npm - @cyanheads/pubchem-mcp-server - Versions diffs - 0.4.3 → 0.5.0 - Mend

@cyanheads/pubchem-mcp-server 0.4.3 → 0.5.0

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Files changed (20) hide show

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![Version](https://img.shields.io/badge/Version-0.4.3-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubchem-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubchem-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubchem-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.3.0-f472b6.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-0.5.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubchem-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubchem-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubchem-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.3.0-f472b6.svg?style=flat-square)](https://bun.sh/)
 </div>

package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js CHANGED Viewed

@@ -8,7 +8,7 @@ import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
 const MAX_RESULTS = 25;
 export const compoundBioactivityResource = resource('pubchem://compound/{cid}/bioactivity', {
     name: 'pubchem-compound-bioactivity',
-    description: 'Bioassay activity profile for a PubChem compound by CID. Returns up to 25 assays; use pubchem_get_bioactivity to filter by outcome or molecular target and to raise the cap.',
+    description: 'Bioassay activity profile for a PubChem compound by CID. Returns up to 25 assays; use pubchem_get_bioactivity to filter by outcome or molecular target, raise the cap, and page through the rest with offset.',
     mimeType: 'application/json',
     params: z.object({
         cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),

package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"compound-bioactivity.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-bioactivity.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,gGAAgG;AAChG,MAAM,WAAW,GAAG,EAAE,CAAC;AAEvB,MAAM,CAAC,MAAM,2BAA2B,GAAG,QAAQ,CAAC,sCAAsC,EAAE;IAC1F,IAAI,EAAE,8BAA8B;IACpC,WAAW,EACT,+MAA+M;IACjN,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACzE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QACtD,MAAM,WAAW,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC,MAAM,CAAC;QACtE,OAAO;YACL,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,WAAW,EAAE,IAAI,CAAC,MAAM;YACxB,WAAW;YACX,OAAO,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,WAAW,CAAC;SACpC,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts CHANGED Viewed

@@ -13,6 +13,7 @@ export declare const getBioactivity: import("@cyanheads/mcp-ts-core").ToolDefini
     }>>;
     targetGeneId: z.ZodOptional<z.ZodNumber>;
     targetAccession: z.ZodOptional<z.ZodString>;
+    offset: z.ZodDefault<z.ZodNumber>;
     maxResults: z.ZodDefault<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     cid: z.ZodNumber;
@@ -36,6 +37,8 @@ export declare const getBioactivity: import("@cyanheads/mcp-ts-core").ToolDefini
     readonly targetFilter: z.ZodOptional<z.ZodString>;
     readonly filteredCount: z.ZodNumber;
     readonly returnedCount: z.ZodNumber;
+    readonly offset: z.ZodNumber;
+    readonly nextOffset: z.ZodOptional<z.ZodNumber>;
     readonly truncated: z.ZodOptional<z.ZodBoolean>;
     readonly shown: z.ZodOptional<z.ZodNumber>;
     readonly cap: z.ZodOptional<z.ZodNumber>;

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

	@@ -1 +1 @@
1	- {"version":3,"file":"get-bioactivity.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,cAAc~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkNzB~~,CAAC"}
1	+ {"version":3,"file":"get-bioactivity.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAoPzB,CAAC"}

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

@@ -34,12 +34,18 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
             .string()
             .optional()
             .describe('Filter to assays against this target protein accession (UniProt/GenBank), e.g. "P35354". Obtain accessions from pubchem_search_assays or the targetAccession field of an unfiltered result here.'),
+        offset: z
+            .number()
+            .int()
+            .min(0)
+            .default(0)
+            .describe('Zero-based index of the first assay to return, applied after the outcome and target filters. Pass the nextOffset from a previous call to read the following page. Default: 0.'),
         maxResults: z
             .number()
             .min(1)
             .max(100)
             .default(20)
-            .describe('Max assay results to return (1-100). Well-studied compounds have thousands of records. Default: 20.'),
+            .describe('Max assay results to return per page (1-100). Well-studied compounds have thousands of records; use offset to reach the ones past this page. Default: 20.'),
     }),
     output: z.object({
         cid: z.number().describe('PubChem Compound ID.'),
@@ -78,9 +84,14 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
             .describe('Assay result entry.'))
             .describe('Assay results matching the filter.'),
     }),
-    // Agent-facing context — filter echo, the filtered/returned cap boundary, and a notice
-    // distinguishing "no data" from "filter excluded everything". Reaches structuredContent
-    // and content[]; keys disjoint from output (cid/totalAssays live there).
+    // Agent-facing context — filter echo, the page boundary, and a notice distinguishing
+    // "no data" from "filter excluded everything". Reaches structuredContent and content[];
+    // keys disjoint from output (cid/totalAssays live there).
+    //
+    // Bounded-total convention: a reported total states only what the server actually
+    // observed, and pairs with an `…AtLeast` floor when the exact figure is unknowable.
+    // Every count here is exact and needs no such twin — PubChem's assay summary has no
+    // pagination of its own, so the full table is in hand before any filter runs.
     enrichment: {
         outcomeFilter: z.string().describe('Outcome filter applied: active, inactive, or all.'),
         targetFilter: z
@@ -89,13 +100,15 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
             .describe('Target filter applied (gene ID and/or protein accession), when set.'),
         filteredCount: z
             .number()
-            .describe('Assays matching the outcome and target filters, before the maxResults cap.'),
-        returnedCount: z.number().describe('Assays returned after the maxResults cap.'),
-        truncated: z
-            .boolean()
+            .describe('Exact number of assays matching the outcome and target filters, across all pages.'),
+        returnedCount: z.number().describe('Assays returned on this page.'),
+        offset: z.number().describe('Zero-based index of the first assay returned.'),
+        nextOffset: z
+            .number()
             .optional()
-            .describe('True when results were capped at maxResults — more matching assays exist.'),
-        shown: z.number().optional().describe('Assays returned after the maxResults cap.'),
+            .describe('Offset to pass on the next call to continue past this page. Omitted when no further assays match.'),
+        truncated: z.boolean().optional().describe('True when matching assays remain past this page.'),
+        shown: z.number().optional().describe('Assays returned on this page.'),
         cap: z.number().optional().describe('The maxResults cap that was applied.'),
         notice: z
             .string()
@@ -128,21 +141,29 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
         if (input.targetAccession) {
             filtered = filtered.filter((r) => r.targetAccession === input.targetAccession);
         }
-        const results = filtered.slice(0, input.maxResults);
+        // Offset is applied client-side: PubChem's assay summary endpoint accepts no
+        // offset/start/limit/page parameter, so getAssaySummary already holds every row.
+        const results = filtered.slice(input.offset, input.offset + input.maxResults);
+        const nextOffset = input.offset + results.length;
+        const hasMore = nextOffset < filtered.length;
         ctx.log.info('Bioactivity fetched', {
             cid: input.cid,
             total: allRows.length,
             active: activeCount,
             filtered: filtered.length,
+            offset: input.offset,
             returned: results.length,
         });
         ctx.enrich({
             outcomeFilter: input.outcomeFilter,
             filteredCount: filtered.length,
             returnedCount: results.length,
+            offset: input.offset,
         });
         if (targetLabel)
             ctx.enrich({ targetFilter: targetLabel });
+        if (hasMore)
+            ctx.enrich({ nextOffset });
         if (allRows.length === 0) {
             ctx.enrich.notice(`No bioactivity data found for CID ${input.cid}. The compound may be uncharacterized, or verify the CID with pubchem_search_compounds.`);
         }
@@ -151,8 +172,15 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
                 ? `CID ${input.cid} has ${allRows.length} assay(s) but none match the target filter (${targetLabel})${input.outcomeFilter !== 'all' ? ` with outcomeFilter="${input.outcomeFilter}"` : ''}. Verify the target identifier appears in this compound's assays, or widen the filter.`
                 : `CID ${input.cid} has ${allRows.length} assay(s) but none match outcomeFilter="${input.outcomeFilter}". Use outcomeFilter="all" to see them.`);
         }
-        else if (filtered.length > results.length) {
-            ctx.enrich.truncated({ shown: results.length, cap: input.maxResults });
+        else if (results.length === 0) {
+            ctx.enrich.notice(`offset ${input.offset} is past the ${filtered.length} assay(s) matching the filter. Pass an offset below ${filtered.length}.`);
+        }
+        else if (hasMore) {
+            ctx.enrich.truncated({
+                shown: results.length,
+                cap: input.maxResults,
+                guidance: `Showing assays ${input.offset + 1}-${nextOffset} of ${filtered.length}. Pass offset=${nextOffset} for the next page.`,
+            });
         }
         return {
             cid: input.cid,

