npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.3.8 → 0.3.9 - Mend

@cyanheads/brapi-mcp-server 0.3.8 → 0.3.9

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Files changed (19) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** brapi-mcp-server
-**Version:** 0.3.8
+**Version:** 0.3.9
 **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 CHANGED Viewed

@@ -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-0.3.8-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-0.3.9-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/0.3.x/0.3.9.md ADDED Viewed

@@ -0,0 +1,25 @@
+---
+summary: "Resolver field-name fix for BrAPI v2.1 trait subobjects + bbox swap-on-zero detection for non-conformant GeoJSON deployments."
+breaking: false
+---
+# 0.3.9 — 2026-04-29
+Two patch-level field fixes from running the read surface against the BrAPI Community Test Server. `find_variables` free-text queries now surface candidates when the match lives on `trait.traitName` (the v2.1 spec key) rather than only the variable name. `find_locations` bbox filtering survives servers that store GeoJSON coordinates as `[lat, lon, alt]` instead of the spec-required `[lon, lat, alt]`.
+## Added
+- **`CoordinateAxisOrder` type + `axisOrder` parameter on `extractCoordinates` (`src/mcp-server/tools/shared/find-helpers.ts`)** — `'spec'` (default) follows the GeoJSON RFC 7946 `[lon, lat, alt?]` convention; `'swapped'` reads the array as `[lat, lon, alt?]` for non-conformant deployments. Legacy top-level `latitude`/`longitude` fields are unambiguous by name and not affected.
+- **`hasPointGeometry` helper** — true when a record carries a GeoJSON `Point` with a 2- or 3-element numeric coordinate array. Used by the bbox swap-on-zero retry to skip Polygon-only result sets where reinterpretation can't help.
+- **`coordinateAxisOrder` field on `brapi_find_locations` output** — surfaces which axis interpretation the bbox filter and renderer used, so callers can correlate displayed coordinates with the warning when a swap fired.
+- **Tests** — new `tests/services/ontology-resolver.test.ts` (8 cases) covers PUI / name / synonym paths, the v2.1 trait-name path, legacy alias fallback, ranking order, and `ontologyDbId` scope. New cases in `brapi-find-variables.tool.test.ts` (trait-only text match) and `brapi-find-locations.tool.test.ts` (Cornell-shape swap recovery, spec-correct preserved, both readings empty, polygon-only skip).
+## Changed
+- **`brapi_find_locations` bbox handler** — when the spec-correct reading produces zero matches and at least one row carries a Point geometry, retries the filter once in-memory with axes swapped. On recovery, sets `coordinateAxisOrder: "swapped"` and emits a dedicated warning naming the deployment as non-conformant. Falls back to the existing "verify the latitude/longitude window" warning when both readings empty or no Point rows present.
+- **`brapi_find_locations` renderer** — threads `result.coordinateAxisOrder` into `extractCoordinates` so printed coordinates match the warning rather than contradicting it.
+## Fixed
+- **`brapi_find_variables` free-text query returned empty `ontologyCandidates` when the match lived on `trait.traitName`** — `OntologyResolver` (`src/services/ontology-resolver/ontology-resolver.ts`) read `trait.name` and `trait.description`, but BrAPI v2.1 servers populate `trait.traitName` and `trait.traitDescription`. Both lookups returned undefined, so candidates were never built and the v0.3.8 dbId-promotion path stayed silently dormant. `scoreOne` and `toCandidate` now read both v2.1 keys with `?? ` fallback to the legacy aliases. Closes [#3](https://github.com/cyanheads/brapi-mcp-server/issues/3).
+- **`brapi_find_locations` bbox excluded all rows on servers that store GeoJSON Points as `[lat, lon, alt]`** — the BrAPI Community Test Server is a known offender (Cornell at 42.44°N, -76.46°W stored as `[42.44423, -76.46313, 123]`). The retry-once-with-swap path described above recovers matches without operator pre-knowledge while keeping the spec-conformant default. Closes [#4](https://github.com/cyanheads/brapi-mcp-server/issues/4).

