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/brapi-find-variables.tool.js CHANGED Viewed

@@ -14,7 +14,7 @@ import { getCapabilityRegistry } from '../../../services/capability-registry/ind
 import { getDatasetStore } from '../../../services/dataset-store/index.js';
 import { getOntologyResolver, } from '../../../services/ontology-resolver/index.js';
 import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, asString, buildRefinementHint, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderDatasetHandle, renderDistributions, } from '../shared/find-helpers.js';
+import { AliasInput, asString, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
 const VariableRowSchema = z
     .object({
     observationVariableDbId: z
@@ -70,6 +70,10 @@ const VariableRowSchema = z
     .describe('One BrAPI observation variable record.');
 const CandidateSchema = z
     .object({
+    observationVariableDbId: z
+        .string()
+        .optional()
+        .describe('Server-side variable DbId of the source row, when present.'),
     termId: z
         .string()
         .optional()
@@ -122,6 +126,17 @@ const OutputSchema = z.object({
         .record(z.string(), z.unknown())
         .describe('The final filter map sent to the server (named + extraFilters).'),
 });
+const SERVER_TO_USER = {
+    observationVariableDbIds: 'variables',
+    observationVariableNames: 'variableNames',
+    observationVariablePUIs: 'variablePUIs',
+    traitClasses: 'traitClasses',
+    ontologyDbIds: 'ontologies',
+    studyDbId: 'studies',
+    methodDbIds: 'methods',
+    scaleDbIds: 'scales',
+    commonCropName: 'crop',
+};
 export const brapiFindVariables = tool('brapi_find_variables', {
     description: 'Find observation variables (traits) by name, trait class, ontology term, or free-text query. Free-text queries are ranked against the returned set and may resolve to ontology URIs when the server advertises them. Returns a dataset handle when the upstream total exceeds loadLimit.',
     annotations: { readOnlyHint: true, openWorldHint: true },
@@ -197,13 +212,19 @@ export const brapiFindVariables = tool('brapi_find_variables', {
         if (input.text) {
             candidates = resolver.match(input.text, fullRows, { limit: 10 });
             if (candidates.length > 0) {
-                const orderedIds = new Set(candidates.map((c) => c.termId).filter(Boolean));
-                // Promote matched rows to the top of the in-context set.
+                // PUI is sparse on real servers (CassavaBase doesn't populate it),
+                // so promote rows by observationVariableDbId — always present —
+                // and fall back to PUI for any candidate that lacked the dbId.
+                const matchedDbIds = new Set(candidates.map((c) => c.observationVariableDbId).filter((v) => Boolean(v)));
+                const matchedPuis = new Set(candidates.map((c) => c.termId).filter((v) => Boolean(v)));
                 const matched = [];
                 const rest = [];
                 for (const row of firstPage.rows) {
+                    const dbId = row.observationVariableDbId;
                     const pui = row.observationVariablePUI;
-                    if (typeof pui === 'string' && orderedIds.has(pui))
+                    const isMatch = (typeof dbId === 'string' && matchedDbIds.has(dbId)) ||
+                        (typeof pui === 'string' && matchedPuis.has(pui));
+                    if (isMatch)
                         matched.push(row);
                     else
                         rest.push(row);
@@ -226,8 +247,34 @@ export const brapiFindVariables = tool('brapi_find_variables', {
                 return asString(scale.scaleName);
             }),
         };
+        checkFilterMatchRates(warnings, fullRows.length, [
+            {
+                paramName: 'traitClasses',
+                requestedValues: input.traitClasses,
+                distribution: distributions.traitClass,
+                caseInsensitive: true,
+            },
+            {
+                paramName: 'ontologies',
+                requestedValues: input.ontologies,
+                distribution: distributions.ontologyDbId,
+            },
+        ]);
         const totalCount = firstPage.totalCount ?? firstPage.rows.length;
-        const refinementHint = buildRefinementHint(totalCount, loadLimit, distributions);
+        const refinementHint = buildRefinementHint(totalCount, loadLimit, distributions, {
+            availableFilters: [
+                'variables',
+                'variableNames',
+                'variablePUIs',
+                'traitClasses',
+                'ontologies',
+                'studies',
+                'methods',
+                'scales',
+                'crop',
+                'text',
+            ],
+        });
         const result = {
             alias: connection.alias,
             results: rankedResults,
@@ -247,7 +294,13 @@ export const brapiFindVariables = tool('brapi_find_variables', {
     },
     format: (result) => {
         const lines = [];
-        lines.push(`# ${result.returnedCount} of ${result.totalCount} variables — \`${result.alias}\``);
+        lines.push(renderFindHeader({
+            noun: 'variables',
+            alias: result.alias,
+            returnedCount: result.returnedCount,
+            totalCount: result.totalCount,
+            dataset: result.dataset,
+        }));
         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.'}`);
@@ -257,7 +310,7 @@ export const brapiFindVariables = tool('brapi_find_variables', {
             lines.push(`**Refinement hint:** ${result.refinementHint}`);
             lines.push('');
         }
-        lines.push(`Applied filters: \`${JSON.stringify(result.appliedFilters)}\``);
+        lines.push(renderAppliedFilters(result.appliedFilters, SERVER_TO_USER));
         lines.push('');
         if (result.ontologyCandidates.length > 0) {
             lines.push('## Ontology candidates (ranked)');
@@ -265,6 +318,8 @@ export const brapiFindVariables = tool('brapi_find_variables', {
                 const parts = [];
                 if (c.name)
                     parts.push(`**${c.name}**`);
+                if (c.observationVariableDbId)
+                    parts.push(`observationVariableDbId=\`${c.observationVariableDbId}\``);
                 if (c.termId)
                     parts.push(`termId=\`${c.termId}\``);
                 if (c.ontologyDbId)

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

	@@ -1 +1 @@
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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;~~AA0GjD~~,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~6BAwJ5B~~,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;AAqHjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAkK5B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-find-variants.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 { getDatasetStore } from '../../../services/dataset-store/index.js';
 import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, asString, buildRefinementHint, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderDatasetHandle, renderDistributions, } from '../shared/find-helpers.js';
+import { AliasInput, asString, buildRefinementHint, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
 const VariantRowSchema = z
     .object({
     variantDbId: z.string().describe('Server-side identifier for the variant.'),
@@ -90,6 +90,14 @@ const OutputSchema = z.object({
         .record(z.string(), z.unknown())
         .describe('The final filter map sent to the server (named + extraFilters).'),
 });
+const SERVER_TO_USER = {
+    variantSetDbIds: 'variantSets',
+    variantDbIds: 'variants',
+    referenceDbIds: 'references',
+    referenceName: 'referenceName',
+    start: 'start',
+    end: 'end',
+};
 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). Returns a dataset handle when the upstream total exceeds loadLimit.',
     annotations: { readOnlyHint: true, openWorldHint: true },
@@ -147,7 +155,9 @@ export const brapiFindVariants = tool('brapi_find_variants', {
             variantSetDbId: computeDistribution(fullRows, (r) => collectVariantSetIds(r)),
         };
         const totalCount = firstPage.totalCount ?? firstPage.rows.length;
-        const refinementHint = buildRefinementHint(totalCount, loadLimit, distributions);
+        const refinementHint = buildRefinementHint(totalCount, loadLimit, distributions, {
+            availableFilters: ['variantSets', 'variants', 'references', 'referenceName', 'start', 'end'],
+        });
         const result = {
             alias: connection.alias,
             results: firstPage.rows,
@@ -166,7 +176,13 @@ export const brapiFindVariants = tool('brapi_find_variants', {
     },
     format: (result) => {
         const lines = [];
-        lines.push(`# ${result.returnedCount} of ${result.totalCount} variants — \`${result.alias}\``);
+        lines.push(renderFindHeader({
+            noun: 'variants',
+            alias: result.alias,
+            returnedCount: result.returnedCount,
+            totalCount: result.totalCount,
+            dataset: result.dataset,
+        }));
         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.'}`);
@@ -176,7 +192,7 @@ export const brapiFindVariants = tool('brapi_find_variants', {
             lines.push(`**Refinement hint:** ${result.refinementHint}`);
             lines.push('');
         }
-        lines.push(`Applied filters: \`${JSON.stringify(result.appliedFilters)}\``);
+        lines.push(renderAppliedFilters(result.appliedFilters, SERVER_TO_USER));
         lines.push('');
         lines.push('## Distributions');
         lines.push(renderDistributions(result.distributions) || '_No values to summarize._');

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

	@@ -1 +1 @@
1	- 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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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~GAqIxB~~,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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAwIxB,CAAC"}

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

@@ -180,12 +180,15 @@ export const brapiGetImage = tool('brapi_get_image', {
             });
         }
         for (const err of result.errors) {
-            blocks.push({ type: 'text', text: `### ${err.imageDbId} — failed\n- error: ${err.error}` });
+            blocks.push({
+                type: 'text',
+                text: `\n### ${err.imageDbId} — failed\n- error: ${err.error}`,
+            });
         }
         for (const w of result.warnings) {
             blocks.push({
                 type: 'text',
-                text: `### ${w.imageDbId} — warning\n- ${w.warning}`,
+                text: `\n### ${w.imageDbId} — warning\n- ${w.warning}`,
             });
         }
         return blocks;

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 CHANGED Viewed

@@ -1,7 +1,7 @@
 /**
  * @fileoverview `brapi_get_study` — fetch a single study by DbId, resolve
  * program/trial/location FKs via ReferenceDataCache, and attach cheap
- * `pageSize=0` counts (observations, observation units, variables) as
+ * `pageSize=1` counts (observations, observation units, variables) as
  * response companions so the agent can decide where to drill next.
  *
  * @module mcp-server/tools/definitions/brapi-get-study.tool
@@ -61,6 +61,7 @@ export declare const brapiGetStudy: import("@cyanheads/mcp-ts-core").ToolDefinit
         latitude: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
         longitude: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
         altitude: z.ZodOptional<z.ZodNullable<z.ZodNumber>>;
+        coordinates: z.ZodOptional<z.ZodNullable<z.ZodObject<{}, z.core.$loose>>>;
     }, z.core.$loose>>;
     observationCount: z.ZodOptional<z.ZodNumber>;
     observationUnitCount: z.ZodOptional<z.ZodNumber>;

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

	@@ -1 +1 @@
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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"}

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

@@ -1,7 +1,7 @@
 /**
  * @fileoverview `brapi_get_study` — fetch a single study by DbId, resolve
  * program/trial/location FKs via ReferenceDataCache, and attach cheap
- * `pageSize=0` counts (observations, observation units, variables) as
+ * `pageSize=1` counts (observations, observation units, variables) as
  * response companions so the agent can decide where to drill next.
  *
  * @module mcp-server/tools/definitions/brapi-get-study.tool
@@ -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, isUpstreamNotFound } from '../shared/find-helpers.js';
+import { AliasInput, buildRequestOptions, extractCoordinates, isUpstreamNotFound, } from '../shared/find-helpers.js';
 const StudySchema = z
     .object({
     studyDbId: z.string().describe('Server-side identifier for the study.'),
@@ -71,9 +71,20 @@ const LocationSchema = z
         .string()
         .nullish()
         .describe('Type of location (e.g. "Research Station", "Field").'),
-    latitude: z.number().nullish().describe('WGS84 latitude in decimal degrees.'),
-    longitude: z.number().nullish().describe('WGS84 longitude in decimal degrees.'),
+    latitude: z
+        .number()
+        .nullish()
+        .describe('WGS84 latitude in decimal degrees (legacy field; modern servers use coordinates).'),
+    longitude: z
+        .number()
+        .nullish()
+        .describe('WGS84 longitude in decimal degrees (legacy field; modern servers use coordinates).'),
     altitude: z.number().nullish().describe('Altitude in meters above sea level.'),
+    coordinates: z
+        .object({})
+        .passthrough()
+        .nullish()
+        .describe('BrAPI v2 GeoJSON Feature carrying [lon, lat, alt?] in geometry.coordinates.'),
 })
     .passthrough();
 const OutputSchema = z.object({
@@ -277,6 +288,14 @@ export const brapiGetStudy = tool('brapi_get_study', {
             lines.push('');
             lines.push('## Location');
             renderKeyValues(lines, result.location);
+            const coords = extractCoordinates(result.location);
+            if (coords && result.location.latitude == null && result.location.longitude == null) {
+                lines.push(`- **latitude:** ${coords.latitude}`);
+                lines.push(`- **longitude:** ${coords.longitude}`);
+                if (coords.altitude != null && result.location.altitude == null) {
+                    lines.push(`- **altitude:** ${coords.altitude}`);
+                }
+            }
         }
         lines.push('');
         lines.push('## Drill-down signals');

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

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

@@ -4,7 +4,7 @@
  * against the study's observation variables and returns a routing breakdown
  * (POST for new rows, PUT for rows carrying `observationDbId`); `mode: 'apply'`
  * elicits confirmation when supported, fans the rows out to POST + PUT in
- * parallel, then verifies the post-state with a cheap `pageSize=0` count.
+ * parallel, then verifies the post-state with a cheap `pageSize=1` count.
  * Additive write — no observation is destroyed by this tool.
  *
  * @module mcp-server/tools/definitions/brapi-submit-observations.tool

package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.js CHANGED Viewed

@@ -4,7 +4,7 @@
  * against the study's observation variables and returns a routing breakdown
  * (POST for new rows, PUT for rows carrying `observationDbId`); `mode: 'apply'`
  * elicits confirmation when supported, fans the rows out to POST + PUT in
- * parallel, then verifies the post-state with a cheap `pageSize=0` count.
+ * parallel, then verifies the post-state with a cheap `pageSize=1` count.
  * Additive write — no observation is destroyed by this tool.
  *
  * @module mcp-server/tools/definitions/brapi-submit-observations.tool