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

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"get-bioactivity.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAEjD,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,yBAAyB,EAAE;IAC5D,KAAK,EAAE,iBAAiB;IACxB,WAAW,EACT,kYAAkY;IACpY,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,QAAQ,EAAE;aACV,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,aAAa,EAAE,CAAC;aACb,IAAI,CAAC,CAAC,QAAQ,EAAE,UAAU,EAAE,KAAK,CAAC,CAAC;aACnC,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,+JAA+J,CAChK;QACH,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,GAAG,EAAE;aACL,QAAQ,EAAE;aACV,QAAQ,EAAE;aACV,QAAQ,CACP,2OAA2O,CAC5O;QACH,eAAe,EAAE,CAAC;aACf,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,kMAAkM,CACnM;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,+KAA+K,CAChL;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,2JAA2J,CAC5J;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC1E,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;QACjE,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QACrE,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YAC7C,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YACnD,OAAO,EAAE,CAAC;iBACP,MAAM,EAAE;iBACR,QAAQ,CAAC,gEAAgE,CAAC;YAC7E,eAAe,EAAE,CAAC;iBACf,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,6CAA6C,CAAC;YAC1D,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;YACpE,cAAc,EAAE,CAAC;iBACd,KAAK,CACJ,CAAC;iBACE,MAAM,CAAC;gBACN,IAAI,EAAE,CAAC;qBACJ,MAAM,EAAE;qBACR,QAAQ,EAAE;qBACV,QAAQ,CACP,oEAAoE,CACrE;gBACH,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;gBAC7C,IAAI,EAAE,CAAC;qBACJ,MAAM,EAAE;qBACR,QAAQ,EAAE;qBACV,QAAQ,CAAC,+DAA+D,CAAC;aAC7E,CAAC;iBACD,QAAQ,CAAC,0CAA0C,CAAC,CACxD;iBACA,QAAQ,CAAC,qCAAqC,CAAC;SACnD,CAAC;aACD,QAAQ,CAAC,qBAAqB,CAAC,CACnC;aACA,QAAQ,CAAC,oCAAoC,CAAC;KAClD,CAAC;IACF,qFAAqF;IACrF,wFAAwF;IACxF,0DAA0D;IAC1D,EAAE;IACF,kFAAkF;IAClF,oFAAoF;IACpF,oFAAoF;IACpF,8EAA8E;IAC9E,UAAU,EAAE;QACV,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACvF,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,qEAAqE,CAAC;QAClF,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,QAAQ,CACP,mFAAmF,CACpF;QACH,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;QACnE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+CAA+C,CAAC;QAC5E,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mGAAmG,CACpG;QACH,SAAS,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kDAAkD,CAAC;QAC9F,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;QACtE,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QAC3E,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,8FAA8F,CAC/F;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;QAExD,MAAM,WAAW,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC,MAAM,CAAC;QACzE,MAAM,aAAa,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,UAAU,CAAC,CAAC,MAAM,CAAC;QAE7E,2EAA2E;QAC3E,yFAAyF;QACzF,IAAI,QAAQ,GAAG,OAAO,CAAC;QACvB,IAAI,KAAK,CAAC,aAAa,KAAK,QAAQ,EAAE,CAAC;YACrC,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC;QAC5D,CAAC;aAAM,IAAI,KAAK,CAAC,aAAa,KAAK,UAAU,EAAE,CAAC;YAC9C,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,UAAU,CAAC,CAAC;QAC9D,CAAC;QAED,MAAM,WAAW,GAAG;YAClB,KAAK,CAAC,YAAY,IAAI,IAAI,CAAC,CAAC,CAAC,UAAU,KAAK,CAAC,YAAY,EAAE,CAAC,CAAC,CAAC,SAAS;YACvE,KAAK,CAAC,eAAe,CAAC,CAAC,CAAC,aAAa,KAAK,CAAC,eAAe,EAAE,CAAC,CAAC,CAAC,SAAS;SACzE;aACE,MAAM,CAAC,OAAO,CAAC;aACf,IAAI,CAAC,GAAG,CAAC,CAAC;QACb,IAAI,KAAK,CAAC,YAAY,IAAI,IAAI,EAAE,CAAC;YAC/B,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,YAAY,KAAK,KAAK,CAAC,YAAY,CAAC,CAAC;QAC3E,CAAC;QACD,IAAI,KAAK,CAAC,eAAe,EAAE,CAAC;YAC1B,QAAQ,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,eAAe,KAAK,KAAK,CAAC,eAAe,CAAC,CAAC;QACjF,CAAC;QAED,6EAA6E;QAC7E,iFAAiF;QACjF,MAAM,OAAO,GAAG,QAAQ,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,MAAM,GAAG,KAAK,CAAC,UAAU,CAAC,CAAC;QAC9E,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC;QACjD,MAAM,OAAO,GAAG,UAAU,GAAG,QAAQ,CAAC,MAAM,CAAC;QAE7C,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,qBAAqB,EAAE;YAClC,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,KAAK,EAAE,OAAO,CAAC,MAAM;YACrB,MAAM,EAAE,WAAW;YACnB,QAAQ,EAAE,QAAQ,CAAC,MAAM;YACzB,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,QAAQ,EAAE,OAAO,CAAC,MAAM;SACzB,CAAC,CAAC;QAEH,GAAG,CAAC,MAAM,CAA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package/dist/mcp-server/tools/definitions/index.d.ts CHANGED Viewed

@@ -145,7 +145,8 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
     readonly recovery: "Pass a positive integer CID string (e.g. \"2244\"), or set queryType \"smiles\" with a SMILES query.";
 }], {
     readonly searchType: import("zod").ZodString;
-    readonly totalFound: import("zod").ZodNumber;
+    readonly totalFound: import("zod").ZodOptional<import("zod").ZodNumber>;
+    readonly totalFoundAtLeast: import("zod").ZodOptional<import("zod").ZodNumber>;
     readonly truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
     readonly shown: import("zod").ZodOptional<import("zod").ZodNumber>;
     readonly cap: import("zod").ZodOptional<import("zod").ZodNumber>;
@@ -247,6 +248,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
     }>>;
     targetGeneId: import("zod").ZodOptional<import("zod").ZodNumber>;
     targetAccession: import("zod").ZodOptional<import("zod").ZodString>;
+    offset: import("zod").ZodDefault<import("zod").ZodNumber>;
     maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
 }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
     cid: import("zod").ZodNumber;
@@ -270,6 +272,8 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
     readonly targetFilter: import("zod").ZodOptional<import("zod").ZodString>;
     readonly filteredCount: import("zod").ZodNumber;
     readonly returnedCount: import("zod").ZodNumber;
+    readonly offset: import("zod").ZodNumber;
+    readonly nextOffset: import("zod").ZodOptional<import("zod").ZodNumber>;
     readonly truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
     readonly shown: import("zod").ZodOptional<import("zod").ZodNumber>;
     readonly cap: import("zod").ZodOptional<import("zod").ZodNumber>;

package/dist/mcp-server/tools/definitions/index.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAaH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAW9B,CAAC"}
1	+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAaH,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAW9B,CAAC"}

package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts CHANGED Viewed

@@ -60,7 +60,8 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
     readonly recovery: "Pass a positive integer CID string (e.g. \"2244\"), or set queryType \"smiles\" with a SMILES query.";
 }], {
     readonly searchType: z.ZodString;
-    readonly totalFound: z.ZodNumber;
+    readonly totalFound: z.ZodOptional<z.ZodNumber>;
+    readonly totalFoundAtLeast: z.ZodOptional<z.ZodNumber>;
     readonly truncated: z.ZodOptional<z.ZodBoolean>;
     readonly shown: z.ZodOptional<z.ZodNumber>;
     readonly cap: z.ZodOptional<z.ZodNumber>;

package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"search-compounds.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-compounds.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA8Y1B,CAAC"}

package/dist/mcp-server/tools/definitions/search-compounds.tool.js CHANGED Viewed

