npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.5.4 → 0.6.0 - Mend

@cyanheads/brapi-mcp-server 0.5.4 → 0.6.0

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 (144) hide show

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

@@ -23,7 +23,7 @@ export declare const brapiFindVariants: import("@cyanheads/mcp-ts-core").ToolDef
     results: z.ZodArray<z.ZodObject<{
         variantDbId: z.ZodString;
         variantNames: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodString>>>;
-        variantSetDbId: z.ZodOptional<z.ZodNullable<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>>;
+        variantSetDbId: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>, z.ZodNull]>>;
         variantSetDbIds: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodString>>>;
         variantType: z.ZodOptional<z.ZodNullable<z.ZodString>>;
         referenceBases: z.ZodOptional<z.ZodNullable<z.ZodString>>;
@@ -56,6 +56,11 @@ export declare const brapiFindVariants: import("@cyanheads/mcp-ts-core").ToolDef
     warnings: z.ZodArray<z.ZodString>;
     appliedFilters: z.ZodRecord<z.ZodString, z.ZodUnknown>;
 }, z.core.$strip>, readonly [{
+    readonly reason: "unknown_alias";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "No connection has been registered under the requested alias";
+    readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_variants.";
+}, {
     readonly reason: "all_filters_dropped";
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.";

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-variants.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variants.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AAiIjE~~,eAAO,MAAM,iBAAiB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsM5B~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-variants.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variants.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmIjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiN5B,CAAC"}

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

@@ -13,8 +13,7 @@ import { getBrapiClient } from '../../../services/brapi-client/index.js';
 import { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCanvasBridge } from '../../../services/canvas-bridge/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
-import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, applyDialectFiltersOrFail, asString, buildExtraFilterChecks, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDataframeHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFiltersOrFail, asString, buildExtraFilterChecks, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, dialectRowMapper, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, resolveFindRoute, } from '../shared/find-helpers.js';
 const VariantRowSchema = z
     .object({
     variantDbId: z.string().describe('Server-side identifier for the variant.'),
@@ -28,8 +27,9 @@ const VariantRowSchema = z
         z
             .array(z.string().describe('One variant-set FK.'))
             .describe('Variant-set FK array — a variant may belong to multiple sets.'),
+        z.null().describe('Field present but null on the upstream.'),
     ])
-        .nullish()
+        .optional()
         .describe('FK to the variant set(s) this variant belongs to. May be a string or string[] depending on server.'),
     variantSetDbIds: z
         .array(z.string().describe('Variant-set FK.'))
@@ -110,6 +110,12 @@ export const brapiFindVariants = tool('brapi_find_variants', {
     description: 'Find variant records by variant set, reference sequence, or genomic region (start/end, 1-based inclusive / exclusive). When the upstream total exceeds loadLimit, the full result set is materialized as a dataframe — query it with brapi_dataframe_query (SQL).',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
+        {
+            reason: 'unknown_alias',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'No connection has been registered under the requested alias',
+            recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_variants.',
+        },
         {
             reason: 'all_filters_dropped',
             code: JsonRpcErrorCode.ValidationError,
@@ -130,12 +136,11 @@ export const brapiFindVariants = tool('brapi_find_variants', {
     }),
     output: OutputSchema,
     async handler(input, ctx) {
-        const registry = getServerRegistry();
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
         const bridge = getCanvasBridge();
         const config = getServerConfig();
-        const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
+        const connection = await requireRegisteredConnection(ctx, input.alias);
         const capabilityLookup = {};
         if (connection.resolvedAuth)
             capabilityLookup.auth = connection.resolvedAuth;
@@ -153,7 +158,8 @@ export const brapiFindVariants = tool('brapi_find_variants', {
             start: input.start,
             end: input.end,
         }, input.extraFilters, warnings);
-        const filters = applyDialectFiltersOrFail(ctx, dialect, 'variants', merged, warnings);
+        const adapted = applyDialectFiltersOrFail(ctx, dialect, 'variants', merged, warnings);
+        const filters = adapted.filters;
         const route = resolveFindRoute({
             profile,
             dialect,
@@ -161,9 +167,11 @@ export const brapiFindVariants = tool('brapi_find_variants', {
             filters,
             searchBody: merged,
             warnings,
+            ...(adapted.requiresEscalation ? { requiresEscalation: true } : {}),
         });
         const loadLimit = input.loadLimit ?? config.loadLimit;
-        const firstPage = await loadInitialFindPage(client, connection, route, loadLimit, ctx);
+        const normalizeRow = dialectRowMapper(dialect, 'variants');
+        const firstPage = await loadInitialFindPage(client, connection, route, loadLimit, ctx, normalizeRow ? { normalizeRow } : {});
         const { fullRows, dataframe } = await maybeSpill({
             firstPage,
             client,
@@ -175,6 +183,7 @@ export const brapiFindVariants = tool('brapi_find_variants', {
             loadLimit,
             ctx,
             bridge,
+            ...(normalizeRow ? { normalizeRow } : {}),
         });
         const distributions = {
             variantType: computeDistribution(fullRows, (r) => asString(r.variantType)),

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

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts CHANGED Viewed

@@ -51,6 +51,11 @@ export declare const brapiGetGermplasm: import("@cyanheads/mcp-ts-core").ToolDef
     directDescendantCount: z.ZodOptional<z.ZodNumber>;
     warnings: z.ZodArray<z.ZodString>;
 }, z.core.$strip>, readonly [{
+    readonly reason: "unknown_alias";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "No connection has been registered under the requested alias";
+    readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_get_germplasm.";
+}, {
     readonly reason: "germplasm_not_found";
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "Upstream returned no germplasm record for the requested DbId";

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

	@@ -1 +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;AA0GjE,eAAO,MAAM,iBAAiB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiP5B~~,CAAC"}
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;AA0GjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAuP5B,CAAC"}

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

@@ -11,8 +11,7 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 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, dedupSynonymsByIdentity, isUpstreamNotFound, } from '../shared/find-helpers.js';
+import { AliasInput, appendPassthroughLines, buildRequestOptions, collectPassthroughParts, dedupSynonymsByIdentity, isUpstreamNotFound, requireRegisteredConnection, } from '../shared/find-helpers.js';
 const GermplasmSchema = z
     .object({
     germplasmDbId: z.string().describe('Server-side identifier for the germplasm.'),
@@ -97,6 +96,12 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
     description: 'Fetch a single germplasm by DbId with attributes and direct parents. Response companions report study count, direct parent count, and direct descendant count — signals for pedigree depth and observation coverage.',
     annotations: { readOnlyHint: true, idempotentHint: true },
     errors: [
+        {
+            reason: 'unknown_alias',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'No connection has been registered under the requested alias',
+            recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_get_germplasm.',
+        },
         {
             reason: 'germplasm_not_found',
             code: JsonRpcErrorCode.NotFound,
@@ -110,10 +115,9 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
     }),
     output: OutputSchema,
     async handler(input, ctx) {
-        const registry = getServerRegistry();
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
-        const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
+        const connection = await requireRegisteredConnection(ctx, input.alias);
         const capabilityLookup = {};
         if (connection.resolvedAuth)
             capabilityLookup.auth = connection.resolvedAuth;
@@ -122,7 +126,7 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
         const warnings = [];
         let germplasmEnv;
         try {
-            germplasmEnv = await client.get(connection.baseUrl, `/germplasm/${id}`, ctx, buildRequestOptions(connection));
+            germplasmEnv = await client.get(connection.baseUrl, `/germplasm/${id}`, ctx, buildRequestOptions(connection, undefined, { singleton: true }));
         }
         catch (err) {
             if (isUpstreamNotFound(err)) {

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

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/brapi-get-image.tool.d.ts CHANGED Viewed

@@ -49,6 +49,11 @@ export declare const brapiGetImage: import("@cyanheads/mcp-ts-core").ToolDefinit
         warning: z.ZodString;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
+    readonly reason: "unknown_alias";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "No connection has been registered under the requested alias";
+    readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_get_image.";
+}, {
     readonly reason: "images_unsupported";
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "BrAPI server does not advertise /images in /serverinfo";

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-get-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-image.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AAsEjE~~,eAAO,MAAM,aAAa~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAyJxB~~,CAAC"}
1	+ {"version":3,"file":"brapi-get-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-image.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0EjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+JxB,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-get-image.tool.js CHANGED Viewed

@@ -11,8 +11,7 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getBrapiClient } from '../../../services/brapi-client/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
-import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, appendPassthroughLines, buildRequestOptions } from '../shared/find-helpers.js';
+import { AliasInput, appendPassthroughLines, buildRequestOptions, requireRegisteredConnection, } from '../shared/find-helpers.js';
 const MAX_IMAGES_PER_CALL = 5;
 const MAX_IMAGE_BYTES = 20 * 1024 * 1024; // 20 MB
 const ImageMetadataSchema = z
@@ -70,6 +69,12 @@ export const brapiGetImage = tool('brapi_get_image', {
     description: `Fetch image bytes for up to ${MAX_IMAGES_PER_CALL} imageDbIds and return them inline as \`type: image\` content blocks. Falls back to the metadata \`imageURL\` when the server lacks dedicated image-content delivery. No filesystem side-effects.`,
     annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: true },
     errors: [
+        {
+            reason: 'unknown_alias',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'No connection has been registered under the requested alias',
+            recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_get_image.',
+        },
         {
             reason: 'images_unsupported',
             code: JsonRpcErrorCode.NotFound,
@@ -87,10 +92,9 @@ export const brapiGetImage = tool('brapi_get_image', {
     }),
     output: OutputSchema,
     async handler(input, ctx) {
-        const registry = getServerRegistry();
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
-        const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
+        const connection = await requireRegisteredConnection(ctx, input.alias);
         const capabilityLookup = {};
         if (connection.resolvedAuth)
             capabilityLookup.auth = connection.resolvedAuth;
@@ -290,13 +294,36 @@ async function fetchBytes(input) {
         source: 'imageURL',
     };
 }
+/**
+ * Resolve an `imageURL` metadata value to an absolute fetchable URL.
+ * Three input shapes are handled:
+ *   1. Absolute URL (`https://host/path`, `http://host/path`) — returned as-is.
+ *   2. Schemeless protocol-relative (`//host/path`) — prefixed with `https:`.
+ *   3. Schemeless domain-shaped (`host.tld/path`, e.g. Breedbase's
+ *      `breedbase.org/data/images/.../medium.jpg`) — prefixed with `https://`.
+ *   4. Root-relative or relative path (`/path` or `path`) — concatenated with
+ *      the BrAPI baseUrl. This is the legitimate "image is hosted on the same
+ *      BrAPI server" case.
+ */
 function resolveImageUrl(baseUrl, imageUrl) {
     if (imageUrl.startsWith('http://') || imageUrl.startsWith('https://'))
         return imageUrl;
+    if (imageUrl.startsWith('//'))
+        return `https:${imageUrl}`;
+    if (SCHEMELESS_DOMAIN.test(imageUrl))
+        return `https://${imageUrl}`;
     const trimmed = baseUrl.replace(/\/$/, '');
     const prefixed = imageUrl.startsWith('/') ? imageUrl : `/${imageUrl}`;
     return `${trimmed}${prefixed}`;
 }
+/**
+ * Matches values that look like `domain.tld/path` or just `domain.tld` — a
+ * leading character that isn't `/`, followed by at least one DNS-style label
+ * with a TLD of two-plus letters. Excludes leading slashes (path) and IPv4
+ * dotted-quads (rare in `imageURL`, and the surrounding flow treats them as
+ * paths under baseUrl just fine).
+ */
+const SCHEMELESS_DOMAIN = /^(?!\/)[a-z0-9](?:[a-z0-9-]*[a-z0-9])?(?:\.[a-z0-9-]+)*\.[a-z]{2,}(?:[/:?#]|$)/i;
 function toBase64(bytes) {
     if (typeof Buffer !== 'undefined') {
         return Buffer.from(bytes).toString('base64');

package/dist/mcp-server/tools/definitions/brapi-get-image.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/brapi-get-study.tool.d.ts CHANGED Viewed

@@ -68,6 +68,11 @@ export declare const brapiGetStudy: import("@cyanheads/mcp-ts-core").ToolDefinit
     variableCount: z.ZodOptional<z.ZodNumber>;
     warnings: z.ZodArray<z.ZodString>;
 }, z.core.$strip>, readonly [{
+    readonly reason: "unknown_alias";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "No connection has been registered under the requested alias";
+    readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_get_study.";
+}, {
     readonly reason: "study_not_found";
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "Upstream returned no study record for the requested DbId";

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-get-study.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-study.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6IjE,eAAO,MAAM,aAAa~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+PxB~~,CAAC"}
1	+ {"version":3,"file":"brapi-get-study.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-study.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6IjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAqQxB,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-get-study.tool.js CHANGED Viewed

@@ -13,8 +13,7 @@ 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 { getReferenceDataCache } from '../../../services/reference-data-cache/index.js';
-import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, appendPassthroughLines, asStringArray, buildRequestOptions, companionRequestOptions, extractCoordinates, isUpstreamNotFound, } from '../shared/find-helpers.js';
+import { AliasInput, appendPassthroughLines, asStringArray, buildRequestOptions, companionRequestOptions, extractCoordinates, isUpstreamNotFound, requireRegisteredConnection, } from '../shared/find-helpers.js';
 const StudySchema = z
     .object({
     studyDbId: z.string().describe('Server-side identifier for the study.'),
@@ -122,6 +121,12 @@ export const brapiGetStudy = tool('brapi_get_study', {
     description: 'Fetch a single study by DbId with program, trial, and location fully resolved. Response includes cheap observation/observation-unit/variable counts as drill-down signals.',
     annotations: { readOnlyHint: true, idempotentHint: true },
     errors: [
+        {
+            reason: 'unknown_alias',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'No connection has been registered under the requested alias',
+            recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_get_study.',
+        },
         {
             reason: 'study_not_found',
             code: JsonRpcErrorCode.NotFound,
@@ -135,12 +140,11 @@ export const brapiGetStudy = tool('brapi_get_study', {
     }),
     output: OutputSchema,
     async handler(input, ctx) {
-        const registry = getServerRegistry();
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
         const referenceData = getReferenceDataCache();
         const config = getServerConfig();
-        const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
+        const connection = await requireRegisteredConnection(ctx, input.alias);
         const capabilityLookup = {};
         if (connection.resolvedAuth)
             capabilityLookup.auth = connection.resolvedAuth;
@@ -152,7 +156,7 @@ export const brapiGetStudy = tool('brapi_get_study', {
             referenceLookup.auth = connection.resolvedAuth;
         let studyEnv;
         try {
-            studyEnv = await client.get(connection.baseUrl, `/studies/${encodeURIComponent(input.studyDbId)}`, ctx, buildRequestOptions(connection));
+            studyEnv = await client.get(connection.baseUrl, `/studies/${encodeURIComponent(input.studyDbId)}`, ctx, buildRequestOptions(connection, undefined, { singleton: true }));
         }
         catch (err) {
             if (isUpstreamNotFound(err)) {

package/dist/mcp-server/tools/definitions/brapi-get-study.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.d.ts CHANGED Viewed

@@ -42,6 +42,11 @@ export declare const brapiRawGet: import("@cyanheads/mcp-ts-core").ToolDefinitio
         maxRows: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
+    readonly reason: "unknown_alias";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "No connection has been registered under the requested alias";
+    readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_raw_get.";
+}, {
     readonly reason: "cross_origin_path";
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "path argument was a full URL instead of a relative BrAPI route";