npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.4.2 → 0.4.4 - Mend

@cyanheads/brapi-mcp-server 0.4.2 → 0.4.4

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 (43) hide show

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

@@ -9,9 +9,10 @@
 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 { 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, buildRequestOptions, isUpstreamNotFound } from '../shared/find-helpers.js';
+import { AliasInput, appendPassthroughLines, buildRequestOptions, collectPassthroughParts, isUpstreamNotFound, } from '../shared/find-helpers.js';
 const GermplasmSchema = z
     .object({
     germplasmDbId: z.string().describe('Server-side identifier for the germplasm.'),
@@ -146,6 +147,9 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
         const supportsAttributes = Boolean(profile.supported['germplasm/{germplasmDbId}/attributes']);
         const supportsProgeny = Boolean(profile.supported['germplasm/{germplasmDbId}/progeny']);
         const supportsStudies = profile.supported.studies?.methods?.includes('GET') ?? false;
+        const dialect = supportsStudies
+            ? await resolveDialect(connection, ctx, capabilityLookup)
+            : undefined;
         const [pedigree, attributes, studyCount, progenyCount] = await Promise.all([
             supportsPedigree
                 ? fetchPedigree(client, connection.baseUrl, id, ctx, buildRequestOptions(connection)).catch((err) => recordWarning(warnings, 'pedigree lookup failed', err))
@@ -153,11 +157,15 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
             supportsAttributes
                 ? fetchAttributes(client, connection.baseUrl, id, ctx, buildRequestOptions(connection)).catch((err) => recordWarning(warnings, 'attributes lookup failed', err))
                 : Promise.resolve(undefined),
-            supportsStudies
-                ? fetchTotalCount(client, connection.baseUrl, '/studies', ctx, buildRequestOptions(connection, {
-                    germplasmDbIds: [input.germplasmDbId],
-                    pageSize: 1,
-                })).catch((err) => recordWarning(warnings, 'study count probe failed', err))
+            supportsStudies && dialect
+                ? fetchValidatedStudyCount({
+                    client,
+                    connection,
+                    germplasmDbId: input.germplasmDbId,
+                    dialect,
+                    ctx,
+                    warnings,
+                }).catch((err) => recordWarning(warnings, 'study count probe failed', err))
                 : Promise.resolve(undefined),
             supportsProgeny
                 ? fetchTotalCount(client, connection.baseUrl, `/germplasm/${id}/progeny`, ctx, buildRequestOptions(connection, { pageSize: 1 })).catch((err) => recordWarning(warnings, 'progeny count probe failed', err))
@@ -182,6 +190,25 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
     format: (result) => {
         const lines = [];
         const g = result.germplasm;
+        const GERMPLASM_RENDERED = new Set([
+            'germplasmDbId',
+            'germplasmName',
+            'germplasmPUI',
+            'commonCropName',
+            'accessionNumber',
+            'genus',
+            'species',
+            'subtaxa',
+            'defaultDisplayName',
+            'pedigree',
+            'biologicalStatusOfAccessionDescription',
+            'germplasmOrigin',
+            'countryOfOriginCode',
+            'collection',
+            'instituteCode',
+            'instituteName',
+            'synonyms',
+        ]);
         lines.push(`# ${g.germplasmName ?? g.defaultDisplayName ?? g.germplasmDbId}`);
         lines.push('');
         lines.push(`- **germplasmDbId:** \`${g.germplasmDbId}\``);
@@ -206,7 +233,7 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
         if (g.biologicalStatusOfAccessionDescription)
             lines.push(`- **biologicalStatus:** ${g.biologicalStatusOfAccessionDescription}`);
         if (g.germplasmOrigin?.length)
-            lines.push(`- **germplasmOrigin:** ${g.germplasmOrigin.length} record(s)`);
+            lines.push(`- **germplasmOrigin:** ${JSON.stringify(g.germplasmOrigin)}`);
         if (g.countryOfOriginCode)
             lines.push(`- **countryOfOriginCode:** ${g.countryOfOriginCode}`);
         if (g.collection)
@@ -221,6 +248,7 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
                 .join(', ');
             lines.push(`- **synonyms:** ${synStr}`);
         }
+        appendPassthroughLines(lines, g, GERMPLASM_RENDERED);
         lines.push(`- **alias:** ${result.alias}`);
         lines.push('');
         lines.push(`## Parents (${result.directParentCount})`);
@@ -228,6 +256,7 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
             lines.push('_No parents recorded._');
         }
         else {
+            const PARENT_RENDERED = new Set(['germplasmDbId', 'germplasmName', 'parentType']);
             for (const p of result.parents) {
                 const parts = [];
                 if (p.germplasmName)
@@ -236,6 +265,7 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
                     parts.push(`id=\`${p.germplasmDbId}\``);
                 if (p.parentType)
                     parts.push(`type=${p.parentType}`);
+                parts.push(...collectPassthroughParts(p, PARENT_RENDERED));
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }
@@ -245,6 +275,12 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
             lines.push('_No attributes recorded._');
         }
         else {
+            const ATTR_RENDERED = new Set([
+                'attributeName',
+                'attributeDbId',
+                'attributeValue',
+                'determinedDate',
+            ]);
             for (const a of result.attributes) {
                 const parts = [];
                 if (a.attributeName)
@@ -255,6 +291,7 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
                     parts.push(`= ${a.attributeValue}`);
                 if (a.determinedDate)
                     parts.push(`[determined ${a.determinedDate}]`);
+                parts.push(...collectPassthroughParts(a, ATTR_RENDERED));
                 lines.push(`- ${parts.join(' ')}`);
             }
         }
@@ -303,4 +340,44 @@ async function fetchTotalCount(client, baseUrl, path, ctx, options) {
     const total = env.metadata?.pagination?.totalCount;
     return typeof total === 'number' ? total : undefined;
 }
+/**
+ * Probe `/studies?germplasmDbIds=X` and a parallel unfiltered baseline.
+ * Some servers (notably the SGN family) silently drop the germplasm filter on
+ * `/studies` and return the global studies total — which would be wildly
+ * misleading as a per-germplasm `studyCount`. The cross-check catches that:
+ * if the filtered total matches the unfiltered baseline, the filter was
+ * ignored and we drop the count rather than report a misleading global.
+ *
+ * Routes the filtered probe through the dialect adapter so any per-server
+ * key translation (or filter drop) takes effect, and surfaces the dialect's
+ * own warnings so the agent sees why a count is missing.
+ */
+async function fetchValidatedStudyCount(input) {
+    const { client, connection, ctx, dialect, germplasmDbId, warnings } = input;
+    const adapted = dialect.adaptGetFilters('studies', {
+        germplasmDbIds: [germplasmDbId],
+    });
+    warnings.push(...adapted.warnings);
+    // If the dialect dropped the filter entirely, the count would be the
+    // global studies total — useless. Skip and let the caller render `—`.
+    if (Object.keys(adapted.filters).length === 0) {
+        warnings.push('studyCount probe skipped: the active dialect dropped the germplasm filter for /studies (server does not honor it).');
+        return;
+    }
+    const filteredParams = {
+        ...adapted.filters,
+        pageSize: 1,
+    };
+    const [filtered, baseline] = await Promise.all([
+        fetchTotalCount(client, connection.baseUrl, '/studies', ctx, buildRequestOptions(connection, filteredParams)),
+        fetchTotalCount(client, connection.baseUrl, '/studies', ctx, buildRequestOptions(connection, { pageSize: 1 })).catch(() => undefined),
+    ]);
+    if (typeof filtered !== 'number')
+        return;
+    if (typeof baseline === 'number' && baseline > 0 && filtered === baseline) {
+        warnings.push(`studyCount omitted: /studies returned the same total (${baseline}) for both the germplasm-filtered probe and an unfiltered baseline — the upstream silently ignored the germplasm filter, so a per-germplasm count cannot be trusted.`);
+        return;
+    }
+    return filtered;
+}
 //# sourceMappingURL=brapi-get-germplasm.tool.js.map

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

	@@ -1 +1 @@
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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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~GAwIxB~~,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;AAsEjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAyJxB,CAAC"}

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

@@ -12,7 +12,7 @@ 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, buildRequestOptions } from '../shared/find-helpers.js';
+import { AliasInput, appendPassthroughLines, buildRequestOptions } from '../shared/find-helpers.js';
 const MAX_IMAGES_PER_CALL = 5;
 const MAX_IMAGE_BYTES = 20 * 1024 * 1024; // 20 MB
 const ImageMetadataSchema = z
@@ -139,6 +139,22 @@ export const brapiGetImage = tool('brapi_get_image', {
             header.push(`⚠ ${result.warnings.length} suspect — see warnings below.`);
         }
         blocks.push({ type: 'text', text: header.join('\n') });
+        const META_RENDERED = new Set([
+            'imageDbId',
+            'imageName',
+            'imageFileName',
+            'imageWidth',
+            'imageHeight',
+            'mimeType',
+            'imageURL',
+            'observationUnitDbId',
+            'observationUnitName',
+            'studyDbId',
+            'studyName',
+            'imageTimeStamp',
+            'copyright',
+            'description',
+        ]);
         for (const img of result.images) {
             const meta = img.metadata;
             const lines = [];
@@ -172,6 +188,7 @@ export const brapiGetImage = tool('brapi_get_image', {
                 lines.push(`- copyright: ${meta.copyright}`);
             if (meta.description)
                 lines.push(`- description: ${meta.description}`);
+            appendPassthroughLines(lines, meta, META_RENDERED);
             blocks.push({ type: 'text', text: lines.join('\n') });
             blocks.push({
                 type: 'image',

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

	@@ -1 +1 @@
1	- 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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;~~AAiIjE~~,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~GA+NxB~~,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;AAkIjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAmPxB,CAAC"}

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

@@ -12,7 +12,7 @@ import { getBrapiClient } from '../../../services/brapi-client/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, buildRequestOptions, extractCoordinates, isUpstreamNotFound, } from '../shared/find-helpers.js';
+import { AliasInput, appendPassthroughLines, buildRequestOptions, extractCoordinates, isUpstreamNotFound, } from '../shared/find-helpers.js';
 const StudySchema = z
     .object({
     studyDbId: z.string().describe('Server-side identifier for the study.'),
@@ -238,6 +238,25 @@ export const brapiGetStudy = tool('brapi_get_study', {
     format: (result) => {
         const lines = [];
         const study = result.study;
+        const STUDY_RENDERED = new Set([
+            'studyDbId',
+            'studyName',
+            'studyType',
+            'studyDescription',
+            'programDbId',
+            'programName',
+            'trialDbId',
+            'trialName',
+            'locationDbId',
+            'locationName',
+            'commonCropName',
+            'seasons',
+            'active',
+            'startDate',
+            'endDate',
+            'studyCode',
+            'studyPUI',
+        ]);
         lines.push(`# ${study.studyName ?? study.studyDbId}`);
         lines.push('');
         lines.push(`- **studyDbId:** \`${study.studyDbId}\``);
@@ -273,6 +292,7 @@ export const brapiGetStudy = tool('brapi_get_study', {
             lines.push(`- **studyCode:** ${study.studyCode}`);
         if (study.studyPUI)
             lines.push(`- **studyPUI:** ${study.studyPUI}`);
+        appendPassthroughLines(lines, study, STUDY_RENDERED);
         lines.push(`- **alias:** ${result.alias}`);
         if (result.program) {
             lines.push('');
@@ -333,6 +353,7 @@ function renderKeyValues(lines, record) {
             lines.push(`- **${key}:** ${value.join(', ')}`);
         }
         else if (typeof value === 'object') {
+            lines.push(`- **${key}:** ${JSON.stringify(value)}`);
         }
         else {
             lines.push(`- **${key}:** ${value}`);

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/shared/find-helpers.d.ts CHANGED Viewed

@@ -56,6 +56,7 @@ export declare function renderFindHeader(opts: {
     totalCount: number;
     dataset?: {
         rowCount: number;
+        expiresAt?: string;
     } | undefined;
 }): string;
 /**
@@ -91,6 +92,14 @@ export interface SpillInput<T> {
     firstPage: T[];
     loadLimit: number;
     path: string;
+    /**
+     * Optional client-side predicate applied to every row (first-page + spilled)
+     * before persistence. When present, only rows that pass are persisted to
+     * DatasetStore and returned in `fullRows`. The unfiltered upstream total is
+     * preserved separately on the LoadedRows envelope so distributions and
+     * headers can still report the true upstream size.
+     */
+    rowFilter?: (row: T) => boolean;
     source: string;
     store: DatasetStore;
     /** Total reported by the server on the first page. */
@@ -98,7 +107,7 @@ export interface SpillInput<T> {
 }
 export interface SpillResult<T> {
     dataset: DatasetMetadata;
-    /** All rows that were persisted — used for distributions. */
+    /** Rows that were persisted (post-filter when `rowFilter` was supplied). */
     fullRows: T[];
     pagesFetched: number;
 }
@@ -121,8 +130,16 @@ export type DatasetHandle = z.infer<typeof DatasetHandleSchema>;
 /**
  * Render a DatasetHandle as bullet lines, matching the existing find_* tool
  * format. Centralized so the truncated/maxRows fields surface consistently.
+ * `expiresAt` is paired with a human-readable `expires in Xh / Xd` so the
+ * agent doesn't have to subtract dates to know when the handle goes stale.
  */
 export declare function renderDatasetHandle(handle: DatasetHandle): string[];
+/**
+ * Render an absolute `expiresAt` timestamp as a relative human label
+ * (`expires in 24h`, `expires in 30m`, `expired 5m ago`). Coarsens to the
+ * most useful unit so the value reads at a glance.
+ */
+export declare function formatExpiresIn(expiresAt: string, now?: Date): string;
 /** Project a `DatasetMetadata` to the in-context handle shape. */
 export declare function toDatasetHandle(metadata: DatasetMetadata): DatasetHandle;
 export interface MaybeSpillInput<T> {
@@ -133,12 +150,18 @@ export interface MaybeSpillInput<T> {
     firstPage: LoadedRows<T>;
     loadLimit: number;
     path: string;
+    /**
+     * Optional client-side predicate applied to every row before persistence.
+     * Forwarded to `spillToDataset`. When present and no spillover happens, the
+     * first-page rows are also filtered before being returned.
+     */
+    rowFilter?: (row: T) => boolean;
     source: string;
     store: DatasetStore;
 }
 export interface MaybeSpillResult<T> {
     dataset?: DatasetHandle;
-    /** Full row set if a spillover happened, otherwise the first-page rows. */
+    /** Row set after `rowFilter` (when supplied), spilled or first-page only. */
     fullRows: T[];
 }
 /**
@@ -243,5 +266,19 @@ export interface RefinementHintOptions {
  * the tool's available filter parameters by name.
  */
 export declare function buildRefinementHint(totalCount: number, loadLimit: number, distributions: Record<string, Record<string, number>>, options?: RefinementHintOptions): string | undefined;
+/**
+ * Collect `key=value` strings for every top-level key in a passthrough row
+ * that was not explicitly rendered by the caller. Ensures format() /
+ * structuredContent parity — server fields beyond the declared schema are
+ * still emitted to text-only clients (Claude Desktop sees content[] only).
+ */
+export declare function collectPassthroughParts(row: Record<string, unknown>, renderedKeys: ReadonlySet<string>): string[];
+/**
+ * Append `- **key:** value` lines for every top-level key in a passthrough
+ * record that was not explicitly rendered. Companion to
+ * `collectPassthroughParts` for detail-view (get_*) tools that use a
+ * line-per-field layout instead of bullet-part lists.
+ */
+export declare function appendPassthroughLines(lines: string[], record: Record<string, unknown>, renderedKeys: ReadonlySet<string>): void;
 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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