@@ -94,11 +94,25 @@ export const searchCompounds = tool('pubchem_search_compounds', {
     }),
     // Agent-facing context — search strategy echo, total before cap, and an empty-result
     // notice. Reaches structuredContent and content[] automatically; not in the domain return.
+    //
+    // Bounded-total convention: a reported total states only what the server actually
+    // observed. `totalFound` carries a true count and appears only when the whole match set
+    // was seen. When the upstream request was itself bounded and came back saturated, the
+    // exact total is unknowable, so `totalFoundAtLeast` carries a floor in its place rather
+    // than a number that reads as a count. Exactly one of the two is populated per call; any
+    // other capped output pairs its count field with an `…AtLeast` twin the same way.
     enrichment: {
         searchType: z
             .string()
             .describe('Search strategy used: identifier, formula, substructure, superstructure, or similarity.'),
-        totalFound: z.number().describe('Total CIDs found before the maxResults cap.'),
+        totalFound: z
+            .number()
+            .optional()
+            .describe('Exact number of matching CIDs, before the maxResults cap. Omitted when a formula, substructure, superstructure, or similarity search filled its page — PubChem returns no match count for those, so totalFoundAtLeast reports a floor instead.'),
+        totalFoundAtLeast: z
+            .number()
+            .optional()
+            .describe('Lower bound on matching CIDs, reported in place of totalFound when the exact count is unavailable. At least this many match, and the true total may be higher; raise maxResults to retrieve more.'),
         truncated: z
             .boolean()
             .optional()
@@ -139,6 +153,11 @@ export const searchCompounds = tool('pubchem_search_compounds', {
     async handler(input, ctx) {
         const client = getPubChemClient();
         let allCids = [];
+        // Formula and structure searches are bounded server-side. One record past the cap is
+        // enough to prove more matches exist without moving the rest of PubChem's match set,
+        // which for a common substructure runs to 16.3 MB of CIDs.
+        const recordCap = input.maxResults + 1;
+        let boundedSearch = false;
         const identifierMap = new Map();
         // Identifier-mode resolution tracking (#29): inputs that resolved to no CID, and
         // CIDs claimed by more than one distinct input (the output row can echo only one).
@@ -202,7 +221,8 @@ export const searchCompounds = tool('pubchem_search_compounds', {
                         ...ctx.recoveryFor('missing_formula'),
                     });
                 }
-                allCids = await client.searchByFormula(input.formula, input.allowOtherElements);
+                boundedSearch = true;
+                allCids = await client.searchByFormula(input.formula, input.allowOtherElements, recordCap);
                 break;
             }
             case 'substructure':
@@ -218,21 +238,28 @@ export const searchCompounds = tool('pubchem_search_compounds', {
                 if (input.queryType === 'cid' && !(/^\d+$/.test(input.query) && Number(input.query) > 0)) {
                     throw ctx.fail('invalid_cid_query', `queryType is "cid" but query "${input.query}" is not a positive integer CID.`, { ...ctx.recoveryFor('invalid_cid_query') });
                 }
-                allCids = await client.searchByStructure(input.searchType, input.query, input.queryType, input.threshold);
+                boundedSearch = true;
+                allCids = await client.searchByStructure(input.searchType, input.query, input.queryType, input.threshold, recordCap);
                 break;
             }
         }
         // Deduplicate and cap
         const uniqueCids = [...new Set(allCids)];
-        const totalFound = uniqueCids.length;
+        const observedTotal = uniqueCids.length;
         const cappedCids = uniqueCids.slice(0, input.maxResults);
+        // A bounded search that came back short of its cap returned everything PubChem had, so
+        // the count is exact. A saturated one only proves a floor.
+        const totalIsExact = !boundedSearch || allCids.length < recordCap;
         ctx.log.info('Search completed', {
             searchType: input.searchType,
-            totalFound,
+            observedTotal,
+            totalIsExact,
             returned: cappedCids.length,
         });
         // Agent-facing context: search strategy echo, total, and empty-result notice.
-        ctx.enrich({ searchType: input.searchType, totalFound });
+        ctx.enrich(totalIsExact
+            ? { searchType: input.searchType, totalFound: observedTotal }
+            : { searchType: input.searchType, totalFoundAtLeast: observedTotal });
         // Identifier-mode signals (#29): name inputs that did not resolve and flag CID
         // collisions, so a partial miss is never silent. Empty for other search types.
         const noticeParts = [];
@@ -248,19 +275,20 @@ export const searchCompounds = tool('pubchem_search_compounds', {
                 ? noticeParts.join(' ')
                 : `No compounds matched the ${input.searchType} search. Try a different identifier, broaden the formula, lower the similarity threshold, or verify the SMILES/CID.`);
         }
-        else if (totalFound > cappedCids.length) {
+        else if (observedTotal > cappedCids.length) {
             // Truncated: fold any identifier notice into the truncation guidance (notice is
-            // last-wins, so compose rather than emit two; restate the cap when overriding).
-            if (noticeParts.length > 0) {
-                ctx.enrich.truncated({
-                    shown: cappedCids.length,
-                    cap: input.maxResults,
-                    guidance: `${noticeParts.join(' ')} Showing ${cappedCids.length} of ${totalFound} matches — raise maxResults (max 200) for more.`,
-                });
-            }
-            else {
-                ctx.enrich.truncated({ shown: cappedCids.length, cap: input.maxResults });
-            }
+            // last-wins, so compose rather than emit two). Without an exact total there is no
+            // "of N" to quote — say more exist and stop.
+            const truncationGuidance = totalIsExact
+                ? `Showing ${cappedCids.length} of ${observedTotal} matches — raise maxResults (max 200) for more.`
+                : `Showing ${cappedCids.length} matches; more exist, but PubChem reports no match count for a ${input.searchType} search — raise maxResults (max 200) for more.`;
+            ctx.enrich.truncated({
+                shown: cappedCids.length,
+                cap: input.maxResults,
+                guidance: noticeParts.length > 0
+                    ? `${noticeParts.join(' ')} ${truncationGuidance}`
+                    : truncationGuidance,
+            });
         }
         else if (noticeParts.length > 0) {
             ctx.enrich.notice(noticeParts.join(' '));

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package/dist/services/pubchem/pubchem-client.d.ts CHANGED Viewed

@@ -19,15 +19,37 @@ export declare class PubChemClient {
     private fetchBinary;
     /** Fetch a text/plain body (e.g. an SDF record). Non-2xx is classified and thrown. */
     private fetchText;
-    /** Fetch CID list, with automatic ListKey polling for async searches */
+    /** Fetch CID list, with automatic ListKey polling for async searches.
+     *
+     * `maxRecords` carries a bounded search's cap into the ListKey retrieval. A search that
+     * answers synchronously is already bounded by the `MaxRecords` on its own URL, but that
+     * bound lives in the request, not the ListKey — so an async answer would otherwise return
+     * the full match set and the caller would read PubChem's ceiling as a real count. Omitted
+     * for identifier lookups, which are unbounded by design. */
     private fetchCids;
-    /** Poll a PubChem ListKey until results are ready */
+    /** Poll a PubChem ListKey until results are ready.
+     *
+     * `listkey_count` asks PubChem to trim the page; the slice enforces the same bound
+     * locally, so the caller's saturation test holds whether or not the parameter is honored. */
     private pollListKey;
     searchByName(name: string): Promise<number[]>;
     searchBySmiles(smiles: string): Promise<number[]>;
     searchByInchiKey(inchikey: string): Promise<number[]>;
-    searchByFormula(formula: string, allowOther?: boolean): Promise<number[]>;
-    searchByStructure(mode: 'substructure' | 'superstructure' | 'similarity', query: string, queryType: 'smiles' | 'cid', threshold?: number): Promise<number[]>;
+    /** Formula search, bounded server-side by `maxRecords`.
+     *
+     * `MaxRecords` is mandatory rather than optional because an unbounded fast search moves
+     * PubChem's entire match set: a benzoic-acid substructure query returns 1,000,000 CIDs in
+     * 16.3 MB, which is PubChem's own ceiling rather than a real count. Callers ask for the
+     * window they will actually use.
+     *
+     * A response shorter than `maxRecords` is the complete match set; a response of exactly
+     * `maxRecords` is saturated, and the true total is not recoverable — PubChem returns the
+     * CID list alone, with no match count beside it. Callers that need to distinguish the two
+     * compare the returned length against the cap they passed. */
+    searchByFormula(formula: string, allowOther: boolean, maxRecords: number): Promise<number[]>;
+    /** Substructure, superstructure, and 2D-similarity search, bounded server-side by
+     * `maxRecords`. Same cap contract as {@link searchByFormula}. */
+    searchByStructure(mode: 'substructure' | 'superstructure' | 'similarity', query: string, queryType: 'smiles' | 'cid', threshold: number | undefined, maxRecords: number): Promise<number[]>;
     getProperties(cids: number[], properties: string[]): Promise<Array<Record<string, unknown> & {
         CID: number;
     }>>;

package/dist/services/pubchem/pubchem-client.d.ts.map CHANGED Viewed

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package/dist/services/pubchem/pubchem-client.js CHANGED Viewed

@@ -455,12 +455,18 @@ export class PubChemClient {
         return response.text();
     }
     // ── CID Resolution ──────────────────────────────────────────────
-    /** Fetch CID list, with automatic ListKey polling for async searches */
-    async fetchCids(url, init) {
+    /** Fetch CID list, with automatic ListKey polling for async searches.
+     *
+     * `maxRecords` carries a bounded search's cap into the ListKey retrieval. A search that
+     * answers synchronously is already bounded by the `MaxRecords` on its own URL, but that
+     * bound lives in the request, not the ListKey — so an async answer would otherwise return
+     * the full match set and the caller would read PubChem's ceiling as a real count. Omitted
+     * for identifier lookups, which are unbounded by design. */
+    async fetchCids(url, init, maxRecords) {
         try {
             const data = await this.fetchJson(url, init);
             if ('Waiting' in data)
-                return this.pollListKey(data.Waiting.ListKey);
+                return this.pollListKey(data.Waiting.ListKey, maxRecords);
             return data.IdentifierList.CID;
         }
         catch (error) {
@@ -469,16 +475,21 @@ export class PubChemClient {
             throw error;
         }
     }
-    /** Poll a PubChem ListKey until results are ready */
-    async pollListKey(listKey, maxAttempts = 20) {
-        const pollUrl = `${this.pugBase}/compound/listkey/${listKey}/cids/JSON`;
+    /** Poll a PubChem ListKey until results are ready.
+     *
+     * `listkey_count` asks PubChem to trim the page; the slice enforces the same bound
+     * locally, so the caller's saturation test holds whether or not the parameter is honored. */
+    async pollListKey(listKey, maxRecords, maxAttempts = 20) {
+        const query = maxRecords === undefined ? '' : `?listkey_count=${maxRecords}`;
+        const pollUrl = `${this.pugBase}/compound/listkey/${listKey}/cids/JSON${query}`;
         for (let attempt = 0; attempt < maxAttempts; attempt++) {
             await sleep(1500);
             try {
                 const data = await this.fetchJson(pollUrl);
                 if ('Waiting' in data)
                     continue;
-                return data.IdentifierList.CID;
+                const cids = data.IdentifierList.CID;
+                return maxRecords === undefined ? cids : cids.slice(0, maxRecords);
             }
             catch (error) {
                 if (isNotFound(error))
@@ -501,27 +512,44 @@ export class PubChemClient {
     searchByInchiKey(inchikey) {
         return this.fetchCids(`${this.pugBase}/compound/inchikey/${encodeURIComponent(inchikey)}/cids/JSON`);
     }
-    searchByFormula(formula, allowOther = false) {
-        const params = allowOther ? '?AllowOtherElements=true' : '';
-        return this.fetchCids(`${this.pugBase}/compound/fastformula/${encodeURIComponent(formula)}/cids/JSON${params}`);
+    /** Formula search, bounded server-side by `maxRecords`.
+     *
+     * `MaxRecords` is mandatory rather than optional because an unbounded fast search moves
+     * PubChem's entire match set: a benzoic-acid substructure query returns 1,000,000 CIDs in
+     * 16.3 MB, which is PubChem's own ceiling rather than a real count. Callers ask for the
+     * window they will actually use.
+     *
+     * A response shorter than `maxRecords` is the complete match set; a response of exactly
+     * `maxRecords` is saturated, and the true total is not recoverable — PubChem returns the
+     * CID list alone, with no match count beside it. Callers that need to distinguish the two
+     * compare the returned length against the cap they passed. */
+    searchByFormula(formula, allowOther, maxRecords) {
+        const params = new URLSearchParams({ MaxRecords: String(maxRecords) });
+        if (allowOther)
+            params.set('AllowOtherElements', 'true');
+        return this.fetchCids(`${this.pugBase}/compound/fastformula/${encodeURIComponent(formula)}/cids/JSON?${params}`, undefined, maxRecords);
     }
-    searchByStructure(mode, query, queryType, threshold) {
+    /** Substructure, superstructure, and 2D-similarity search, bounded server-side by
+     * `maxRecords`. Same cap contract as {@link searchByFormula}. */
+    searchByStructure(mode, query, queryType, threshold, maxRecords) {
         const endpoint = mode === 'similarity'
             ? 'fastsimilarity_2d'
             : mode === 'substructure'
                 ? 'fastsubstructure'
                 : 'fastsuperstructure';
-        const thresholdParam = mode === 'similarity' ? `?Threshold=${threshold ?? 90}` : '';
+        const params = new URLSearchParams({ MaxRecords: String(maxRecords) });
+        if (mode === 'similarity')
+            params.set('Threshold', String(threshold ?? 90));
         if (queryType === 'cid') {
-            return this.fetchCids(`${this.pugBase}/compound/${endpoint}/cid/${query}/cids/JSON${thresholdParam}`);
+            return this.fetchCids(`${this.pugBase}/compound/${endpoint}/cid/${query}/cids/JSON?${params}`, undefined, maxRecords);
         }
         // POST for SMILES to avoid encoding issues
-        const url = `${this.pugBase}/compound/${endpoint}/smiles/cids/JSON${thresholdParam}`;
+        const url = `${this.pugBase}/compound/${endpoint}/smiles/cids/JSON?${params}`;
         return this.fetchCids(url, {
             method: 'POST',
             headers: { 'Content-Type': 'application/x-www-form-urlencoded' },
             body: new URLSearchParams({ smiles: query }).toString(),
-        });
+        }, maxRecords);
     }
     // ── Compound Data ───────────────────────────────────────────────
     async getProperties(cids, properties) {

package/dist/services/pubchem/pubchem-client.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/manifest.json CHANGED Viewed

@@ -1,7 +1,7 @@
 {
   "manifest_version": "0.3",
   "name": "pubchem-mcp-server",
-  "version": "0.4.3",
+  "version": "0.5.0",
   "description": "Search the PubChem chemical database for compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP. STDIO or Streamable HTTP.",
   "author": {
     "name": "cyanheads"

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubchem-mcp-server",
-  "version": "0.4.3",
+  "version": "0.5.0",
   "description": "Search the PubChem chemical database for compounds, properties, safety data, bioactivity, cross-references, and entity summaries via MCP. STDIO or Streamable HTTP.",
   "mcpName": "io.github.cyanheads/pubchem-mcp-server",
   "type": "module",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubchem-mcp-server",
     "source": "github"
   },
-  "version": "0.4.3",
+  "version": "0.5.0",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubchem-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.4.3",
+      "version": "0.5.0",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:stdio" }
@@ -42,7 +42,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubchem-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.4.3",
+      "version": "0.5.0",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }