@cyanheads/brapi-mcp-server 0.4.3 → 0.4.4

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

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

@@ -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"}
+{"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;AA2HjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAsO3B,CAAC"}

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

@@ -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, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
 const StudyRowSchema = z
     .object({
     studyDbId: z.string().describe('Server-side identifier for the study.'),
@@ -248,6 +248,25 @@ 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 +300,7 @@ 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

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

@@ -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"}
+{"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;AAgLjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAsR7B,CAAC"}

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

@@ -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, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
 const VariableRowSchema = z
     .object({
     observationVariableDbId: z
@@ -354,6 +354,17 @@ 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 +376,13 @@ 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(' · ')}`);
             }
         }

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

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

@@ -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;AA6HjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAsK5B,CAAC"}
+{"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;AA8HjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAsL5B,CAAC"}

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

@@ -13,7 +13,7 @@ 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, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFilters, asString, buildRefinementHint, collectPassthroughParts, 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.'),
@@ -211,6 +211,21 @@ export const brapiFindVariants = tool('brapi_find_variants', {
             lines.push('_No rows returned._');
         }
         else {
+            const RENDERED = new Set([
+                'variantNames',
+                'variantDbId',
+                'variantType',
+                'variantSetDbId',
+                'variantSetDbIds',
+                'referenceName',
+                'start',
+                'end',
+                'referenceBases',
+                'alternateBases',
+                'filtersApplied',
+                'filtersPassed',
+                'filtersFailed',
+            ]);
             for (const v of result.results) {
                 const label = v.variantNames?.[0] ?? v.variantDbId;
                 const parts = [`**${label}**`];
@@ -238,6 +253,7 @@ export const brapiFindVariants = tool('brapi_find_variants', {
                     parts.push(`filtersFailed=${v.filtersFailed.join(',')}`);
                 if (v.variantNames?.length)
                     parts.push(`names=${v.variantNames.join(',')}`);
+                parts.push(...collectPassthroughParts(v, RENDERED));
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }

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

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

@@ -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;AAmGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAgN5B,CAAC"}
+{"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;AAyGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA6O5B,CAAC"}

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

@@ -12,7 +12,7 @@ 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 { 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.'),
@@ -190,6 +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}\``);
@@ -214,7 +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)
@@ -229,6 +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})`);
@@ -236,6 +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)
@@ -244,6 +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(' · ')}`);
             }
         }
@@ -253,6 +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)
@@ -263,6 +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(' ')}`);
             }
         }

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

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

@@ -1 +1 @@
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+{"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"}