@cyanheads/brapi-mcp-server 0.4.1 → 0.4.2

package/CLAUDE.md

@@ -1,7 +1,7 @@
 # Agent Protocol
 
 **Server:** brapi-mcp-server
-**Version:** 0.4.1
+**Version:** 0.4.2
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
 
 > **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

@@ -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-0.4.1-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-0.4.2-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/0.4.2.md

@@ -0,0 +1,23 @@
+---
+summary: "Row schemas accept null fields from sparse upstreams. FK match-rate checks across find_studies / find_observations / find_images surface silently-ignored filters as warnings. CassavaBase locationDbIds dropped on /studies."
+breaking: false
+---
+
+# 0.4.2 — 2026-04-30
+
+Field testing against `https://cassavabase.org/brapi/v2` after 0.4.1 surfaced two classes of correctness gaps: (1) several upstream record types return `null` for missing optional fields where row schemas required `string | undefined` — Zod parse failed before the agent ever saw the data; (2) the post-fetch `checkFilterMatchRates` heuristic was wired up unevenly across find tools, so when a CassavaBase-side filter was silently ignored (e.g. `locationDbId` on `/studies`), the result envelope arrived clean with no signal that the filter had been dropped. This release closes both gaps and removes the one mapping that field testing proved doesn't filter even after dialect translation.
+
+## Added
+
+- **`fkMatchCheck(paramName, requestedValues, rows, fieldName)` helper in `find-helpers`** — builds a `FilterMatchCheck` for an FK identifier filter inline. Replaces the 4-line `computeDistribution(...)` + `{ paramName, requestedValues, distribution }` construction repeated nine times across the three find tools that gained match-rate coverage. The DbId distribution is computed only for the check; not exposed in `result.distributions` (raw FK frequencies don't carry semantic meaning to agents).
+- **FK filter match-rate checks** — `brapi_find_studies` now checks `locations` / `programs` / `trials`; `brapi_find_observations` adds `studies` / `germplasm` / `variables` / `observationUnits`; `brapi_find_images` adds `studies` / `observationUnits`. When the upstream silently ignores a filter and returns an unrelated row set, the user receives a `Filter 'X' requested […] but no returned row matches — the server may not honor this filter` warning instead of a clean envelope they'll trust.
+- **Tests** — 9 new cases. `tests/tools/brapi-find-{observations,images}.tool.test.ts` cover explicit-null upstream rows (the CassavaBase shape that broke 0.4.1 in the wild). `tests/tools/brapi-find-studies.tool.test.ts` covers the new locations/programs/trials warnings. `tests/services/brapi-dialect/cassavabase-dialect.test.ts` covers the `locationDbIds` drop on `/studies` for both plural and singular forms.
+
+## Changed
+
+- **`ObservationRowSchema` (14 fields), `ImageRowSchema` (12 fields), `VariantRowSchema` (3 top-level identifier fields), `CallRowSchema` (5 fields + `genotype` block), and `callFormatting` echo block converted from `.optional()` to `.nullish()`** — accepts the explicit `null` values CassavaBase and other sparse-upstream servers return for missing optional fields. Pre-0.4.2, a row like `{ observationDbId: 'obs-1', observationTimeStamp: null, germplasmName: null, ... }` failed Zod parse on the entire envelope. Post-0.4.2, the agent receives the row with the nulls preserved on output. `StudyRowSchema`, `GermplasmRowSchema`, `VariableRowSchema`, and `LocationRowSchema` already used `.nullish()` from prior live-testing rounds — this release brings the remaining row schemas to parity.
+- **`brapi_find_variables.text` description rewritten** to make the rank-not-subset behavior explicit and call out the divergence from `brapi_find_germplasm.text` (which subsets). Same parameter name, different semantics — the documentation now says so loudly. Use exact filters (`variables`, `variableNames`, `variablePUIs`, `traitClasses`, `ontologies`) to actually narrow the result set.
+
+## Fixed
+
+- **CassavaBase `locationDbIds` on `/studies` moved to `DROPPED_FILTERS`** — empirically verified that the singular `locationDbId` form is silently ignored too: requesting `locationDbId=3` against the live `/studies` endpoint returned studies for unrelated locations (Mokwa, Zaria). 0.4.0's plural→singular translation produced a wire shape that looked correct but didn't filter. The dialect now drops the filter from the wire entirely and surfaces a `dropped filter 'locationDbIds'` warning so the agent knows the request can't be served as-is. Until we have a working alternative, narrow location-wise post-fetch via `locationName` distribution or a follow-up `brapi_get_study` call. See [#5](https://github.com/cyanheads/brapi-mcp-server/issues/5) for the broader verified-flag-per-mapping work this is one step toward.

package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts

@@ -27,25 +27,25 @@ export declare const brapiFindGenotypeCalls: import("@cyanheads/mcp-ts-core").To
 }, z.core.$strip>, z.ZodObject<{
     alias: z.ZodString;
     results: z.ZodArray<z.ZodObject<{
-        callSetDbId: z.ZodOptional<z.ZodString>;
-        callSetName: z.ZodOptional<z.ZodString>;
-        variantDbId: z.ZodOptional<z.ZodString>;
-        variantName: z.ZodOptional<z.ZodString>;
-        variantSetDbId: z.ZodOptional<z.ZodString>;
-        genotype: z.ZodOptional<z.ZodObject<{
-            values: z.ZodOptional<z.ZodArray<z.ZodString>>;
-        }, z.core.$loose>>;
-        genotypeValue: z.ZodOptional<z.ZodString>;
-        phaseSet: z.ZodOptional<z.ZodString>;
+        callSetDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        callSetName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        variantDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        variantName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        variantSetDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        genotype: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+            values: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodString>>>;
+        }, z.core.$loose>>>;
+        genotypeValue: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        phaseSet: z.ZodOptional<z.ZodNullable<z.ZodString>>;
     }, z.core.$loose>>;
     returnedCount: z.ZodNumber;
     totalCount: z.ZodNumber;
     hasMore: z.ZodBoolean;
     callFormatting: z.ZodObject<{
-        expandHomozygotes: z.ZodOptional<z.ZodBoolean>;
-        unknownString: z.ZodOptional<z.ZodString>;
-        sepPhased: z.ZodOptional<z.ZodString>;
-        sepUnphased: z.ZodOptional<z.ZodString>;
+        expandHomozygotes: z.ZodOptional<z.ZodNullable<z.ZodBoolean>>;
+        unknownString: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        sepPhased: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        sepUnphased: z.ZodOptional<z.ZodNullable<z.ZodString>>;
     }, z.core.$strip>;
     distributions: z.ZodObject<{
         callSetName: z.ZodRecord<z.ZodString, z.ZodNumber>;

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

@@ -22,29 +22,29 @@ const CallRowSchema = z
     .object({
     callSetDbId: z
         .string()
-        .optional()
+        .nullish()
         .describe('FK to the call set (one germplasm × one variant set = one call set).'),
-    callSetName: z.string().optional().describe('Display name of the call set.'),
-    variantDbId: z.string().optional().describe('FK to the variant being called.'),
-    variantName: z.string().optional().describe('Display name / alias of the variant.'),
-    variantSetDbId: z.string().optional().describe('FK to the variant set the call belongs to.'),
+    callSetName: z.string().nullish().describe('Display name of the call set.'),
+    variantDbId: z.string().nullish().describe('FK to the variant being called.'),
+    variantName: z.string().nullish().describe('Display name / alias of the variant.'),
+    variantSetDbId: z.string().nullish().describe('FK to the variant set the call belongs to.'),
     genotype: z
         .object({
         values: z
             .array(z.string().describe('Per-allele value string.'))
-            .optional()
+            .nullish()
             .describe('Encoded allele values — interpret using top-level `callFormatting`.'),
     })
         .passthrough()
-        .optional()
+        .nullish()
         .describe('Structured genotype payload (array of allele values plus server-specific fields).'),
     genotypeValue: z
         .string()
-        .optional()
+        .nullish()
         .describe('Legacy flat string form of the call (provided by some servers instead of `genotype`).'),
     phaseSet: z
         .string()
-        .optional()
+        .nullish()
         .describe('Phase-set identifier linking calls that share a haplotype phase.'),
 })
     .passthrough()
@@ -65,19 +65,19 @@ const OutputSchema = z.object({
         .object({
         expandHomozygotes: z
             .boolean()
-            .optional()
+            .nullish()
             .describe('When true, homozygous calls are expanded to both alleles.'),
         unknownString: z
             .string()
-            .optional()
+            .nullish()
             .describe('String used for unknown / missing calls (often "." or "N").'),
         sepPhased: z
             .string()
-            .optional()
+            .nullish()
             .describe('Separator between phased allele values (typically "|").'),
         sepUnphased: z
             .string()
-            .optional()
+            .nullish()
             .describe('Separator between unphased allele values (typically "/").'),
     })
         .describe('Genotype-encoding hints echoed by the server.'),

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

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package/dist/mcp-server/tools/definitions/brapi-find-images.tool.d.ts

@@ -22,22 +22,22 @@ export declare const brapiFindImages: import("@cyanheads/mcp-ts-core").ToolDefin
     alias: z.ZodString;
     results: z.ZodArray<z.ZodObject<{
         imageDbId: z.ZodString;
-        imageName: z.ZodOptional<z.ZodString>;
-        imageFileName: z.ZodOptional<z.ZodString>;
-        imageFileSize: z.ZodOptional<z.ZodNumber>;
-        imageHeight: z.ZodOptional<z.ZodNumber>;
-        imageWidth: z.ZodOptional<z.ZodNumber>;
-        mimeType: z.ZodOptional<z.ZodString>;
-        imageTimeStamp: z.ZodOptional<z.ZodString>;
-        imageURL: z.ZodOptional<z.ZodString>;
-        observationUnitDbId: z.ZodOptional<z.ZodString>;
-        observationUnitName: z.ZodOptional<z.ZodString>;
-        observationDbIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
-        studyDbId: z.ZodOptional<z.ZodString>;
-        studyName: z.ZodOptional<z.ZodString>;
-        descriptiveOntologyTerms: z.ZodOptional<z.ZodArray<z.ZodString>>;
-        copyright: z.ZodOptional<z.ZodString>;
-        description: z.ZodOptional<z.ZodString>;
+        imageName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        imageFileName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        imageFileSize: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
+        imageHeight: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
+        imageWidth: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
+        mimeType: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        imageTimeStamp: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        imageURL: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        observationUnitDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        observationUnitName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        observationDbIds: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodString>>>;
+        studyDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        studyName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        descriptiveOntologyTerms: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodString>>>;
+        copyright: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        description: z.ZodOptional<z.ZodNullable<z.ZodString>>;
     }, z.core.$loose>>;
     returnedCount: z.ZodNumber;
     totalCount: z.ZodNumber;

package/dist/mcp-server/tools/definitions/brapi-find-images.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-find-images.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-images.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAyHjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BA2M1B,CAAC"}
+{"version":3,"file":"brapi-find-images.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-images.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA0HjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BA6M1B,CAAC"}

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

@@ -13,38 +13,38 @@ 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, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
 const ImageRowSchema = z
     .object({
     imageDbId: z.string().describe('Server-side identifier for the image.'),
-    imageName: z.string().optional().describe('Display name.'),
-    imageFileName: z.string().optional().describe('Original uploaded filename.'),
-    imageFileSize: z.number().optional().describe('File size in bytes.'),
-    imageHeight: z.number().optional().describe('Pixel height.'),
-    imageWidth: z.number().optional().describe('Pixel width.'),
-    mimeType: z.string().optional().describe('MIME type (e.g. "image/jpeg").'),
-    imageTimeStamp: z.string().optional().describe('ISO 8601 capture timestamp.'),
+    imageName: z.string().nullish().describe('Display name.'),
+    imageFileName: z.string().nullish().describe('Original uploaded filename.'),
+    imageFileSize: z.number().nullish().describe('File size in bytes.'),
+    imageHeight: z.number().nullish().describe('Pixel height.'),
+    imageWidth: z.number().nullish().describe('Pixel width.'),
+    mimeType: z.string().nullish().describe('MIME type (e.g. "image/jpeg").'),
+    imageTimeStamp: z.string().nullish().describe('ISO 8601 capture timestamp.'),
     imageURL: z
         .string()
-        .optional()
+        .nullish()
         .describe('URL where the bytes live (may be relative to baseUrl or absolute).'),
     observationUnitDbId: z
         .string()
-        .optional()
+        .nullish()
         .describe('FK to the observation unit this image depicts.'),
-    observationUnitName: z.string().optional().describe('Display name of the observation unit.'),
+    observationUnitName: z.string().nullish().describe('Display name of the observation unit.'),
     observationDbIds: z
         .array(z.string().describe('Observation identifier.'))
-        .optional()
+        .nullish()
         .describe('FKs to observations this image is evidence for.'),
-    studyDbId: z.string().optional().describe('FK to the study the image belongs to.'),
-    studyName: z.string().optional().describe('Display name of the study.'),
+    studyDbId: z.string().nullish().describe('FK to the study the image belongs to.'),
+    studyName: z.string().nullish().describe('Display name of the study.'),
     descriptiveOntologyTerms: z
         .array(z.string().describe('Ontology term ID or label.'))
-        .optional()
+        .nullish()
         .describe('Descriptive ontology tags (e.g. "CO_334:plot").'),
-    copyright: z.string().optional().describe('Copyright or rights notice.'),
-    description: z.string().optional().describe('Free-text description.'),
+    copyright: z.string().nullish().describe('Copyright or rights notice.'),
+    description: z.string().nullish().describe('Free-text description.'),
 })
     .passthrough()
     .describe('One BrAPI image metadata record.');
@@ -183,6 +183,8 @@ export const brapiFindImages = tool('brapi_find_images', {
                 requestedValues: input.descriptiveOntologyTerms,
                 distribution: distributions.descriptiveOntologyTerms,
             },
+            fkMatchCheck('studies', input.studies, fullRows, 'studyDbId'),
+            fkMatchCheck('observationUnits', input.observationUnits, fullRows, 'observationUnitDbId'),
         ]);
         const totalCount = firstPage.totalCount ?? firstPage.rows.length;
         const refinementHint = buildRefinementHint(totalCount, loadLimit, distributions, {

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

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package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts

@@ -26,26 +26,26 @@ export declare const brapiFindObservations: import("@cyanheads/mcp-ts-core").Too
 }, z.core.$strip>, z.ZodObject<{
     alias: z.ZodString;
     results: z.ZodArray<z.ZodObject<{
-        observationDbId: z.ZodOptional<z.ZodString>;
-        observationUnitDbId: z.ZodOptional<z.ZodString>;
-        observationUnitName: z.ZodOptional<z.ZodString>;
-        observationVariableDbId: z.ZodOptional<z.ZodString>;
-        observationVariableName: z.ZodOptional<z.ZodString>;
-        studyDbId: z.ZodOptional<z.ZodString>;
-        studyName: z.ZodOptional<z.ZodString>;
-        germplasmDbId: z.ZodOptional<z.ZodString>;
-        germplasmName: z.ZodOptional<z.ZodString>;
-        observationLevel: z.ZodOptional<z.ZodString>;
-        season: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodObject<{
-            seasonDbId: z.ZodOptional<z.ZodString>;
-            year: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodNumber]>>;
-            season: z.ZodOptional<z.ZodString>;
-            seasonName: z.ZodOptional<z.ZodString>;
-        }, z.core.$loose>]>>;
-        value: z.ZodOptional<z.ZodString>;
-        observationTimeStamp: z.ZodOptional<z.ZodString>;
-        collector: z.ZodOptional<z.ZodString>;
-        uploadedBy: z.ZodOptional<z.ZodString>;
+        observationDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        observationUnitDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        observationUnitName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        observationVariableDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        observationVariableName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        studyDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        studyName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        germplasmDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        germplasmName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        observationLevel: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        season: z.ZodOptional<z.ZodNullable<z.ZodUnion<readonly [z.ZodString, z.ZodObject<{
+            seasonDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+            year: z.ZodOptional<z.ZodNullable<z.ZodUnion<readonly [z.ZodString, z.ZodNumber]>>>;
+            season: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+            seasonName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        }, z.core.$loose>]>>>;
+        value: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        observationTimeStamp: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        collector: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        uploadedBy: z.ZodOptional<z.ZodNullable<z.ZodString>>;
     }, z.core.$loose>>;
     returnedCount: z.ZodNumber;
     totalCount: z.ZodNumber;

package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-find-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA6JjD,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BA6MhC,CAAC"}
+{"version":3,"file":"brapi-find-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA8JjD,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAiNhC,CAAC"}

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

@@ -14,62 +14,62 @@ 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, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
 const ObservationRowSchema = z
     .object({
-    observationDbId: z.string().optional().describe('Server-side identifier for the observation.'),
+    observationDbId: z.string().nullish().describe('Server-side identifier for the observation.'),
     observationUnitDbId: z
         .string()
-        .optional()
+        .nullish()
         .describe('FK to the observation unit (plot / plant / sample) that carries the measurement.'),
-    observationUnitName: z.string().optional().describe('Display name of the observation unit.'),
+    observationUnitName: z.string().nullish().describe('Display name of the observation unit.'),
     observationVariableDbId: z
         .string()
-        .optional()
+        .nullish()
         .describe('FK to the observation variable (trait) measured.'),
     observationVariableName: z
         .string()
-        .optional()
+        .nullish()
         .describe('Display name of the observation variable.'),
-    studyDbId: z.string().optional().describe('FK to the study the observation belongs to.'),
-    studyName: z.string().optional().describe('Display name of the study.'),
+    studyDbId: z.string().nullish().describe('FK to the study the observation belongs to.'),
+    studyName: z.string().nullish().describe('Display name of the study.'),
     germplasmDbId: z
         .string()
-        .optional()
+        .nullish()
         .describe('FK to the germplasm the observation was taken on.'),
-    germplasmName: z.string().optional().describe('Display name of the germplasm.'),
-    observationLevel: z.string().optional().describe('Unit level — e.g. "plot", "plant", "field".'),
+    germplasmName: z.string().nullish().describe('Display name of the germplasm.'),
+    observationLevel: z.string().nullish().describe('Unit level — e.g. "plot", "plant", "field".'),
     season: z
         .union([
         z.string().describe('Season identifier as a flat string (older BrAPI servers).'),
         z
             .object({
-            seasonDbId: z.string().optional().describe('Server-side season identifier.'),
+            seasonDbId: z.string().nullish().describe('Server-side season identifier.'),
             year: z
                 .union([
                 z.string().describe('Calendar year as a string (e.g. "2024").'),
                 z.number().describe('Calendar year as an integer (e.g. 2024).'),
             ])
-                .optional()
+                .nullish()
                 .describe('Calendar year — accepts string or numeric form depending on server.'),
-            season: z.string().optional().describe('Season label (e.g. "wet", "dry", "Q1").'),
+            season: z.string().nullish().describe('Season label (e.g. "wet", "dry", "Q1").'),
             seasonName: z
                 .string()
-                .optional()
+                .nullish()
                 .describe('Season display name (BrAPI v2.1 alternate field).'),
         })
             .passthrough()
             .describe('Structured season block per BrAPI v2.1.'),
     ])
-        .optional()
+        .nullish()
         .describe('Season — either a flat string or a structured `{seasonDbId, year, season}` object depending on the server.'),
     value: z
         .string()
-        .optional()
+        .nullish()
         .describe('Recorded measurement value (stringified per BrAPI spec).'),
-    observationTimeStamp: z.string().optional().describe('ISO 8601 timestamp of the observation.'),
-    collector: z.string().optional().describe('Name or ID of the person who collected the value.'),
-    uploadedBy: z.string().optional().describe('Name or ID of the user who uploaded the record.'),
+    observationTimeStamp: z.string().nullish().describe('ISO 8601 timestamp of the observation.'),
+    collector: z.string().nullish().describe('Name or ID of the person who collected the value.'),
+    uploadedBy: z.string().nullish().describe('Name or ID of the user who uploaded the record.'),
 })
     .passthrough()
     .describe('One BrAPI observation record.');
@@ -215,6 +215,10 @@ export const brapiFindObservations = tool('brapi_find_observations', {
                 distribution: distributions.observationLevel,
                 caseInsensitive: true,
             },
+            fkMatchCheck('studies', input.studies, fullRows, 'studyDbId'),
+            fkMatchCheck('germplasm', input.germplasm, fullRows, 'germplasmDbId'),
+            fkMatchCheck('variables', input.variables, fullRows, 'observationVariableDbId'),
+            fkMatchCheck('observationUnits', input.observationUnits, fullRows, 'observationUnitDbId'),
         ]);
         const totalCount = firstPage.totalCount ?? firstPage.rows.length;
         const refinementHint = buildRefinementHint(totalCount, loadLimit, distributions, {