.create(input.ctx, createInput);
     return { dataset, fullRows: persistedRows, pagesFetched };
@@ -502,6 +530,52 @@ export function extractRows(result) {
 export function asString(value) {
     return typeof value === 'string' && value.length > 0 ? value : undefined;
 }
+/**
+ * Drop entries from a `synonyms` array that are structurally identical to an
+ * entry already kept. Some Breedbase deployments (notably CassavaBase) return
+ * each registered synonym repeated 11× per germplasm record — the bloat is
+ * purely upstream and carries no information beyond the unique set.
+ *
+ * Identity is taken via a stable serialization (keys sorted recursively) so
+ * that two entries with the same fields but different property insertion
+ * order are recognized as duplicates — observed live: CassavaBase emits two
+ * key orderings on the same record. Two entries that genuinely differ on
+ * any field (e.g. same `synonym` text but different `type`) still hash to
+ * distinct keys and are both kept. When no duplicates are present the
+ * input row is returned by reference — the helper is allocation-free on
+ * the common case.
+ */
+export function dedupSynonymsByIdentity(row) {
+    if (!Array.isArray(row.synonyms))
+        return row;
+    const seen = new Set();
+    const out = [];
+    for (const entry of row.synonyms) {
+        const key = stableStringify(entry);
+        if (seen.has(key))
+            continue;
+        seen.add(key);
+        out.push(entry);
+    }
+    if (out.length === row.synonyms.length)
+        return row;
+    return { ...row, synonyms: out };
+}
+/**
+ * Order-invariant `JSON.stringify` for structural identity hashing. Sorts
+ * object keys recursively so insertion order doesn't affect the output.
+ * Arrays preserve element order — order is semantically meaningful there.
+ */
+function stableStringify(value) {
+    if (value === null || typeof value !== 'object')
+        return JSON.stringify(value);
+    if (Array.isArray(value)) {
+        return `[${value.map(stableStringify).join(',')}]`;
+    }
+    const obj = value;
+    const keys = Object.keys(obj).sort();
+    return `{${keys.map((k) => `${JSON.stringify(k)}:${stableStringify(obj[k])}`).join(',')}}`;
+}
 /** Return the input as a non-empty string array, or undefined. */
 export function asStringArray(value) {
     if (!Array.isArray(value))

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package/dist/services/canvas-bridge/canvas-bridge.d.ts.map

@@ -1 +1 @@
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package/dist/services/canvas-bridge/canvas-bridge.js

@@ -92,7 +92,16 @@ export class CanvasBridge {
         const tableName = datasetTableName(metadata.datasetId);
         try {
             const instance = await this.getInstance(ctx);
-            await instance.registerTable(tableName, rows);
+            // Pre-compute an explicit all-nullable schema. The framework's default
+            // path sniffs the first N rows and infers `nullable: false` for any
+            // column that happened to be non-null in the sample — DuckDB then
+            // creates the table with NOT NULL constraints, and the appender rolls
+            // back the entire batch the first time a later row carries a null for
+            // that column. Sniffed schemas can never prove non-nullability from a
+            // sample, so we walk every row, classify types ourselves, and emit
+            // `nullable: true` for every column.
+            const schema = deriveAllNullableSchema(rows);
+            await instance.registerTable(tableName, rows, { schema });
             const tableMeta = {
                 datasetId: metadata.datasetId,
                 source: metadata.source,
@@ -238,6 +247,83 @@ function tableMetaKey(tableName) {
 function isCanvasNotFound(err) {
     return err instanceof McpError && err.code === JsonRpcErrorCode.NotFound;
 }
+/**
+ * Walk every row, union the JS-side types per column, and emit a
+ * `ColumnSchema[]` with `nullable: true` on every column. Mirrors the
+ * framework's sniffer type classification (string/integer/double/bigint/
+ * boolean/object) so the inferred DuckDB types stay identical, but never
+ * emits NOT NULL constraints — sample-based sniffing cannot prove the
+ * absence of nulls, and a wrong NOT NULL inference rolls back the entire
+ * appender batch when the first violating row appears later.
+ *
+ * Walks the full row set rather than a sample so that columns appearing
+ * only in late rows still show up in the schema. We already hold every
+ * row in memory at this point (the spillover persisted them), so the
+ * extra pass is cheap.
+ */
+function deriveAllNullableSchema(rows) {
+    const observedByCol = new Map();
+    const columnOrder = [];
+    for (const row of rows) {
+        for (const key of Object.keys(row)) {
+            let bag = observedByCol.get(key);
+            if (!bag) {
+                bag = new Set();
+                observedByCol.set(key, bag);
+                columnOrder.push(key);
+            }
+            bag.add(classifyValue(row[key]));
+        }
+    }
+    return columnOrder.map((name) => ({
+        name,
+        type: unionToColumnType(observedByCol.get(name) ?? new Set(['null'])),
+        nullable: true,
+    }));
+}
+function classifyValue(value) {
+    if (value === null || value === undefined)
+        return 'null';
+    if (typeof value === 'string')
+        return 'string';
+    if (typeof value === 'boolean')
+        return 'boolean';
+    if (typeof value === 'bigint')
+        return 'bigint';
+    if (typeof value === 'number')
+        return Number.isInteger(value) ? 'integer' : 'double';
+    return 'object';
+}
+function unionToColumnType(observed) {
+    const nonNull = new Set(observed);
+    nonNull.delete('null');
+    if (nonNull.size === 0)
+        return 'VARCHAR';
+    if (nonNull.size === 1) {
+        const [only] = nonNull;
+        switch (only) {
+            case 'string':
+                return 'VARCHAR';
+            case 'integer':
+            case 'bigint':
+                return 'BIGINT';
+            case 'double':
+                return 'DOUBLE';
+            case 'boolean':
+                return 'BOOLEAN';
+            case 'object':
+                return 'JSON';
+            default:
+                return 'VARCHAR';
+        }
+    }
+    const allNumeric = [...nonNull].every((t) => t === 'integer' || t === 'double' || t === 'bigint');
+    if (allNumeric)
+        return nonNull.has('double') ? 'DOUBLE' : 'BIGINT';
+    if (!nonNull.has('string') && nonNull.has('object'))
+        return 'JSON';
+    return 'VARCHAR';
+}
 /**
  * Compose the caller's AbortSignal with a wall-clock timeout. Returns the
  * caller's signal directly when no timeout is configured or the parent is

package/dist/services/canvas-bridge/canvas-bridge.js.map

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package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@cyanheads/brapi-mcp-server",
   "mcpName": "io.github.cyanheads/brapi-mcp-server",
-  "version": "0.4.13",
+  "version": "0.4.14",
   "description": "BrAPI v2.1 MCP server — studies, germplasm, observations, genotypes, images, and pedigrees.",
   "author": "Casey Hand @cyanheads (https://github.com/cyanheads/brapi-mcp-server#readme)",
   "type": "module",
@@ -71,7 +71,7 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.8.13",
+    "@cyanheads/mcp-ts-core": "^0.8.14",
     "pino-pretty": "^13.1.3"
   },
   "devDependencies": {

package/server.json

@@ -6,14 +6,14 @@
     "url": "https://github.com/cyanheads/brapi-mcp-server",
     "source": "github"
   },
-  "version": "0.4.13",
+  "version": "0.4.14",
   "packages": [
     {
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.4.13",
+      "version": "0.4.14",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:stdio" }
@@ -49,7 +49,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.4.13",
+      "version": "0.4.14",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }