npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.3.6 → 0.3.8 - Mend

@cyanheads/brapi-mcp-server 0.3.6 → 0.3.8

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (68) hide show

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

@@ -0,0 +1 @@

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package/dist/mcp-server/tools/definitions/index.js ADDED Viewed

@@ -0,0 +1,50 @@
+/**
+ * @fileoverview Tool registration barrel. The write tool
+ * (`brapi_submit_observations`) is exported separately so callers can decide
+ * whether to register it based on the `BRAPI_ENABLE_WRITES` flag — keeping
+ * this module free of eager config reads.
+ * @module mcp-server/tools/definitions/index
+ */
+import { brapiConnect } from './brapi-connect.tool.js';
+import { brapiDescribeFilters } from './brapi-describe-filters.tool.js';
+import { brapiFindGenotypeCalls } from './brapi-find-genotype-calls.tool.js';
+import { brapiFindGermplasm } from './brapi-find-germplasm.tool.js';
+import { brapiFindImages } from './brapi-find-images.tool.js';
+import { brapiFindLocations } from './brapi-find-locations.tool.js';
+import { brapiFindObservations } from './brapi-find-observations.tool.js';
+import { brapiFindStudies } from './brapi-find-studies.tool.js';
+import { brapiFindVariables } from './brapi-find-variables.tool.js';
+import { brapiFindVariants } from './brapi-find-variants.tool.js';
+import { brapiGetGermplasm } from './brapi-get-germplasm.tool.js';
+import { brapiGetImage } from './brapi-get-image.tool.js';
+import { brapiGetStudy } from './brapi-get-study.tool.js';
+import { brapiManageDataset } from './brapi-manage-dataset.tool.js';
+import { brapiRawGet } from './brapi-raw-get.tool.js';
+import { brapiRawSearch } from './brapi-raw-search.tool.js';
+import { brapiServerInfo } from './brapi-server-info.tool.js';
+import { brapiSubmitObservations } from './brapi-submit-observations.tool.js';
+import { brapiWalkPedigree } from './brapi-walk-pedigree.tool.js';
+/** Read-only tools registered unconditionally on every server. */
+export const readOnlyToolDefinitions = [
+    brapiConnect,
+    brapiServerInfo,
+    brapiDescribeFilters,
+    brapiFindStudies,
+    brapiGetStudy,
+    brapiFindGermplasm,
+    brapiGetGermplasm,
+    brapiWalkPedigree,
+    brapiFindVariables,
+    brapiFindObservations,
+    brapiFindImages,
+    brapiGetImage,
+    brapiFindLocations,
+    brapiFindVariants,
+    brapiFindGenotypeCalls,
+    brapiManageDataset,
+    brapiRawGet,
+    brapiRawSearch,
+];
+/** Write tools — registered only when `BRAPI_ENABLE_WRITES=true`. */
+export const writeToolDefinitions = [brapiSubmitObservations];
+//# sourceMappingURL=index.js.map

package/dist/mcp-server/tools/definitions/index.js.map ADDED Viewed

@@ -0,0 +1 @@

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

@@ -34,6 +34,29 @@ export declare function buildRequestOptions(connection: RegisteredServer, params
  * exploded. Returns `{value -> count}` sorted by count desc.
  */
 export declare function computeDistribution<T>(rows: readonly T[], accessor: (row: T) => string | readonly string[] | undefined | null): Record<string, number>;
+/**
+ * Render the standardized header line for `find_*` tools. When a dataset
+ * spillover is present, surfaces the dataset row count alongside the
+ * in-context count and the upstream total — `{returned} of {total}` alone
+ * hides the middle number and confuses readers when filters miss server-
+ * side and the dataset row count diverges from both.
+ */
+export declare function renderFindHeader(opts: {
+    noun: string;
+    alias: string;
+    returnedCount: number;
+    totalCount: number;
+    dataset?: {
+        rowCount: number;
+    } | undefined;
+}): string;
+/**
+ * Render the applied-filters block, optionally translating server-side
+ * keys to the user-facing parameter names declared by the tool. Server
+ * keys without a user-facing alias (e.g. anything from `extraFilters`) are
+ * rendered as-is.
+ */
+export declare function renderAppliedFilters(filters: Record<string, unknown>, serverToUser?: Record<string, string>): string;
 /** Cheap sanity-render for a distributions block in markdown. */
 export declare function renderDistributions(distributions: Record<string, Record<string, number>>): string;
 export interface LoadedRows<T> {
@@ -133,11 +156,57 @@ 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;
+/**
+ * Extract WGS84 coordinates from a BrAPI v2 record. Modern servers carry
+ * coordinates as a GeoJSON Feature (`coordinates.geometry.coordinates =
+ * [lon, lat, alt?]`); some legacy and mixed-mode servers also expose
+ * 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.
+ */
+export declare function extractCoordinates(record: unknown): {
+    latitude: number;
+    longitude: number;
+    altitude?: number;
+} | undefined;
+/**
+ * One filter → distribution mapping for `checkFilterMatchRates`. Used to
+ * detect upstream servers that silently ignore a filter and return the
+ * unfiltered set instead of the requested subset.
+ */
+export interface FilterMatchCheck {
+    /** Compare case-insensitively (default: false). */
+    caseInsensitive?: boolean;
+    /** Distribution computed from the returned rows for the corresponding field. */
+    distribution: Record<string, number>;
+    /** User-facing filter name (e.g. "seasons"). Surfaces in the warning. */
+    paramName: string;
+    /** Requested values from the agent. Undefined or empty means skip this check. */
+    requestedValues: readonly (string | number | boolean)[] | undefined;
+}
+/**
+ * Verify that requested filter values appear in the returned distributions.
+ * When the upstream silently drops a filter, all requested values miss the
+ * distribution — the warning lets the agent (and the user) know the result
+ * set may not actually match the query. Skips checks where the distribution
+ * is empty (no signal) or where no values were requested.
+ */
+export declare function checkFilterMatchRates(warnings: string[], fullRowCount: number, checks: readonly FilterMatchCheck[]): void;
+export interface RefinementHintOptions {
+    /**
+     * Filter parameter names available on the calling tool. Used to suggest
+     * concrete narrowers when no distribution has enough cardinality to
+     * pick a specific value. Skipped when omitted.
+     */
+    availableFilters?: readonly string[];
+}
 /**
  * Compose a refinement hint for a too-large result set. Picks the highest-
  * cardinality non-empty distribution to suggest as a narrower. Returns
- * undefined when the result set fits under `loadLimit`.
+ * undefined when the result set fits under `loadLimit`. When distributions
+ * are too sparse to surface a specific value, falls back to suggesting
+ * the tool's available filter parameters by name.
  */
-export declare function buildRefinementHint(totalCount: number, loadLimit: number, distributions: Record<string, Record<string, number>>): string | undefined;
+export declare function buildRefinementHint(totalCount: number, loadLimit: number, distributions: Record<string, Record<string, number>>, options?: RefinementHintOptions): string | undefined;
 export type { BrapiEnvelope, BrapiPagination, ResolvedAuth, ServerConfig };
 //# sourceMappingURL=find-helpers.d.ts.map

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

@@ -102,6 +102,37 @@ export function computeDistribution(rows, accessor) {
     }
     return Object.fromEntries([...counts.entries()].sort(([, a], [, b]) => b - a));
 }
+/**
+ * Render the standardized header line for `find_*` tools. When a dataset
+ * spillover is present, surfaces the dataset row count alongside the
+ * in-context count and the upstream total — `{returned} of {total}` alone
+ * hides the middle number and confuses readers when filters miss server-
+ * side and the dataset row count diverges from both.
+ */
+export function renderFindHeader(opts) {
+    if (opts.dataset) {
+        return `# ${opts.returnedCount} returned · ${opts.dataset.rowCount} in dataset · ${opts.totalCount} total ${opts.noun} — \`${opts.alias}\``;
+    }
+    return `# ${opts.returnedCount} of ${opts.totalCount} ${opts.noun} — \`${opts.alias}\``;
+}
+/**
+ * Render the applied-filters block, optionally translating server-side
+ * keys to the user-facing parameter names declared by the tool. Server
+ * keys without a user-facing alias (e.g. anything from `extraFilters`) are
+ * rendered as-is.
+ */
+export function renderAppliedFilters(filters, serverToUser = {}) {
+    const entries = Object.entries(filters);
+    if (entries.length === 0)
+        return 'Applied filters: `{}`';
+    const lines = ['Applied filters:'];
+    for (const [serverKey, value] of entries) {
+        const userKey = serverToUser[serverKey];
+        const label = userKey ? `${userKey} → ${serverKey}` : serverKey;
+        lines.push(`- \`${label}\`: ${JSON.stringify(value)}`);
+    }
+    return lines.join('\n');
+}
 /** Cheap sanity-render for a distributions block in markdown. */
 export function renderDistributions(distributions) {
     const lines = [];
@@ -290,12 +321,80 @@ export function asStringArray(value) {
         return;
     return value.filter((v) => typeof v === 'string' && v.length > 0);
 }
+/**
+ * Extract WGS84 coordinates from a BrAPI v2 record. Modern servers carry
+ * coordinates as a GeoJSON Feature (`coordinates.geometry.coordinates =
+ * [lon, lat, alt?]`); some legacy and mixed-mode servers also expose
+ * 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.
+ */
+export function extractCoordinates(record) {
+    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 result = {
+                latitude: lat,
+                longitude: lon,
+            };
+            if (typeof alt === 'number')
+                result.altitude = alt;
+            return result;
+        }
+    }
+    const lat = r.latitude;
+    const lon = r.longitude;
+    if (typeof lat === 'number' && typeof lon === 'number') {
+        const result = {
+            latitude: lat,
+            longitude: lon,
+        };
+        const alt = r.altitude;
+        if (typeof alt === 'number')
+            result.altitude = alt;
+        return result;
+    }
+    return;
+}
+/**
+ * Verify that requested filter values appear in the returned distributions.
+ * When the upstream silently drops a filter, all requested values miss the
+ * distribution — the warning lets the agent (and the user) know the result
+ * set may not actually match the query. Skips checks where the distribution
+ * is empty (no signal) or where no values were requested.
+ */
+export function checkFilterMatchRates(warnings, fullRowCount, checks) {
+    if (fullRowCount === 0)
+        return;
+    for (const check of checks) {
+        if (!check.requestedValues || check.requestedValues.length === 0)
+            continue;
+        const distKeys = Object.keys(check.distribution);
+        if (distKeys.length === 0)
+            continue;
+        const norm = (v) => (check.caseInsensitive ? v.toLowerCase() : v);
+        const haystack = new Set(distKeys.map(norm));
+        const matched = check.requestedValues.some((v) => haystack.has(norm(String(v))));
+        if (matched)
+            continue;
+        const sample = distKeys.slice(0, 5).join(', ');
+        const overflow = distKeys.length > 5 ? `, …+${distKeys.length - 5} more` : '';
+        warnings.push(`Filter '${check.paramName}' requested ${JSON.stringify(check.requestedValues)} but no returned row matches — the server may not honor this filter. Observed values: ${sample}${overflow}.`);
+    }
+}
 /**
  * Compose a refinement hint for a too-large result set. Picks the highest-
  * cardinality non-empty distribution to suggest as a narrower. Returns
- * undefined when the result set fits under `loadLimit`.
+ * undefined when the result set fits under `loadLimit`. When distributions
+ * are too sparse to surface a specific value, falls back to suggesting
+ * the tool's available filter parameters by name.
  */
-export function buildRefinementHint(totalCount, loadLimit, distributions) {
+export function buildRefinementHint(totalCount, loadLimit, distributions, options = {}) {
     if (totalCount <= loadLimit)
         return;
     let best;
@@ -311,9 +410,13 @@ export function buildRefinementHint(totalCount, loadLimit, distributions) {
             best = { field, topValue, count, cardinality: entries.length };
         }
     }
-    if (!best) {
-        return `${totalCount} rows exceed loadLimit=${loadLimit}. Add more specific filters or raise loadLimit.`;
+    if (best) {
+        return `${totalCount} rows exceed loadLimit=${loadLimit}. The ${best.field} distribution spans ${best.cardinality} values — narrowing to \`${best.topValue}\` would cut to ~${best.count} rows.`;
+    }
+    if (options.availableFilters && options.availableFilters.length > 0) {
+        const suggestions = options.availableFilters.map((f) => `\`${f}\``).join(', ');
+        return `${totalCount} rows exceed loadLimit=${loadLimit}. Distributions are too sparse to surface a specific narrower — try filtering on ${suggestions}, or raise loadLimit.`;
     }
-    return `${totalCount} rows exceed loadLimit=${loadLimit}. The ${best.field} distribution spans ${best.cardinality} values — narrowing to \`${best.topValue}\` would cut to ~${best.count} rows.`;
+    return `${totalCount} rows exceed loadLimit=${loadLimit}. Add more specific filters or raise loadLimit.`;
 }
 //# sourceMappingURL=find-helpers.js.map

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

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/shared/orientation-envelope.d.ts CHANGED Viewed

@@ -3,7 +3,7 @@
  * by both `brapi_connect` (inlined after registration) and
  * `brapi_server_info` (on-demand). Pulls from CapabilityRegistry and the
  * active ServerRegistry entry, then layers in cheap opportunistic counts via
- * `pageSize=0` probes. Counts degrade silently — a server that doesn't
+ * `pageSize=1` probes. Counts degrade silently — a server that doesn't
  * honor the probe just omits the field rather than failing the whole call.
  *
  * @module mcp-server/tools/shared/orientation-envelope
@@ -90,7 +90,10 @@ export interface BuildEnvelopeDeps {
 /**
  * Compose the orientation envelope for a connected server. Runs the
  * CapabilityRegistry profile (cached after the first call) plus a parallel
- * set of cheap `pageSize=0` probes for totals.
+ * set of cheap `pageSize=1` probes for totals. BrAPI v2.1 mandates
+ * `pageSize >= 1` — strict servers reject `pageSize=0` with HTTP 400, so
+ * we ask for one row and ignore it; only `metadata.pagination.totalCount`
+ * matters here.
  */
 export declare function buildOrientationEnvelope(ctx: Context, connection: RegisteredServer, deps: BuildEnvelopeDeps): Promise<OrientationEnvelope>;
 export declare function formatOrientationEnvelope(envelope: OrientationEnvelope): string;

package/dist/mcp-server/tools/shared/orientation-envelope.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"orientation-envelope.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/orientation-envelope.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAE,KAAK,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACzD,OAAO,KAAK,EAAE,WAAW,EAAuB,MAAM,kCAAkC,CAAC;AACzF,OAAO,KAAK,EAEV,kBAAkB,EACnB,MAAM,yCAAyC,CAAC;AACjD,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,qCAAqC,CAAC;AAsB5E,eAAO,MAAM,oBAAoB;;;;;;;;iBAUmD,CAAC;AAErF,eAAO,MAAM,qBAAqB;;;;;;;;;;iBAQ0C,CAAC;AAE7E,eAAO,MAAM,6BAA6B;;;;iBAciD,CAAC;AAE5F,eAAO,MAAM,wBAAwB;;;;;;iBA8B2D,CAAC;AAEjG,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAapC,CAAC;AAEH,MAAM,MAAM,mBAAmB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,yBAAyB,CAAC,CAAC;AAE5E,MAAM,WAAW,iBAAiB;IAChC,MAAM,EAAE,WAAW,CAAC;IACpB,QAAQ,EAAE,kBAAkB,CAAC;CAC9B;AAED~~;;;;GAIG~~;AACH,wBAAsB,wBAAwB,CAC5C,GAAG,EAAE,OAAO,EACZ,UAAU,EAAE,gBAAgB,EAC5B,IAAI,EAAE,iBAAiB,GACtB,OAAO,CAAC,mBAAmB,CAAC,CAwD9B;AAqDD,wBAAgB,yBAAyB,CAAC,QAAQ,EAAE,mBAAmB,GAAG,MAAM,CA6D/E"}
1	+ {"version":3,"file":"orientation-envelope.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/orientation-envelope.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAE,KAAK,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACzD,OAAO,KAAK,EAAE,WAAW,EAAuB,MAAM,kCAAkC,CAAC;AACzF,OAAO,KAAK,EAEV,kBAAkB,EACnB,MAAM,yCAAyC,CAAC;AACjD,OAAO,KAAK,EAAE,gBAAgB,EAAE,MAAM,qCAAqC,CAAC;AAsB5E,eAAO,MAAM,oBAAoB;;;;;;;;iBAUmD,CAAC;AAErF,eAAO,MAAM,qBAAqB;;;;;;;;;;iBAQ0C,CAAC;AAE7E,eAAO,MAAM,6BAA6B;;;;iBAciD,CAAC;AAE5F,eAAO,MAAM,wBAAwB;;;;;;iBA8B2D,CAAC;AAEjG,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAapC,CAAC;AAEH,MAAM,MAAM,mBAAmB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,yBAAyB,CAAC,CAAC;AAE5E,MAAM,WAAW,iBAAiB;IAChC,MAAM,EAAE,WAAW,CAAC;IACpB,QAAQ,EAAE,kBAAkB,CAAC;CAC9B;AAED;;;;;;;GAOG;AACH,wBAAsB,wBAAwB,CAC5C,GAAG,EAAE,OAAO,EACZ,UAAU,EAAE,gBAAgB,EAC5B,IAAI,EAAE,iBAAiB,GACtB,OAAO,CAAC,mBAAmB,CAAC,CAwD9B;AAqDD,wBAAgB,yBAAyB,CAAC,QAAQ,EAAE,mBAAmB,GAAG,MAAM,CA6D/E"}

package/dist/mcp-server/tools/shared/orientation-envelope.js CHANGED Viewed

@@ -3,7 +3,7 @@
  * by both `brapi_connect` (inlined after registration) and
  * `brapi_server_info` (on-demand). Pulls from CapabilityRegistry and the
  * active ServerRegistry entry, then layers in cheap opportunistic counts via
- * `pageSize=0` probes. Counts degrade silently — a server that doesn't
+ * `pageSize=1` probes. Counts degrade silently — a server that doesn't
  * honor the probe just omits the field rather than failing the whole call.
  *
  * @module mcp-server/tools/shared/orientation-envelope
@@ -109,7 +109,10 @@ export const OrientationEnvelopeSchema = z.object({
 /**
  * Compose the orientation envelope for a connected server. Runs the
  * CapabilityRegistry profile (cached after the first call) plus a parallel
- * set of cheap `pageSize=0` probes for totals.
+ * set of cheap `pageSize=1` probes for totals. BrAPI v2.1 mandates
+ * `pageSize >= 1` — strict servers reject `pageSize=0` with HTTP 400, so
+ * we ask for one row and ignore it; only `metadata.pagination.totalCount`
+ * matters here.
  */
 export async function buildOrientationEnvelope(ctx, connection, deps) {
     const baseRequestOptions = {};
@@ -172,7 +175,7 @@ async function fetchOpportunisticCounts(client, baseUrl, ctx, supportedSet, base
         try {
             const env = await client.get(baseUrl, probe.path, ctx, {
                 ...baseOptions,
-                params: { pageSize: 0 },
+                params: { pageSize: 1 },
             });
             const total = env.metadata?.pagination?.totalCount;
             if (typeof total === 'number' && Number.isFinite(total)) {

package/dist/mcp-server/tools/shared/orientation-envelope.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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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;~~AAmBD~~,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;;;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"}

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

@@ -69,6 +69,9 @@ export class OntologyResolver {
 }
 function toCandidate(variable, source) {
     const candidate = { source };
+    if (variable.observationVariableDbId) {
+        candidate.observationVariableDbId = variable.observationVariableDbId;
+    }
     if (variable.observationVariablePUI)
         candidate.termId = variable.observationVariablePUI;
     const name = variable.observationVariableName ?? variable.trait?.name;

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

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

@@ -14,6 +14,12 @@ export interface OntologyCandidate {
     description?: string;
     /** Display name of the trait/variable/term. */
     name?: string;
+    /**
+     * Server-side variable DbId of the row this candidate was scored from.
+     * Always populated when the source variable carries one; used by callers
+     * to map candidates back to rows (PUI is too sparse on real servers).
+     */
+    observationVariableDbId?: string;
     /** Originating ontology (e.g. "CO_334"). */
     ontologyDbId?: string;
     /**

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

	@@ -1 +1 @@
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package/dist/services/reference-data-cache/types.d.ts CHANGED Viewed

@@ -30,13 +30,23 @@ export interface Trial {
 export interface Location {
     abbreviation?: string;
     altitude?: number;
+    /** BrAPI v2 GeoJSON Feature carrying [lon, lat, alt?] in geometry.coordinates. */
+    coordinates?: {
+        type?: string;
+        geometry?: {
+            type?: string;
+            coordinates?: number[];
+        };
+    };
     countryCode?: string;
     countryName?: string;
     documentationURL?: string;
+    /** Legacy WGS84 latitude — modern BrAPI v2 servers use `coordinates` instead. */
     latitude?: number;
     locationDbId: string;
     locationName?: string;
     locationType?: string;
+    /** Legacy WGS84 longitude — modern BrAPI v2 servers use `coordinates` instead. */
     longitude?: number;
 }
 //# sourceMappingURL=types.d.ts.map

package/dist/services/reference-data-cache/types.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/services/reference-data-cache/types.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,MAAM,WAAW,OAAO;IACtB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB;AAED,MAAM,WAAW,KAAK;IACpB,MAAM,CAAC,EAAE,OAAO,CAAC;IACjB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;IAClB,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,QAAQ;IACvB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,kFAAkF;IAClF,WAAW,CAAC,EAAE;QAAE,IAAI,CAAC,EAAE,MAAM,CAAC;QAAC,QAAQ,CAAC,EAAE;YAAE,IAAI,CAAC,EAAE,MAAM,CAAC;YAAC,WAAW,CAAC,EAAE,MAAM,EAAE,CAAA;SAAE,CAAA;KAAE,CAAC;IACtF,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,iFAAiF;IACjF,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,kFAAkF;IAClF,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB"}

package/package.json CHANGED Viewed

@@ -1,7 +1,7 @@
 {
   "name": "@cyanheads/brapi-mcp-server",
   "mcpName": "io.github.cyanheads/brapi-mcp-server",
-  "version": "0.3.6",
+  "version": "0.3.8",
   "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",