npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.4.3 → 0.4.5 - Mend

@cyanheads/brapi-mcp-server 0.4.3 → 0.4.5

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 (88) hide show

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

@@ -14,7 +14,7 @@ import { resolveDialect } from '../../../services/brapi-dialect/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, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, extractCoordinates, hasPointGeometry, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, extractCoordinates, hasPointGeometry, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
 const LocationRowSchema = z
     .object({
     locationDbId: z.string().describe('Server-side identifier for the location.'),
@@ -157,7 +157,7 @@ export const brapiFindLocations = tool('brapi_find_locations', {
         const capabilityLookup = {};
         if (connection.resolvedAuth)
             capabilityLookup.auth = connection.resolvedAuth;
-        await capabilities.ensure(connection.baseUrl, { service: 'locations', method: 'GET' }, ctx, capabilityLookup);
+        const profile = await capabilities.profile(connection.baseUrl, ctx, capabilityLookup);
         const dialect = await resolveDialect(connection, ctx, capabilityLookup);
         const warnings = [];
         const merged = mergeFilters({
@@ -168,14 +168,23 @@ export const brapiFindLocations = tool('brapi_find_locations', {
             abbreviations: input.abbreviations,
         }, input.extraFilters, warnings);
         const filters = applyDialectFilters(dialect, 'locations', merged, warnings);
+        const route = resolveFindRoute({
+            profile,
+            dialect,
+            endpoint: 'locations',
+            filters,
+            searchBody: merged,
+            warnings,
+        });
         const loadLimit = input.loadLimit ?? config.loadLimit;
-        const firstPage = await loadInitialPage(client, connection, '/locations', filters, loadLimit, ctx);
+        const firstPage = await loadInitialFindPage(client, connection, route, loadLimit, ctx);
         const { fullRows, dataset: datasetMeta } = await maybeSpill({
             firstPage,
             client,
             connection,
             path: '/locations',
             filters,
+            route,
             source: 'find_locations',
             loadLimit,
             ctx,
@@ -249,7 +258,7 @@ export const brapiFindLocations = tool('brapi_find_locations', {
             hasMore: firstPage.hasMore,
             distributions,
             warnings,
-            appliedFilters: filters,
+            appliedFilters: route.kind === 'search' ? route.searchBody : filters,
             coordinateAxisOrder,
         };
         if (refinementHint)
@@ -287,6 +296,22 @@ export const brapiFindLocations = tool('brapi_find_locations', {
             lines.push('_No rows returned._');
         }
         else {
+            // `coordinates` intentionally excluded: passthrough helper renders the full
+            // GeoJSON object so text-only clients see it alongside the extracted lat/lon.
+            const RENDERED = new Set([
+                'locationName',
+                'locationDbId',
+                'abbreviation',
+                'locationType',
+                'countryCode',
+                'countryName',
+                'latitude',
+                'longitude',
+                'altitude',
+                'instituteName',
+                'instituteAddress',
+                'documentationURL',
+            ]);
             for (const loc of result.results) {
                 const parts = [`**${loc.locationName ?? loc.locationDbId}**`];
                 parts.push(`id=\`${loc.locationDbId}\``);
@@ -314,6 +339,7 @@ export const brapiFindLocations = tool('brapi_find_locations', {
                     parts.push(`addr=${loc.instituteAddress}`);
                 if (loc.documentationURL)
                     parts.push(`docs=${loc.documentationURL}`);
+                parts.push(...collectPassthroughParts(loc, RENDERED));
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }

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

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAsKjD~~,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~6BAsPhC~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwKjD,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAqQhC,CAAC"}

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

@@ -14,7 +14,7 @@ import { resolveDialect } from '../../../services/brapi-dialect/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, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
 const ObservationRowSchema = z
     .object({
     observationDbId: z.string().nullish().describe('Server-side identifier for the observation.'),
@@ -177,7 +177,7 @@ export const brapiFindObservations = tool('brapi_find_observations', {
         const capabilityLookup = {};
         if (connection.resolvedAuth)
             capabilityLookup.auth = connection.resolvedAuth;
-        await capabilities.ensure(connection.baseUrl, { service: 'observations', method: 'GET' }, ctx, capabilityLookup);
+        const profile = await capabilities.profile(connection.baseUrl, ctx, capabilityLookup);
         const dialect = await resolveDialect(connection, ctx, capabilityLookup);
         const warnings = [];
         const merged = mergeFilters({
@@ -194,8 +194,16 @@ export const brapiFindObservations = tool('brapi_find_observations', {
             observationTimeStampRangeEnd: input.timestampTo,
         }, input.extraFilters, warnings);
         const filters = applyDialectFilters(dialect, 'observations', merged, warnings);
+        const route = resolveFindRoute({
+            profile,
+            dialect,
+            endpoint: 'observations',
+            filters,
+            searchBody: merged,
+            warnings,
+        });
         const loadLimit = input.loadLimit ?? config.loadLimit;
-        const loadObservations = (pageSize) => loadInitialPage(client, connection, '/observations', filters, pageSize, ctx);
+        const loadObservations = (pageSize) => loadInitialFindPage(client, connection, route, pageSize, ctx);
         /**
          * Danger pattern: querying /observations by germplasm with no anchoring
          * scope (study, trial, observation, observation-unit). On large servers
@@ -233,6 +241,7 @@ export const brapiFindObservations = tool('brapi_find_observations', {
                 connection,
                 path: '/observations',
                 filters,
+                route,
                 source: 'find_observations',
                 loadLimit,
                 ctx,
@@ -282,7 +291,7 @@ export const brapiFindObservations = tool('brapi_find_observations', {
             hasMore: firstPage.hasMore,
             distributions,
             warnings,
-            appliedFilters: filters,
+            appliedFilters: route.kind === 'search' ? route.searchBody : filters,
         };
         if (refinementHint)
             result.refinementHint = refinementHint;
@@ -318,6 +327,23 @@ export const brapiFindObservations = tool('brapi_find_observations', {
             lines.push('_No rows returned._');
         }
         else {
+            const RENDERED = new Set([
+                'observationVariableName',
+                'observationVariableDbId',
+                'value',
+                'observationDbId',
+                'observationUnitName',
+                'observationUnitDbId',
+                'germplasmName',
+                'germplasmDbId',
+                'studyName',
+                'studyDbId',
+                'observationLevel',
+                'season',
+                'observationTimeStamp',
+                'collector',
+                'uploadedBy',
+            ]);
             for (const o of result.results) {
                 const parts = [];
                 const label = o.observationVariableName ?? o.observationVariableDbId ?? '?';
@@ -351,6 +377,7 @@ export const brapiFindObservations = tool('brapi_find_observations', {
                     parts.push(`collector=${o.collector}`);
                 if (o.uploadedBy)
                     parts.push(`uploadedBy=${o.uploadedBy}`);
+                parts.push(...collectPassthroughParts(o, RENDERED));
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }

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

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-studies.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-studies.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AA0HjD~~,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~6BAkN3B~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-studies.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-studies.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA4HjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAyO3B,CAAC"}

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

@@ -14,7 +14,7 @@ import { resolveDialect } from '../../../services/brapi-dialect/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, applyDialectFilters, asString, asStringArray, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFilters, asString, asStringArray, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
 const StudyRowSchema = z
     .object({
     studyDbId: z.string().describe('Server-side identifier for the study.'),
@@ -132,7 +132,7 @@ export const brapiFindStudies = tool('brapi_find_studies', {
         const capabilityLookup = {};
         if (connection.resolvedAuth)
             capabilityLookup.auth = connection.resolvedAuth;
-        await capabilities.ensure(connection.baseUrl, { service: 'studies', method: 'GET' }, ctx, capabilityLookup);
+        const profile = await capabilities.profile(connection.baseUrl, ctx, capabilityLookup);
         const dialect = await resolveDialect(connection, ctx, capabilityLookup);
         const warnings = [];
         const merged = mergeFilters({
@@ -146,14 +146,23 @@ export const brapiFindStudies = tool('brapi_find_studies', {
             active: input.active,
         }, input.extraFilters, warnings);
         const filters = applyDialectFilters(dialect, 'studies', merged, warnings);
+        const route = resolveFindRoute({
+            profile,
+            dialect,
+            endpoint: 'studies',
+            filters,
+            searchBody: merged,
+            warnings,
+        });
         const loadLimit = input.loadLimit ?? config.loadLimit;
-        const firstPage = await loadInitialPage(client, connection, '/studies', filters, loadLimit, ctx);
+        const firstPage = await loadInitialFindPage(client, connection, route, loadLimit, ctx);
         const { fullRows, dataset: datasetMeta } = await maybeSpill({
             firstPage,
             client,
             connection,
             path: '/studies',
             filters,
+            route,
             source: 'find_studies',
             loadLimit,
             ctx,
@@ -211,7 +220,7 @@ export const brapiFindStudies = tool('brapi_find_studies', {
             hasMore: firstPage.hasMore,
             distributions,
             warnings,
-            appliedFilters: filters,
+            appliedFilters: route.kind === 'search' ? route.searchBody : filters,
         };
         if (refinementHint)
             result.refinementHint = refinementHint;
@@ -248,6 +257,25 @@ export const brapiFindStudies = tool('brapi_find_studies', {
             lines.push('_No rows returned._');
         }
         else {
+            const RENDERED = new Set([
+                'studyName',
+                'studyDbId',
+                'studyType',
+                'programName',
+                'programDbId',
+                'trialName',
+                'trialDbId',
+                'locationName',
+                'locationDbId',
+                'seasons',
+                'commonCropName',
+                'active',
+                'startDate',
+                'endDate',
+                'studyCode',
+                'studyPUI',
+                'studyDescription',
+            ]);
             for (const study of result.results) {
                 const parts = [`**${study.studyName ?? study.studyDbId}**`];
                 parts.push(`id=\`${study.studyDbId}\``);
@@ -281,6 +309,7 @@ export const brapiFindStudies = tool('brapi_find_studies', {
                     parts.push(`pui=${study.studyPUI}`);
                 if (study.studyDescription)
                     parts.push(`desc=${study.studyDescription}`);
+                parts.push(...collectPassthroughParts(study, RENDERED));
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }

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

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-variables.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variables.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AA+KjD~~,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~6BAiR7B~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-variables.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variables.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAiLjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAuR7B,CAAC"}

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

@@ -15,7 +15,7 @@ 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, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
 const VariableRowSchema = z
     .object({
     observationVariableDbId: z
@@ -184,7 +184,6 @@ export const brapiFindVariables = tool('brapi_find_variables', {
         const capabilityLookup = {};
         if (connection.resolvedAuth)
             capabilityLookup.auth = connection.resolvedAuth;
-        await capabilities.ensure(connection.baseUrl, { service: 'variables', method: 'GET' }, ctx, capabilityLookup);
         const profile = await capabilities.profile(connection.baseUrl, ctx, capabilityLookup);
         const hasOntologyEndpoint = Boolean(profile.supported.ontologies);
         const dialect = await resolveDialect(connection, ctx, capabilityLookup);
@@ -201,6 +200,14 @@ export const brapiFindVariables = tool('brapi_find_variables', {
             commonCropName: input.crop,
         }, input.extraFilters, warnings);
         const filters = applyDialectFilters(dialect, 'variables', merged, warnings);
+        const route = resolveFindRoute({
+            profile,
+            dialect,
+            endpoint: 'variables',
+            filters,
+            searchBody: merged,
+            warnings,
+        });
         if ((input.studies?.length ?? 0) > 1) {
             warnings.push('BrAPI /variables accepts only one studyDbId per call; using the first value from `studies`.');
         }
@@ -208,13 +215,14 @@ export const brapiFindVariables = tool('brapi_find_variables', {
             warnings.push('Server does not expose /ontologies — free-text matching falls back to local substring + synonym matching on the returned rows.');
         }
         const loadLimit = input.loadLimit ?? config.loadLimit;
-        const firstPage = await loadInitialPage(client, connection, '/variables', filters, loadLimit, ctx);
+        const firstPage = await loadInitialFindPage(client, connection, route, loadLimit, ctx);
         const { fullRows, dataset: datasetMeta } = await maybeSpill({
             firstPage,
             client,
             connection,
             path: '/variables',
             filters,
+            route,
             source: 'find_variables',
             loadLimit,
             ctx,
@@ -297,7 +305,7 @@ export const brapiFindVariables = tool('brapi_find_variables', {
             distributions,
             ontologyCandidates: candidates,
             warnings,
-            appliedFilters: filters,
+            appliedFilters: route.kind === 'search' ? route.searchBody : filters,
         };
         if (refinementHint)
             result.refinementHint = refinementHint;
@@ -354,6 +362,17 @@ export const brapiFindVariables = tool('brapi_find_variables', {
             lines.push('_No rows returned._');
         }
         else {
+            const RENDERED = new Set([
+                'observationVariableName',
+                'observationVariableDbId',
+                'observationVariablePUI',
+                'ontologyDbId',
+                'ontologyName',
+                'commonCropName',
+                'trait',
+                'scale',
+                'method',
+            ]);
             for (const v of result.results) {
                 const parts = [`**${v.observationVariableName ?? v.observationVariableDbId}**`];
                 parts.push(`id=\`${v.observationVariableDbId}\``);
@@ -365,26 +384,13 @@ export const brapiFindVariables = tool('brapi_find_variables', {
                     parts.push(`ontologyName=${v.ontologyName}`);
                 if (v.commonCropName)
                     parts.push(`crop=${v.commonCropName}`);
-                if (v.trait?.traitName)
-                    parts.push(`trait=${v.trait.traitName}`);
-                if (v.trait?.traitDbId)
-                    parts.push(`traitDbId=${v.trait.traitDbId}`);
-                if (v.trait?.traitClass)
-                    parts.push(`class=${v.trait.traitClass}`);
-                if (v.trait?.description)
-                    parts.push(`desc=${v.trait.description}`);
-                if (v.trait?.synonyms?.length)
-                    parts.push(`synonyms=${v.trait.synonyms.join(',')}`);
-                if (v.scale?.scaleName)
-                    parts.push(`scale=${v.scale.scaleName}`);
-                if (v.scale?.scaleDbId)
-                    parts.push(`scaleDbId=${v.scale.scaleDbId}`);
-                if (v.scale?.dataType)
-                    parts.push(`dataType=${v.scale.dataType}`);
-                if (v.method?.methodName)
-                    parts.push(`method=${v.method.methodName}`);
-                if (v.method?.methodDbId)
-                    parts.push(`methodDbId=${v.method.methodDbId}`);
+                if (v.trait)
+                    parts.push(`trait=${JSON.stringify(v.trait)}`);
+                if (v.scale)
+                    parts.push(`scale=${JSON.stringify(v.scale)}`);
+                if (v.method)
+                    parts.push(`method=${JSON.stringify(v.method)}`);
+                parts.push(...collectPassthroughParts(v, RENDERED));
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }