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-find-locations.tool.js.map CHANGED Viewed

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

	@@ -1 +1 @@
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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;AAuKjD,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAwQhC,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, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
 const ObservationRowSchema = z
     .object({
     observationDbId: z.string().nullish().describe('Server-side identifier for the observation.'),
@@ -112,6 +112,13 @@ const OutputSchema = z.object({
         .record(z.string(), z.unknown())
         .describe('The final filter map sent to the server (named + extraFilters).'),
 });
+/**
+ * Upstream observation totals above this threshold trigger the preflight
+ * bail-out: the bulk pull is skipped and the user is told to narrow the
+ * query. Empirically, CassavaBase germplasm-only queries above ~5k rows
+ * stall past the default request timeout.
+ */
+const PREFLIGHT_BULK_THRESHOLD = 5_000;
 const SERVER_TO_USER = {
     // Plurals — BrAPI v2.1 spec, used by the `spec` dialect.
     studyDbIds: 'studies',
@@ -188,18 +195,49 @@ export const brapiFindObservations = tool('brapi_find_observations', {
         }, input.extraFilters, warnings);
         const filters = applyDialectFilters(dialect, 'observations', merged, warnings);
         const loadLimit = input.loadLimit ?? config.loadLimit;
-        const firstPage = await loadInitialPage(client, connection, '/observations', filters, loadLimit, ctx);
-        const { fullRows, dataset: datasetMeta } = await maybeSpill({
-            firstPage,
-            client,
-            connection,
-            path: '/observations',
-            filters,
-            source: 'find_observations',
-            loadLimit,
-            ctx,
-            store: datasetStore,
-        });
+        const loadObservations = (pageSize) => loadInitialPage(client, connection, '/observations', filters, pageSize, ctx);
+        /**
+         * Danger pattern: querying /observations by germplasm with no anchoring
+         * scope (study, trial, observation, observation-unit). On large servers
+         * (CassavaBase, T3) `germplasmDbIds=X` alone joins across every study the
+         * germplasm appeared in — the upstream count query takes tens of seconds
+         * and a `pageSize=loadLimit` pull stalls past the request timeout. Probe
+         * with `pageSize=1` first; if the upstream advertises more rows than we'd
+         * safely pull, skip the bulk fetch and surface a warning recommending a
+         * study scope. Other unscoped patterns (variable-only, bare query) are
+         * left alone — they don't carry the same join blow-up risk and adding a
+         * preflight to every call would double HTTP for the common case.
+         */
+        const hasScope = (input.studies?.length ?? 0) > 0 ||
+            (input.trials?.length ?? 0) > 0 ||
+            (input.observationUnits?.length ?? 0) > 0 ||
+            (input.observations?.length ?? 0) > 0;
+        const shouldPreflight = !hasScope && (input.germplasm?.length ?? 0) > 0;
+        let firstPage;
+        let bulkPullSkipped = false;
+        if (shouldPreflight) {
+            const preflight = await loadObservations(1);
+            const upstreamTotal = preflight.totalCount;
+            if (typeof upstreamTotal === 'number' && upstreamTotal > PREFLIGHT_BULK_THRESHOLD) {
+                warnings.push(`Preflight detected ${upstreamTotal} observations matching this query (germplasm/variable/season scope, no study or trial anchor). Bulk pull skipped to avoid an upstream timeout — narrow with \`studies: ['…']\` or \`trials: ['…']\`, or accept a partial view by re-calling with a tighter scope. Returning the 1-row preflight as the only in-context observation.`);
+                firstPage = preflight;
+                bulkPullSkipped = true;
+            }
+        }
+        firstPage ??= await loadObservations(loadLimit);
+        const { fullRows, dataset: datasetMeta } = bulkPullSkipped
+            ? { fullRows: firstPage.rows, dataset: undefined }
+            : await maybeSpill({
+                firstPage,
+                client,
+                connection,
+                path: '/observations',
+                filters,
+                source: 'find_observations',
+                loadLimit,
+                ctx,
+                store: datasetStore,
+            });
         const distributions = {
             observationVariableName: computeDistribution(fullRows, (r) => asString(r.observationVariableName)),
             studyName: computeDistribution(fullRows, (r) => asString(r.studyName)),
@@ -280,6 +318,23 @@ 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 ?? '?';
@@ -313,6 +368,7 @@ 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;AA2HjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAsO3B,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, 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 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;AAgLjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAsR7B,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, 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 CHANGED Viewed

	@@ -1 +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;~~AA6HjD~~,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~6BAsK5B~~,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;AA8HjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAsL5B,CAAC"}

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

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
1	- 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