package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.d.ts CHANGED Viewed

@@ -60,5 +60,9 @@ export declare const brapiFindLocations: import("@cyanheads/mcp-ts-core").ToolDe
     }, z.core.$strip>>;
     warnings: z.ZodArray<z.ZodString>;
     appliedFilters: z.ZodRecord<z.ZodString, z.ZodUnknown>;
+    coordinateAxisOrder: z.ZodEnum<{
+        spec: "spec";
+        swapped: "swapped";
+    }>;
 }, z.core.$strip>, undefined>;
 //# sourceMappingURL=brapi-find-locations.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-locations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-locations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAoHjD~~,eAAO,MAAM,kBAAkB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAqO7B~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-locations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-locations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA2HjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BA4P7B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.js CHANGED Viewed

@@ -13,7 +13,7 @@ import { getBrapiClient } from '../../../services/brapi-client/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, asString, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, extractCoordinates, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, asString, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, extractCoordinates, hasPointGeometry, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
 const LocationRowSchema = z
     .object({
     locationDbId: z.string().describe('Server-side identifier for the location.'),
@@ -82,6 +82,9 @@ const OutputSchema = z.object({
     appliedFilters: z
         .record(z.string(), z.unknown())
         .describe('The final filter map sent to the server (named + extraFilters).'),
+    coordinateAxisOrder: z
+        .enum(['spec', 'swapped'])
+        .describe('Axis interpretation used when reading GeoJSON Point coordinates. "spec" follows the GeoJSON RFC 7946 [lon, lat, alt?] convention. "swapped" indicates the upstream server stores [lat, lon, alt?] (non-conformant) and bbox + rendered coordinates were interpreted accordingly.'),
 });
 const SERVER_TO_USER = {
     locationDbIds: 'locations',
@@ -91,7 +94,7 @@ const SERVER_TO_USER = {
     abbreviations: 'abbreviations',
 };
 export const brapiFindLocations = tool('brapi_find_locations', {
-    description: 'Find research stations / field sites by country, abbreviation, type, location ID, or free-text. Optional bbox parameter restricts rows to a latitude/longitude window. Returns a dataset handle when the upstream total exceeds loadLimit.',
+    description: 'Find research stations / field sites by country, abbreviation, type, location ID, or free-text. Optional bbox parameter restricts rows to a latitude/longitude window. When the spec-correct GeoJSON [lon, lat, alt] reading produces zero matches and at least one row carries a Point geometry, the bbox filter retries once with axes swapped (handles non-conformant servers that store [lat, lon, alt]) and surfaces a warning + `coordinateAxisOrder: "swapped"`. Returns a dataset handle when the upstream total exceeds loadLimit.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     input: z.object({
         alias: AliasInput,
@@ -169,12 +172,32 @@ export const brapiFindLocations = tool('brapi_find_locations', {
             store: datasetStore,
         });
         const bbox = normalizeBbox(input.bbox, warnings);
-        const filteredFull = bbox ? fullRows.filter((r) => insideBbox(r, bbox)) : fullRows;
-        const filteredReturned = bbox
-            ? firstPage.rows.filter((r) => insideBbox(r, bbox))
+        let coordinateAxisOrder = 'spec';
+        let filteredFull = bbox ? fullRows.filter((r) => insideBbox(r, bbox, 'spec')) : fullRows;
+        let filteredReturned = bbox
+            ? firstPage.rows.filter((r) => insideBbox(r, bbox, 'spec'))
             : firstPage.rows;
         if (bbox && fullRows.length > 0 && filteredFull.length === 0) {
-            warnings.push(`bbox excluded all ${fullRows.length} upstream location(s). Verify the latitude/longitude window matches the server's coordinate convention.`);
+            // Spec pass excluded everything. If at least one row carries a Point
+            // geometry, the server may store coordinates as [lat, lon, alt] rather
+            // than the GeoJSON-standard [lon, lat, alt] (the BrAPI Community Test
+            // Server is a known offender). Retry once with axes swapped — the
+            // retry is in-memory over already-fetched rows. If the swap recovers
+            // matches, surface a loud warning so operators can chase the upstream
+            // quirk; if it still produces zero, fall through to the existing
+            // verify-coordinate-convention warning.
+            const swappedFull = fullRows.some(hasPointGeometry)
+                ? fullRows.filter((r) => insideBbox(r, bbox, 'swapped'))
+                : [];
+            if (swappedFull.length > 0) {
+                coordinateAxisOrder = 'swapped';
+                filteredFull = swappedFull;
+                filteredReturned = firstPage.rows.filter((r) => insideBbox(r, bbox, 'swapped'));
+                warnings.push(`Server appears to store GeoJSON coordinates as [lat, lon, alt] rather than the spec-required [lon, lat, alt]. Bbox matches returned under the swapped interpretation; report to the server operator so the source quirk gets fixed upstream.`);
+            }
+            else {
+                warnings.push(`bbox excluded all ${fullRows.length} upstream location(s). Verify the latitude/longitude window matches the server's coordinate convention.`);
+            }
         }
         else if (bbox && filteredFull.length < fullRows.length) {
             warnings.push(`bbox excluded ${fullRows.length - filteredFull.length} of ${fullRows.length} upstream location(s).`);
@@ -217,6 +240,7 @@ export const brapiFindLocations = tool('brapi_find_locations', {
             distributions,
             warnings,
             appliedFilters: filters,
+            coordinateAxisOrder,
         };
         if (refinementHint)
             result.refinementHint = refinementHint;
@@ -233,6 +257,7 @@ export const brapiFindLocations = tool('brapi_find_locations', {
             totalCount: result.totalCount,
             dataset: result.dataset,
         }));
+        lines.push(`**Coordinate axis order:** ${result.coordinateAxisOrder}`);
         lines.push('');
         if (result.hasMore) {
             lines.push(`⚠ More rows exist beyond the returned set. ${result.dataset ? `Full set persisted as dataset \`${result.dataset.datasetId}\`.` : 'Narrow filters or raise loadLimit.'}`);
@@ -263,7 +288,7 @@ export const brapiFindLocations = tool('brapi_find_locations', {
                     parts.push(`country=${loc.countryCode}`);
                 if (loc.countryName)
                     parts.push(`countryName=${loc.countryName}`);
-                const coords = extractCoordinates(loc);
+                const coords = extractCoordinates(loc, result.coordinateAxisOrder);
                 if (coords) {
                     parts.push(`lat=${coords.latitude}`);
                     parts.push(`lon=${coords.longitude}`);
@@ -319,8 +344,8 @@ function normalizeBbox(bbox, warnings) {
     }
     return { minLat, maxLat, minLon, maxLon };
 }
-function insideBbox(row, bbox) {
-    const coords = extractCoordinates(row);
+function insideBbox(row, bbox, axisOrder) {
+    const coords = extractCoordinates(row, axisOrder);
     if (!coords)
         return false;
     const { latitude: lat, longitude: lon } = coords;

package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/index.d.ts CHANGED Viewed

@@ -482,6 +482,10 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
     }, import("zod/v4/core").$strip>>;
     warnings: import("zod").ZodArray<import("zod").ZodString>;
     appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
+    coordinateAxisOrder: import("zod").ZodEnum<{
+        spec: "spec";
+        swapped: "swapped";
+    }>;
 }, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     alias: import("zod").ZodOptional<import("zod").ZodString>;
     studies: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;

package/dist/mcp-server/tools/definitions/index.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAsBH,kEAAkE;AAClE,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;+CAmBnC,CAAC;AAEF,qEAAqE;AACrE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAA4B,CAAC"}
1	+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAsBH,kEAAkE;AAClE,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;+CAmBnC,CAAC;AAEF,qEAAqE;AACrE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAA4B,CAAC"}

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

@@ -156,6 +156,14 @@ export declare function extractRows<T>(result: BrapiListResult<T> | T[]): T[];
 export declare function asString(value: unknown): string | undefined;
 /** Return the input as a non-empty string array, or undefined. */
 export declare function asStringArray(value: unknown): string[] | undefined;
+/**
+ * Axis interpretation for GeoJSON Point coordinates:
+ *   - `spec` — RFC 7946 standard `[lon, lat, alt?]` (default)
+ *   - `swapped` — non-conformant `[lat, lon, alt?]` deployments (e.g. the
+ *     BrAPI Community Test Server). `find_locations` falls back to this
+ *     reading when a bbox filter under spec ordering returns zero matches.
+ */
+export type CoordinateAxisOrder = 'spec' | 'swapped';
 /**
  * Extract WGS84 coordinates from a BrAPI v2 record. Modern servers carry
  * coordinates as a GeoJSON Feature (`coordinates.geometry.coordinates =
@@ -163,12 +171,23 @@ export declare function asStringArray(value: unknown): string[] | undefined;
  * top-level `latitude`/`longitude`/`altitude`. Returns `undefined` only
  * when both shapes are missing or malformed. Accepts `unknown` so callers
  * can pass Zod-passthrough rows without an explicit cast.
+ *
+ * `axisOrder` controls how a GeoJSON `Point.coordinates` array is read.
+ * Legacy top-level `latitude`/`longitude` fields are unambiguous by name
+ * and are not affected.
  */
-export declare function extractCoordinates(record: unknown): {
+export declare function extractCoordinates(record: unknown, axisOrder?: CoordinateAxisOrder): {
     latitude: number;
     longitude: number;
     altitude?: number;
 } | undefined;
+/**
+ * True when a BrAPI record carries a GeoJSON `Point` geometry with a
+ * 2- or 3-element numeric coordinate array. Used by the bbox swap-on-zero
+ * heuristic to decide whether retrying with axes swapped is worth doing —
+ * Polygon-only or geometry-less rows can't be reinterpreted.
+ */
+export declare function hasPointGeometry(record: unknown): boolean;
 /**
  * One filter → distribution mapping for `checkFilterMatchRates`. Used to
  * detect upstream servers that silently ignore a filter and return the

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

	@@ -1 +1 @@
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package/dist/mcp-server/tools/shared/find-helpers.js CHANGED Viewed

@@ -328,16 +328,21 @@ export function asStringArray(value) {
  * top-level `latitude`/`longitude`/`altitude`. Returns `undefined` only
  * when both shapes are missing or malformed. Accepts `unknown` so callers
  * can pass Zod-passthrough rows without an explicit cast.
+ *
+ * `axisOrder` controls how a GeoJSON `Point.coordinates` array is read.
+ * Legacy top-level `latitude`/`longitude` fields are unambiguous by name
+ * and are not affected.
  */
-export function extractCoordinates(record) {
+export function extractCoordinates(record, axisOrder = 'spec') {
     if (typeof record !== 'object' || record === null)
         return;
     const r = record;
     const geometry = r.coordinates?.geometry;
     const geoCoords = geometry?.coordinates;
     if (Array.isArray(geoCoords) && geoCoords.length >= 2) {
-        const [lon, lat, alt] = geoCoords;
-        if (typeof lat === 'number' && typeof lon === 'number') {
+        const [a, b, alt] = geoCoords;
+        if (typeof a === 'number' && typeof b === 'number') {
+            const [lon, lat] = axisOrder === 'spec' ? [a, b] : [b, a];
             const result = {
                 latitude: lat,
                 longitude: lon,
@@ -361,6 +366,27 @@ export function extractCoordinates(record) {
     }
     return;
 }
+/**
+ * True when a BrAPI record carries a GeoJSON `Point` geometry with a
+ * 2- or 3-element numeric coordinate array. Used by the bbox swap-on-zero
+ * heuristic to decide whether retrying with axes swapped is worth doing —
+ * Polygon-only or geometry-less rows can't be reinterpreted.
+ */
+export function hasPointGeometry(record) {
+    if (typeof record !== 'object' || record === null)
+        return false;
+    const r = record;
+    const geometry = r.coordinates?.geometry;
+    if (!geometry || typeof geometry !== 'object')
+        return false;
+    const g = geometry;
+    if (g.type !== 'Point')
+        return false;
+    return (Array.isArray(g.coordinates) &&
+        g.coordinates.length >= 2 &&
+        typeof g.coordinates[0] === 'number' &&
+        typeof g.coordinates[1] === 'number');
+}
 /**
  * Verify that requested filter values appear in the returned distributions.
  * When the upstream silently drops a filter, all requested values miss the

package/dist/mcp-server/tools/shared/find-helpers.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/services/ontology-resolver/ontology-resolver.d.ts CHANGED Viewed

@@ -12,6 +12,9 @@ import type { OntologyCandidate, ResolveOptions } from './types.js';
 /**
  * Loose shape of a BrAPI observation-variable record. Every field is
  * optional because server implementations vary in what they populate.
+ * Trait subobject fields follow BrAPI v2.1 naming (`traitName`,
+ * `traitDescription`); both legacy `name` / `description` aliases are
+ * accepted for older or non-conformant servers.
  */
 export interface VariableLike {
     method?: {
@@ -28,9 +31,13 @@ export interface VariableLike {
     synonyms?: string[] | undefined;
     trait?: {
         traitClass?: string;
+        /** Legacy alias for `traitDescription` — accepted for older servers. */
         description?: string;
+        /** Legacy alias for `traitName` — accepted for older servers. */
         name?: string;
         synonyms?: string[];
+        traitDescription?: string;
+        traitName?: string;
     };
 }
 export declare class OntologyResolver {

package/dist/services/ontology-resolver/ontology-resolver.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"ontology-resolver.d.ts","sourceRoot":"","sources":["../../../src/services/ontology-resolver/ontology-resolver.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,iBAAiB,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AAEpE~~;;;GAGG~~;AACH,MAAM,WAAW,YAAY;IAC3B,MAAM,CAAC,EAAE;QAAE,UAAU,CAAC,EAAE,MAAM,CAAA;KAAE,CAAC;IACjC,uBAAuB,CAAC,EAAE,MAAM,CAAC;IACjC,uBAAuB,CAAC,EAAE,MAAM,CAAC;IACjC,sBAAsB,CAAC,EAAE,MAAM,CAAC;IAChC,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,KAAK,CAAC,EAAE;QAAE,SAAS,CAAC,EAAE,MAAM,CAAA;KAAE,CAAC;IAC/B,QAAQ,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;IAChC,KAAK,CAAC,EAAE;QACN,UAAU,CAAC,EAAE,MAAM,CAAC;QACpB,WAAW,CAAC,EAAE,MAAM,CAAC;QACrB,IAAI,CAAC,EAAE,MAAM,CAAC;QACd,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;~~KACrB~~,CAAC;CACH;AAED,qBAAa,gBAAgB;IAC3B;;;;;OAKG;IACH,KAAK,CACH,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,SAAS,YAAY,EAAE,EAClC,OAAO,GAAE,cAAmB,GAC3B,iBAAiB,EAAE;IAoBtB,OAAO,CAAC,QAAQ;~~CA4CjB~~;~~AAsBD~~,wBAAgB,oBAAoB,IAAI,IAAI,CAE3C;AAED,wBAAgB,mBAAmB,IAAI,gBAAgB,CAKtD;AAED,wBAAgB,qBAAqB,IAAI,IAAI,CAE5C"}
1	+ {"version":3,"file":"ontology-resolver.d.ts","sourceRoot":"","sources":["../../../src/services/ontology-resolver/ontology-resolver.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,iBAAiB,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AAEpE;;;;;;GAMG;AACH,MAAM,WAAW,YAAY;IAC3B,MAAM,CAAC,EAAE;QAAE,UAAU,CAAC,EAAE,MAAM,CAAA;KAAE,CAAC;IACjC,uBAAuB,CAAC,EAAE,MAAM,CAAC;IACjC,uBAAuB,CAAC,EAAE,MAAM,CAAC;IACjC,sBAAsB,CAAC,EAAE,MAAM,CAAC;IAChC,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,KAAK,CAAC,EAAE;QAAE,SAAS,CAAC,EAAE,MAAM,CAAA;KAAE,CAAC;IAC/B,QAAQ,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;IAChC,KAAK,CAAC,EAAE;QACN,UAAU,CAAC,EAAE,MAAM,CAAC;QACpB,wEAAwE;QACxE,WAAW,CAAC,EAAE,MAAM,CAAC;QACrB,iEAAiE;QACjE,IAAI,CAAC,EAAE,MAAM,CAAC;QACd,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;QACpB,gBAAgB,CAAC,EAAE,MAAM,CAAC;QAC1B,SAAS,CAAC,EAAE,MAAM,CAAC;KACpB,CAAC;CACH;AAED,qBAAa,gBAAgB;IAC3B;;;;;OAKG;IACH,KAAK,CACH,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,SAAS,YAAY,EAAE,EAClC,OAAO,GAAE,cAAmB,GAC3B,iBAAiB,EAAE;IAoBtB,OAAO,CAAC,QAAQ;CA8CjB;AAwBD,wBAAgB,oBAAoB,IAAI,IAAI,CAE3C;AAED,wBAAgB,mBAAmB,IAAI,gBAAgB,CAKtD;AAED,wBAAgB,qBAAqB,IAAI,IAAI,CAE5C"}

package/dist/services/ontology-resolver/ontology-resolver.js CHANGED Viewed

@@ -52,7 +52,7 @@ export class OntologyResolver {
         if (traitSynonymMatch) {
             return { candidate: toCandidate(variable, 'synonymMatch'), score: 40 };
         }
-        const traitName = variable.trait?.name?.toLowerCase();
+        const traitName = (variable.trait?.traitName ?? variable.trait?.name)?.toLowerCase();
         if (traitName?.includes(query)) {
             return { candidate: toCandidate(variable, 'nameMatch'), score: 35 };
         }
@@ -60,7 +60,7 @@ export class OntologyResolver {
         if (traitClass && traitClass === query) {
             return { candidate: toCandidate(variable, 'traitClassMatch'), score: 30 };
         }
-        const traitDescription = variable.trait?.description?.toLowerCase();
+        const traitDescription = (variable.trait?.traitDescription ?? variable.trait?.description)?.toLowerCase();
         if (traitDescription?.includes(query)) {
             return { candidate: toCandidate(variable, 'nameMatch'), score: 20 };
         }
@@ -74,11 +74,12 @@ function toCandidate(variable, source) {
     }
     if (variable.observationVariablePUI)
         candidate.termId = variable.observationVariablePUI;
-    const name = variable.observationVariableName ?? variable.trait?.name;
+    const name = variable.observationVariableName ?? variable.trait?.traitName ?? variable.trait?.name;
     if (name)
         candidate.name = name;
-    if (variable.trait?.description)
-        candidate.description = variable.trait.description;
+    const description = variable.trait?.traitDescription ?? variable.trait?.description;
+    if (description)
+        candidate.description = description;
     if (variable.ontologyDbId)
         candidate.ontologyDbId = variable.ontologyDbId;
     const combinedSynonyms = [...(variable.synonyms ?? []), ...(variable.trait?.synonyms ?? [])];

package/dist/services/ontology-resolver/ontology-resolver.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"ontology-resolver.js","sourceRoot":"","sources":["../../../src/services/ontology-resolver/ontology-resolver.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAgCH,MAAM,OAAO,gBAAgB;IAC3B;;;;;OAKG;IACH,KAAK,CACH,KAAa,EACb,SAAkC,EAClC,UAA0B,EAAE;QAE5B,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,IAAI,EAAE,CAAC;QAClC,MAAM,UAAU,GAAG,KAAK,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;QAE9C,IAAI,CAAC,UAAU,EAAE,CAAC;YAChB,OAAO,SAAS,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,WAAW,CAAC,CAAC,EAAE,WAAW,CAAC,CAAC,CAAC;QAC3E,CAAC;QAED,MAAM,MAAM,GAAsD,EAAE,CAAC;QAErE,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE,CAAC;YACjC,IAAI,OAAO,CAAC,YAAY,IAAI,QAAQ,CAAC,YAAY,KAAK,OAAO,CAAC,YAAY;gBAAE,SAAS;YACrF,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,CAAC,QAAQ,EAAE,UAAU,CAAC,CAAC;YAClD,IAAI,KAAK;gBAAE,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QAChC,CAAC;QAED,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC;QACzC,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IACxD,CAAC;IAEO,QAAQ,CACd,QAAsB,EACtB,KAAa;QAEb,MAAM,GAAG,GAAG,QAAQ,CAAC,sBAAsB,EAAE,WAAW,EAAE,CAAC;QAC3D,IAAI,GAAG,IAAI,GAAG,KAAK,KAAK,EAAE,CAAC;YACzB,OAAO,EAAE,SAAS,EAAE,WAAW,CAAC,QAAQ,EAAE,UAAU,CAAC,EAAE,KAAK,EAAE,GAAG,EAAE,CAAC;QACtE,CAAC;QAED,MAAM,IAAI,GAAG,QAAQ,CAAC,uBAAuB,EAAE,WAAW,EAAE,CAAC;QAC7D,IAAI,IAAI,EAAE,CAAC;YACT,IAAI,IAAI,KAAK,KAAK;gBAAE,OAAO,EAAE,SAAS,EAAE,WAAW,CAAC,QAAQ,EAAE,WAAW,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,CAAC;YACxF,IAAI,IAAI,CAAC,QAAQ,CAAC,KAAK,CAAC;gBAAE,OAAO,EAAE,SAAS,EAAE,WAAW,CAAC,QAAQ,EAAE,WAAW,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,CAAC;QAChG,CAAC;QAED,MAAM,YAAY,GAAG,QAAQ,CAAC,QAAQ,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC;QACrF,IAAI,YAAY,EAAE,CAAC;YACjB,OAAO,EAAE,SAAS,EAAE,WAAW,CAAC,QAAQ,EAAE,cAAc,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,CAAC;QACzE,CAAC;QAED,MAAM,iBAAiB,GAAG,QAAQ,CAAC,KAAK,EAAE,QAAQ,EAAE,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAC7D,CAAC,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,CAChC,CAAC;QACF,IAAI,iBAAiB,EAAE,CAAC;YACtB,OAAO,EAAE,SAAS,EAAE,WAAW,CAAC,QAAQ,EAAE,cAAc,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,CAAC;QACzE,CAAC;QAED,MAAM,SAAS,GAAG,CAAC,QAAQ,CAAC,KAAK,EAAE,SAAS,IAAI,QAAQ,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,WAAW,EAAE,CAAC;QACrF,IAAI,SAAS,EAAE,QAAQ,CAAC,KAAK,CAAC,EAAE,CAAC;YAC/B,OAAO,EAAE,SAAS,EAAE,WAAW,CAAC,QAAQ,EAAE,WAAW,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,CAAC;QACtE,CAAC;QAED,MAAM,UAAU,GAAG,QAAQ,CAAC,KAAK,EAAE,UAAU,EAAE,WAAW,EAAE,CAAC;QAC7D,IAAI,UAAU,IAAI,UAAU,KAAK,KAAK,EAAE,CAAC;YACvC,OAAO,EAAE,SAAS,EAAE,WAAW,CAAC,QAAQ,EAAE,iBAAiB,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,CAAC;QAC5E,CAAC;QAED,MAAM,gBAAgB,GAAG,CACvB,QAAQ,CAAC,KAAK,EAAE,gBAAgB,IAAI,QAAQ,CAAC,KAAK,EAAE,WAAW,CAChE,EAAE,WAAW,EAAE,CAAC;QACjB,IAAI,gBAAgB,EAAE,QAAQ,CAAC,KAAK,CAAC,EAAE,CAAC;YACtC,OAAO,EAAE,SAAS,EAAE,WAAW,CAAC,QAAQ,EAAE,WAAW,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,CAAC;QACtE,CAAC;QAED,OAAO;IACT,CAAC;CACF;AAED,SAAS,WAAW,CAClB,QAAsB,EACtB,MAAmC;IAEnC,MAAM,SAAS,GAAsB,EAAE,MAAM,EAAE,CAAC;IAChD,IAAI,QAAQ,CAAC,uBAAuB,EAAE,CAAC;QACrC,SAAS,CAAC,uBAAuB,GAAG,QAAQ,CAAC,uBAAuB,CAAC;IACvE,CAAC;IACD,IAAI,QAAQ,CAAC,sBAAsB;QAAE,SAAS,CAAC,MAAM,GAAG,QAAQ,CAAC,sBAAsB,CAAC;IACxF,MAAM,IAAI,GACR,QAAQ,CAAC,uBAAuB,IAAI,QAAQ,CAAC,KAAK,EAAE,SAAS,IAAI,QAAQ,CAAC,KAAK,EAAE,IAAI,CAAC;IACxF,IAAI,IAAI;QAAE,SAAS,CAAC,IAAI,GAAG,IAAI,CAAC;IAChC,MAAM,WAAW,GAAG,QAAQ,CAAC,KAAK,EAAE,gBAAgB,IAAI,QAAQ,CAAC,KAAK,EAAE,WAAW,CAAC;IACpF,IAAI,WAAW;QAAE,SAAS,CAAC,WAAW,GAAG,WAAW,CAAC;IACrD,IAAI,QAAQ,CAAC,YAAY;QAAE,SAAS,CAAC,YAAY,GAAG,QAAQ,CAAC,YAAY,CAAC;IAC1E,MAAM,gBAAgB,GAAG,CAAC,GAAG,CAAC,QAAQ,CAAC,QAAQ,IAAI,EAAE,CAAC,EAAE,GAAG,CAAC,QAAQ,CAAC,KAAK,EAAE,QAAQ,IAAI,EAAE,CAAC,CAAC,CAAC;IAC7F,IAAI,gBAAgB,CAAC,MAAM,GAAG,CAAC;QAAE,SAAS,CAAC,QAAQ,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,GAAG,CAAC,gBAAgB,CAAC,CAAC,CAAC;IAC5F,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,IAAI,SAAuC,CAAC;AAE5C,MAAM,UAAU,oBAAoB;IAClC,SAAS,GAAG,IAAI,gBAAgB,EAAE,CAAC;AACrC,CAAC;AAED,MAAM,UAAU,mBAAmB;IACjC,IAAI,CAAC,SAAS,EAAE,CAAC;QACf,MAAM,IAAI,KAAK,CAAC,2EAA2E,CAAC,CAAC;IAC/F,CAAC;IACD,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,MAAM,UAAU,qBAAqB;IACnC,SAAS,GAAG,SAAS,CAAC;AACxB,CAAC"}

package/package.json CHANGED Viewed

@@ -1,7 +1,7 @@
 {
   "name": "@cyanheads/brapi-mcp-server",
   "mcpName": "io.github.cyanheads/brapi-mcp-server",
-  "version": "0.3.8",
+  "version": "0.3.9",
   "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",

package/server.json CHANGED Viewed

@@ -6,14 +6,14 @@
     "url": "https://github.com/cyanheads/brapi-mcp-server",
     "source": "github"
   },
-  "version": "0.3.8",
+  "version": "0.3.9",
   "packages": [
     {
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.3.8",
+      "version": "0.3.9",
       "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": "0.3.8",
+      "version": "0.3.9",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }