npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.4.14 → 0.5.1 - Mend

@cyanheads/brapi-mcp-server 0.4.14 → 0.5.1

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 (116) hide show

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

@@ -6,8 +6,8 @@
  * (operator policy, default 100k, max 500k) so a single query can't trigger
  * unbounded sequential paginated GETs against the upstream BrAPI server.
  * `loadLimit` bounds the rows returned inline; when the pull exceeds
- * loadLimit, the full collected set spills to DatasetStore for paged
- * follow-up.
+ * loadLimit, the full collected set is materialized as a dataframe
+ * for SQL-based follow-up.
  *
  * @module mcp-server/tools/definitions/brapi-find-genotype-calls.tool
  */
@@ -16,10 +16,10 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getServerConfig } from '../../../config/server-config.js';
 import { getBrapiClient } from '../../../services/brapi-client/index.js';
 import { resolveDialect } from '../../../services/brapi-dialect/index.js';
+import { getCanvasBridge, } from '../../../services/canvas-bridge/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, buildRequestOptions, collectPassthroughParts, computeDistribution, DatasetHandleSchema, renderDatasetHandle, renderDistributions, renderFindHeader, toDatasetHandle, } from '../shared/find-helpers.js';
+import { AliasInput, asString, buildRequestOptions, collectPassthroughParts, computeDistribution, DataframeHandleSchema, renderDataframeHandle, renderDistributions, renderFindHeader, toDataframeHandle, } from '../shared/find-helpers.js';
 const PAGE_SIZE = 10_000;
 const CallRowSchema = z
     .object({
@@ -97,17 +97,17 @@ const OutputSchema = z.object({
             .describe('Variant set ID → count of calls from that set.'),
     })
         .describe('Value frequency per field across the full collected call set.'),
-    dataset: DatasetHandleSchema.optional().describe('Dataset handle when the full collected calls exceed loadLimit and were spilled to DatasetStore.'),
+    dataframe: DataframeHandleSchema.optional().describe('Dataframe handle when the full collected calls exceed loadLimit and were materialized as a dataframe. Query it with brapi_dataframe_query (SQL).'),
     truncated: z
         .boolean()
-        .describe('True when the deployment-wide pull limit was reached and more calls exist upstream. Narrow the filters and re-pull, or query the spilled dataset/dataframe.'),
+        .describe('True when the deployment-wide pull limit was reached and more calls exist upstream. Narrow the filters and re-pull, or query the spilled dataframe.'),
     warnings: z
         .array(z.string())
         .describe('Advisory messages (truncation, capability gaps, partial pulls).'),
     searchBody: z.record(z.string(), z.unknown()).describe('The body sent to /search/calls.'),
 });
 export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
-    description: 'Pull genotype calls for a germplasm × variant set. Filter to bound cost — at minimum, set `variantSetDbId` or `germplasmDbIds`. The upstream pull is capped by deployment policy (default 100,000 rows, max 500,000); when the pull is truncated, narrow the filters or query the spilled dataframe. `loadLimit` (default 200) bounds the rows returned inline; the full collected set spills to a dataset handle for paged follow-up via brapi_manage_dataset.',
+    description: 'Pull genotype calls for a germplasm × variant set. Filter to bound cost — at minimum, set `variantSetDbId` or `germplasmDbIds`. The upstream pull is capped by deployment policy; when the pull is truncated, narrow the filters or query the spilled dataframe. `loadLimit` bounds the rows returned inline; the full collected set is materialized as a dataframe — query it with brapi_dataframe_query (SQL) instead of paging row-by-row.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -149,14 +149,14 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
             .int()
             .positive()
             .optional()
-            .describe('Cap on rows returned inline in the response (default 200). When the upstream pull exceeds this, the full collected set spills to a dataset handle and only the first `loadLimit` rows return inline. Use brapi_manage_dataset (paging) or brapi_dataframe_query (SQL) to work with the full set.'),
+            .describe('Cap on rows returned inline. Omit for the deployment default. When the collected set exceeds this, the full result lands in a dataframe and only the first `loadLimit` rows return inline — query the dataframe with brapi_dataframe_query (SQL) for the rest. Upstream pageSize is fixed for genotype calls, so this knob only affects the inline preview here (no spillover capacity tradeoff).'),
     }),
     output: OutputSchema,
     async handler(input, ctx) {
         const registry = getServerRegistry();
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
-        const datasetStore = getDatasetStore();
+        const bridge = getCanvasBridge();
         const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
         const capabilityLookup = {};
         if (connection.resolvedAuth)
@@ -166,11 +166,11 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
         if (dialect.disabledSearchEndpoints?.has('calls')) {
             throw ctx.fail('search_endpoint_disabled', `Dialect '${dialect.id}' marks POST /search/calls as known-dead on this server. Genotype-call workflows are not viable here without bypassing the dialect.`, { dialectId: dialect.id, ...ctx.recoveryFor('search_endpoint_disabled') });
         }
-        const maxCalls = getServerConfig().genotypeCallsMaxPull;
-        const loadLimit = input.loadLimit ?? 200;
+        const config = getServerConfig();
+        const maxCalls = config.genotypeCallsMaxPull;
+        const loadLimit = input.loadLimit ?? config.loadLimit;
         const searchBody = buildSearchBody(input);
         if (!searchBody.variantSetDbIds &&
-            !searchBody.variantSetDbId &&
             !searchBody.germplasmDbIds &&
             !searchBody.callSetDbIds &&
             !searchBody.variantDbIds) {
@@ -191,14 +191,14 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
             variantName: computeDistribution(collected.rows, (r) => asString(r.variantName)),
             variantSetDbId: computeDistribution(collected.rows, (r) => asString(r.variantSetDbId)),
         };
-        if (collected.rows.length === 0 && hasNamedFilter(searchBody)) {
+        if (collected.rows.length === 0) {
             warnings.push('Upstream returned 0 calls for the requested filters. The variant set or filter combination may not match any data on this server.');
         }
         const shouldSpill = collected.rows.length > loadLimit;
-        let datasetMeta;
+        let dataframeHandle;
         if (shouldSpill) {
-            datasetMeta = await spillCalls({
-                store: datasetStore,
+            dataframeHandle = await spillCalls({
+                bridge,
                 ctx,
                 connection,
                 body: searchBody,
@@ -219,8 +219,8 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
             warnings,
             searchBody,
         };
-        if (datasetMeta)
-            result.dataset = datasetMeta;
+        if (dataframeHandle)
+            result.dataframe = dataframeHandle;
         return result;
     },
     format: (result) => {
@@ -230,7 +230,7 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
             alias: result.alias,
             returnedCount: result.returnedCount,
             totalCount: result.totalCount,
-            dataset: result.dataset,
+            dataframe: result.dataframe,
         });
         lines.push(result.truncated ? `${headerBase} (truncated at deployment pull limit)` : headerBase);
         lines.push('');
@@ -281,10 +281,10 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }
-        if (result.dataset) {
+        if (result.dataframe) {
             lines.push('');
-            lines.push('## Dataset handle');
-            lines.push(...renderDatasetHandle(result.dataset));
+            lines.push('## Dataframe handle');
+            lines.push(...renderDataframeHandle(result.dataframe));
         }
         if (result.warnings.length > 0) {
             lines.push('');
@@ -359,7 +359,7 @@ async function collectCalls(input) {
     if (rows.length > input.maxCalls) {
         rows.length = input.maxCalls;
         truncated = true;
-        input.warnings.push(`Truncated at the deployment pull limit (${input.maxCalls} rows). Narrow the filters and re-pull; the captured slice is preserved in the spilled dataset.`);
+        input.warnings.push(`Truncated at the deployment pull limit (${input.maxCalls} rows). Narrow the filters and re-pull; the captured slice is preserved in the spilled dataframe.`);
     }
     return { rows, callFormatting, truncated };
 }
@@ -388,25 +388,17 @@ function consumePage(envelope, rows, setCallFormatting) {
     }
 }
 async function spillCalls(input) {
-    const createInput = {
+    const registerInput = {
         source: 'find_genotype_calls',
         baseUrl: input.connection.baseUrl,
         query: input.body,
         rows: input.rows,
     };
     if (input.truncated) {
-        createInput.truncated = true;
-        createInput.maxRows = input.maxRows;
+        registerInput.truncated = true;
+        registerInput.maxRows = input.maxRows;
     }
-    const metadata = await input.store.create(input.ctx, createInput);
-    return toDatasetHandle(metadata);
-}
-function hasNamedFilter(body) {
-    const isNonEmptyArray = (v) => Array.isArray(v) && v.length > 0;
-    return (typeof body.variantSetDbId === 'string' ||
-        isNonEmptyArray(body.variantSetDbIds) ||
-        isNonEmptyArray(body.germplasmDbIds) ||
-        isNonEmptyArray(body.callSetDbIds) ||
-        isNonEmptyArray(body.variantDbIds));
+    const result = await input.bridge.registerDataframe(input.ctx, registerInput);
+    return toDataframeHandle(result);
 }
 //# sourceMappingURL=brapi-find-genotype-calls.tool.js.map

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

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

@@ -2,7 +2,7 @@
  * @fileoverview `brapi_find_germplasm` — search germplasm by name, synonym,
  * accession, attribute, or free text. Matches BrAPI's registered-synonym
  * semantics. Returns distributions for crop / genus / species / collection
- * and spills to DatasetStore when the upstream total exceeds loadLimit.
+ * and spills to a dataframe when the upstream total exceeds loadLimit.
  *
  * @module mcp-server/tools/definitions/brapi-find-germplasm.tool
  */
@@ -57,16 +57,14 @@ export declare const brapiFindGermplasm: import("@cyanheads/mcp-ts-core").ToolDe
         countryOfOriginCode: z.ZodRecord<z.ZodString, z.ZodNumber>;
     }, z.core.$strip>;
     refinementHint: z.ZodOptional<z.ZodString>;
-    dataset: z.ZodOptional<z.ZodObject<{
-        datasetId: z.ZodString;
+    dataframe: z.ZodOptional<z.ZodObject<{
+        tableName: z.ZodString;
         rowCount: z.ZodNumber;
-        sizeBytes: z.ZodNumber;
         columns: z.ZodArray<z.ZodString>;
         createdAt: z.ZodString;
         expiresAt: z.ZodString;
         truncated: z.ZodOptional<z.ZodBoolean>;
         maxRows: z.ZodOptional<z.ZodNumber>;
-        dataframe: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;
     warnings: z.ZodArray<z.ZodString>;
     appliedFilters: z.ZodRecord<z.ZodString, z.ZodUnknown>;

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AA8IjE~~,eAAO,MAAM,kBAAkB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAqT7B~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA+IjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsT7B,CAAC"}

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

@@ -2,7 +2,7 @@
  * @fileoverview `brapi_find_germplasm` — search germplasm by name, synonym,
  * accession, attribute, or free text. Matches BrAPI's registered-synonym
  * semantics. Returns distributions for crop / genus / species / collection
- * and spills to DatasetStore when the upstream total exceeds loadLimit.
+ * and spills to a dataframe when the upstream total exceeds loadLimit.
  *
  * @module mcp-server/tools/definitions/brapi-find-germplasm.tool
  */
@@ -11,10 +11,10 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getServerConfig } from '../../../config/server-config.js';
 import { getBrapiClient } from '../../../services/brapi-client/index.js';
 import { resolveDialect } from '../../../services/brapi-dialect/index.js';
+import { getCanvasBridge } from '../../../services/canvas-bridge/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, applyDialectFiltersOrFail, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, dedupSynonymsByIdentity, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFiltersOrFail, asString, buildExtraFilterChecks, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, dedupSynonymsByIdentity, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDataframeHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
 const GermplasmRowSchema = z
     .object({
     germplasmDbId: z.string().describe('Server-side identifier for the germplasm.'),
@@ -87,7 +87,7 @@ const OutputSchema = z.object({
         .string()
         .optional()
         .describe('Suggested next-step query refinement when the result set is large.'),
-    dataset: DatasetHandleSchema.optional().describe('Dataset handle when the full result set was persisted to DatasetStore.'),
+    dataframe: DataframeHandleSchema.optional().describe('Dataframe handle when the full result set was materialized as a dataframe. Query it with brapi_dataframe_query (SQL).'),
     warnings: z
         .array(z.string())
         .describe('Advisory messages (filter overrides, partial data, capability gaps, etc.).'),
@@ -117,7 +117,7 @@ const SERVER_TO_USER = {
     species: 'species',
 };
 export const brapiFindGermplasm = tool('brapi_find_germplasm', {
-    description: 'Find germplasm by name, synonym, accession number, PUI, crop, or free-text query. Matches across registered synonyms. Returns a dataset handle when the upstream total exceeds loadLimit.',
+    description: 'Find germplasm by name, synonym, accession number, PUI, crop, or free-text query. Matches across registered synonyms. When the upstream total exceeds loadLimit, the full result set is materialized as a dataframe — query it with brapi_dataframe_query (SQL) instead of paging row-by-row.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -153,7 +153,7 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
         const registry = getServerRegistry();
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
-        const datasetStore = getDatasetStore();
+        const bridge = getCanvasBridge();
         const config = getServerConfig();
         const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
         const capabilityLookup = {};
@@ -209,15 +209,15 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             source: 'find_germplasm',
             loadLimit,
             ctx,
-            store: datasetStore,
+            bridge,
             // CassavaBase repeats every synonym entry 11× per record. Dedup at the
-            // spillover layer so the in-context view, the persisted dataset, and
-            // the canvas dataframe all see the cleaned shape consistently.
+            // spillover layer so the in-context view and the dataframe see
+            // the cleaned shape consistently.
             rowMapper: dedupSynonymsByIdentity,
         };
         if (text)
             spillInput.rowFilter = (row) => rowMatchesText(row, text);
-        const { fullRows, dataset: datasetMeta } = await maybeSpill(spillInput);
+        const { fullRows, dataframe } = await maybeSpill(spillInput);
         const distributions = {
             commonCropName: computeDistribution(fullRows, (r) => asString(r.commonCropName)),
             genus: computeDistribution(fullRows, (r) => asString(r.genus)),
@@ -250,6 +250,7 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
                 distribution: distributions.collection,
                 caseInsensitive: true,
             },
+            ...buildExtraFilterChecks(input.extraFilters, fullRows, warnings),
         ]);
         const totalCount = firstPage.totalCount ?? firstPage.rows.length;
         const refinementHint = buildRefinementHint(totalCount, loadLimit, distributions, {
@@ -273,8 +274,8 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             else if (fullRows.length === 0 && firstPage.rows.length > 0) {
                 warnings.push(`Free-text '${text}' matched 0 of ${firstPage.rows.length} returned rows. Use exact filters (\`names\`, \`accessionNumbers\`, \`germplasmDbIds\`) for direct lookup, or check spelling.`);
             }
-            else if (datasetMeta) {
-                warnings.push(`Free-text '${text}' filtered the dataset to ${datasetMeta.rowCount} matched row(s) across the upstream union.`);
+            else if (dataframe) {
+                warnings.push(`Free-text '${text}' filtered the dataframe to ${dataframe.rowCount} matched row(s) across the upstream union.`);
             }
             else if (fullRows.length < firstPage.rows.length) {
                 warnings.push(`Free-text '${text}' narrowed in-context view to ${fullRows.length} of ${firstPage.rows.length} returned rows.`);
@@ -293,8 +294,8 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
         };
         if (refinementHint)
             result.refinementHint = refinementHint;
-        if (datasetMeta)
-            result.dataset = datasetMeta;
+        if (dataframe)
+            result.dataframe = dataframe;
         return result;
     },
     format: (result) => {
@@ -304,11 +305,11 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             alias: result.alias,
             returnedCount: result.returnedCount,
             totalCount: result.totalCount,
-            dataset: result.dataset,
+            dataframe: result.dataframe,
         }));
         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.'}`);
+            lines.push(`⚠ More rows exist beyond the returned set. ${result.dataframe ? `Full set materialized as dataframe \`${result.dataframe.tableName}\` — query with brapi_dataframe_query.` : 'Narrow filters or raise loadLimit.'}`);
             lines.push('');
         }
         if (result.refinementHint) {
@@ -387,10 +388,10 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }
-        if (result.dataset) {
+        if (result.dataframe) {
             lines.push('');
-            lines.push('## Dataset handle');
-            lines.push(...renderDatasetHandle(result.dataset));
+            lines.push('## Dataframe handle');
+            lines.push(...renderDataframeHandle(result.dataframe));
         }
         if (result.warnings.length > 0) {
             lines.push('');

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

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

@@ -1,8 +1,8 @@
 /**
  * @fileoverview `brapi_find_images` — filter images by observation unit,
  * study, observation, descriptive ontology, file name, or MIME type. Returns
- * metadata only; pull bytes via `brapi_get_image`. Spills the full set to
- * DatasetStore when the upstream total exceeds loadLimit.
+ * metadata only; pull bytes via `brapi_get_image`. Materializes the full set
+ * as a dataframe when the upstream total exceeds loadLimit.
  *
  * @module mcp-server/tools/definitions/brapi-find-images.tool
  */
@@ -50,16 +50,14 @@ export declare const brapiFindImages: import("@cyanheads/mcp-ts-core").ToolDefin
         descriptiveOntologyTerms: z.ZodRecord<z.ZodString, z.ZodNumber>;
     }, z.core.$strip>;
     refinementHint: z.ZodOptional<z.ZodString>;
-    dataset: z.ZodOptional<z.ZodObject<{
-        datasetId: z.ZodString;
+    dataframe: z.ZodOptional<z.ZodObject<{
+        tableName: z.ZodString;
         rowCount: z.ZodNumber;
-        sizeBytes: z.ZodNumber;
         columns: z.ZodArray<z.ZodString>;
         createdAt: z.ZodString;
         expiresAt: z.ZodString;
         truncated: z.ZodOptional<z.ZodBoolean>;
         maxRows: z.ZodOptional<z.ZodNumber>;
-        dataframe: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;
     warnings: z.ZodArray<z.ZodString>;
     appliedFilters: z.ZodRecord<z.ZodString, z.ZodUnknown>;

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

	@@ -1 +1 @@
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