npm - @cyanheads/pubchem-mcp-server - Versions diffs - 0.5.0 → 0.5.2 - Mend

@cyanheads/pubchem-mcp-server 0.5.0 → 0.5.2

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 (35) hide show

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![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/)
+[![Version](https://img.shields.io/badge/Version-0.5.2-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>
@@ -52,6 +52,7 @@ Search PubChem for chemical compounds across five search modes.
 - **Formula search** — find compounds by molecular formula in Hill notation
 - **Substructure/superstructure** — find compounds containing or contained within a query structure
 - **2D similarity** — find structurally similar compounds by Tanimoto similarity (configurable threshold)
+- Caps at 200 CIDs per page; `offset` pages further, to a ceiling of 10,000. Identifier lookups page over the set already resolved; formula and structure searches widen their bounded upstream request to reach a page, so deep pages cost more upstream
 - Optionally hydrate results with properties to avoid a follow-up details call
 ---
@@ -62,8 +63,9 @@ Get detailed compound information by CID.
 - Batches up to 100 CIDs in a single request
 - 27 available properties: molecular weight, SMILES, InChIKey, XLogP, TPSA, complexity, stereo counts, and more
-- Optionally includes textual descriptions (pharmacology, mechanism, therapeutic use) from PUG View
-- Optionally includes all known synonyms (trade names, systematic names, registry numbers)
+- Optionally includes textual descriptions (pharmacology, mechanism, therapeutic use) from PUG View — fetched for the first 10 CIDs of a batch, with the skipped CIDs named in the response
+- Optionally includes known synonyms (trade names, systematic names, registry numbers)
+- Synonyms and descriptions are paged: `synonymOffset` and `descriptionOffset` window every compound in the batch at the same position, reaching the entries past a page
 - Optionally computes drug-likeness assessment (Lipinski Rule of Five + Veber rules) from fetched properties
 - Optionally fetches pharmacological classification (FDA classes, mechanisms of action, MeSH classes, ATC codes)
@@ -75,7 +77,7 @@ Get a compound's bioactivity profile from PubChem BioAssay.
 - Returns assay outcomes (Active/Inactive/Inconclusive), target info (protein accessions, NCBI Gene IDs), and quantitative values (IC50, EC50, Ki)
 - Filter by outcome and/or a specific molecular target (NCBI Gene ID or protein accession)
-- Caps at 100 results per request (well-studied compounds may have thousands)
+- Caps at 100 results per page; `offset` reaches the rest (well-studied compounds may have thousands)
 ---
@@ -95,6 +97,7 @@ Get a compound's interaction data by CID.
 - Drug-drug interactions (DrugBank), drug-food interactions, and chemical-target binding/activity (BindingDB, ChEMBL, and others)
 - Select which interaction kinds to fetch and cap entries per kind
+- Paged per kind: each reports its source-record total and its own `nextOffset`, and `offset` reaches the records past a page
 - Each entry carries its originating source — coverage is richest for approved drugs
 ---

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

@@ -9,7 +9,7 @@ const RESOURCE_XREF_TYPES = ['RN', 'RegistryID', 'PubMedID'];
 const MAX_PER_TYPE = 25;
 export const compoundXrefsResource = resource('pubchem://compound/{cid}/xrefs', {
     name: 'pubchem-compound-xrefs',
-    description: 'External cross-references (CAS RN, registry IDs, PubMed) for a PubChem compound by CID, up to 25 per type. Use pubchem_get_compound_xrefs for the full set of xref types and a higher per-type cap.',
+    description: 'External cross-references (CAS RN, registry IDs, PubMed) for a PubChem compound by CID, up to 25 per type. Use pubchem_get_compound_xrefs for the full set of xref types, a higher per-type cap, and to 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-xrefs.resource.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts CHANGED Viewed

@@ -10,8 +10,10 @@ export declare const getCompoundDetails: import("@cyanheads/mcp-ts-core").ToolDe
         [x: string]: string;
     }>>>;
     includeDescription: z.ZodDefault<z.ZodBoolean>;
+    descriptionOffset: z.ZodDefault<z.ZodNumber>;
     maxDescriptions: z.ZodDefault<z.ZodNumber>;
     includeSynonyms: z.ZodDefault<z.ZodBoolean>;
+    synonymOffset: z.ZodDefault<z.ZodNumber>;
     maxSynonyms: z.ZodDefault<z.ZodNumber>;
     includeDrugLikeness: z.ZodDefault<z.ZodBoolean>;
     includeClassification: z.ZodDefault<z.ZodBoolean>;
@@ -76,5 +78,13 @@ export declare const getCompoundDetails: import("@cyanheads/mcp-ts-core").ToolDe
             meshClasses: z.ZodArray<z.ZodString>;
         }, z.core.$strip>>;
     }, z.core.$strip>>;
-}, z.core.$strip>, undefined, undefined>;
+}, z.core.$strip>, undefined, {
+    readonly enrichedCids: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+    readonly skippedCids: z.ZodOptional<z.ZodArray<z.ZodNumber>>;
+    readonly synonymOffset: z.ZodOptional<z.ZodNumber>;
+    readonly nextSynonymOffset: z.ZodOptional<z.ZodNumber>;
+    readonly descriptionOffset: z.ZodOptional<z.ZodNumber>;
+    readonly nextDescriptionOffset: z.ZodOptional<z.ZodNumber>;
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
 //# sourceMappingURL=get-compound-details.tool.d.ts.map

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"get-compound-details.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-details.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAmHjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAijB7B,CAAC"}

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

@@ -93,10 +93,16 @@ function computeDrugLikeness(properties) {
         veber: { rotatableBonds, tpsa, violations: veberViolations },
     };
 }
+/**
+ * PUG View is a per-CID endpoint, so descriptions and classification fan out one request per
+ * compound. The batch accepts up to 100 CIDs; this bounds that fan-out. CIDs past it come back
+ * without descriptions or classification — disclosed via enrichment (#40).
+ */
+const PUG_VIEW_CID_CAP = 10;
 // ── Tool definition ────────────────────────────────────────────────────
 export const getCompoundDetails = tool('pubchem_get_compound_details', {
     title: 'Get Compound Details',
-    description: 'Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), all known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Accepts up to 100 CIDs per call.',
+    description: 'Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Accepts up to 100 CIDs per call.',
     annotations: {
         readOnlyHint: true,
         idempotentHint: true,
@@ -115,25 +121,37 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
         includeDescription: z
             .boolean()
             .default(false)
-            .describe('Include textual descriptions (pharmacology, mechanism, therapeutic use) attributed by source. Well-studied compounds have many overlapping summaries — capped via maxDescriptions. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without descriptions.'),
+            .describe(`Include textual descriptions (pharmacology, mechanism, therapeutic use) attributed by source. Well-studied compounds have many overlapping summaries — paged via descriptionOffset/maxDescriptions. Fetched only for the first ${PUG_VIEW_CID_CAP} CIDs in the batch; remaining CIDs return without descriptions and are listed in the response's skippedCids.`),
+        descriptionOffset: z
+            .number()
+            .int()
+            .min(0)
+            .default(0)
+            .describe("Zero-based index of the first description to return within each compound's description list. The same offset is applied to every compound in the batch. Pass the nextDescriptionOffset from a previous call to read the following page. Default: 0."),
         maxDescriptions: z
             .number()
             .int()
             .min(1)
             .max(20)
             .default(3)
-            .describe('Max number of distinct description entries per compound (1-20). PubChem returns near-duplicate summaries from many depositors; duplicates are collapsed before this cap applies. Default: 3.'),
+            .describe('Max number of distinct description entries per compound per page (1-20). PubChem returns near-duplicate summaries from many depositors; duplicates are collapsed before this cap applies. Default: 3.'),
         includeSynonyms: z
             .boolean()
             .default(false)
-            .describe('Fetch all known names and synonyms (trade names, systematic names, registry numbers). Slower for large CID lists.'),
+            .describe('Fetch known names and synonyms (trade names, systematic names, registry numbers), paged via synonymOffset/maxSynonyms. Fetched for every found CID in the batch. Slower for large CID lists.'),
+        synonymOffset: z
+            .number()
+            .int()
+            .min(0)
+            .default(0)
+            .describe("Zero-based index of the first synonym to return within each compound's synonym list. The same offset is applied to every compound in the batch. Pass the nextSynonymOffset from a previous call to read the following page. Default: 0."),
         maxSynonyms: z
             .number()
             .int()
             .min(1)
             .max(100)
             .default(20)
-            .describe('Max synonyms returned per compound (1-100). PubChem lists hundreds for common drugs; capped to keep the response focused. Default: 20.'),
+            .describe('Max synonyms returned per compound per page (1-100). PubChem lists hundreds for common drugs; use synonymOffset to reach the ones past this page. Default: 20.'),
         includeDrugLikeness: z
             .boolean()
             .default(false)
@@ -141,7 +159,7 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
         includeClassification: z
             .boolean()
             .default(false)
-            .describe('Include pharmacological classification: FDA Established Pharmacologic Classes, mechanisms of action, MeSH classes, and ATC codes. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without classification.'),
+            .describe(`Include pharmacological classification: FDA Established Pharmacologic Classes, mechanisms of action, MeSH classes, and ATC codes. Fetched only for the first ${PUG_VIEW_CID_CAP} CIDs in the batch; remaining CIDs return without classification and are listed in the response's skippedCids.`),
     }),
     output: z.object({
         compounds: z
@@ -165,16 +183,19 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
             })
                 .describe('Description entry with optional source attribution.'))
                 .optional()
-                .describe('Textual descriptions, deduplicated and capped at maxDescriptions. Each entry carries optional source attribution.'),
+                .describe('Textual descriptions on this page, deduplicated then windowed by descriptionOffset/maxDescriptions. Each entry carries optional source attribution. Empty when descriptionOffset runs past descriptionsTotal.'),
             descriptionsTotal: z
                 .number()
                 .optional()
-                .describe('Total distinct descriptions available before truncation. Larger than descriptions.length when more sources exist — increase maxDescriptions to see them.'),
-            synonyms: z.array(z.string()).optional().describe('Known names and synonyms.'),
+                .describe('Total distinct descriptions available for this compound, across all pages. Larger than descriptions.length when more sources exist — raise maxDescriptions or page with descriptionOffset to see them.'),
+            synonyms: z
+                .array(z.string())
+                .optional()
+                .describe('Known names and synonyms on this page, windowed by synonymOffset/maxSynonyms. Empty when synonymOffset runs past synonymsTotal.'),
             synonymsTotal: z
                 .number()
                 .optional()
-                .describe('Total synonyms available before truncation. Larger than synonyms.length when more exist — increase maxSynonyms to see them.'),
+                .describe('Total synonyms available for this compound, across all pages. Larger than synonyms.length when more exist — raise maxSynonyms or page with synonymOffset to see them.'),
             drugLikeness: drugLikenessSchema
                 .optional()
                 .describe('Drug-likeness assessment. lipinski.violations ≤ 1 and veber.violations = 0 → pass.'),
@@ -185,6 +206,54 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
             .describe('Per-CID compound detail record.'))
             .describe('Compound detail records.'),
     }),
+    // Agent-facing context for the two things a per-compound record cannot say on its own:
+    // which CIDs the PUG View fan-out reached (#40), and where the synonym/description windows
+    // sit within each compound's full list (#38). Both are batch-wide — one offset and one cap
+    // apply to every compound — so they belong here rather than repeated per record. Reaches
+    // structuredContent and content[]; keys disjoint from output (compounds lives there).
+    //
+    // A full page is exactly maxSynonyms/maxDescriptions long, so one nextOffset serves every
+    // compound that still has entries left, whatever its individual total.
+    enrichment: {
+        enrichedCids: z
+            .array(z.number())
+            .optional()
+            .describe('CIDs whose descriptions and classification were fetched. Present only when the batch exceeded the per-call fan-out limit and other CIDs were skipped.'),
+        skippedCids: z
+            .array(z.number())
+            .optional()
+            .describe('CIDs found in PubChem whose descriptions and classification were NOT fetched because the batch exceeded the per-call fan-out limit. Their absence from a record means "not requested", not "PubChem has none" — re-request these CIDs in a follow-up call. Present only when CIDs were skipped.'),
+        synonymOffset: z
+            .number()
+            .optional()
+            .describe("Zero-based index of the first synonym returned within each compound's list. Present when includeSynonyms is true."),
+        nextSynonymOffset: z
+            .number()
+            .optional()
+            .describe('synonymOffset to pass on the next call to continue past this page. Omitted when no compound in the batch has further synonyms.'),
+        descriptionOffset: z
+            .number()
+            .optional()
+            .describe("Zero-based index of the first description returned within each compound's list. Present when includeDescription is true."),
+        nextDescriptionOffset: z
+            .number()
+            .optional()
+            .describe('descriptionOffset to pass on the next call to continue past this page. Omitted when no compound in the batch has further descriptions.'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Recovery guidance covering the skipped CIDs, an offset that runs past every compound, and pages that remain. Absent when nothing was skipped or truncated.'),
+    },
+    // Both fields are optional, so `render` sees `number[] | undefined` at the type level; the
+    // framework only calls it for a populated field.
+    enrichmentTrailer: {
+        enrichedCids: {
+            render: (cids) => `**Descriptions/classification fetched for:** CID ${(cids ?? []).join(', ')}`,
+        },
+        skippedCids: {
+            render: (cids) => `**Descriptions/classification skipped for:** CID ${(cids ?? []).join(', ')}`,
+        },
+    },
     async handler(input, ctx) {
         const client = getPubChemClient();
         const requestedProps = input.properties ?? [...DEFAULT_PROPERTIES];
@@ -207,12 +276,14 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 return false;
             return Object.keys(row).some((k) => k !== 'CID');
         };
-        // PUG View calls (per-CID, capped at 10) — skip CIDs that aren't in PubChem
+        // PUG View calls (per-CID, capped) — skip CIDs that aren't in PubChem
         const foundCids = input.cids.filter(isFound);
-        const viewCids = foundCids.slice(0, 10);
-        if ((input.includeDescription || input.includeClassification) &&
-            viewCids.length < foundCids.length) {
-            ctx.log.info('PUG View fetch capped at 10 CIDs', {
+        const viewCids = foundCids.slice(0, PUG_VIEW_CID_CAP);
+        const skippedViewCids = foundCids.slice(PUG_VIEW_CID_CAP);
+        const viewCapEngaged = (input.includeDescription || input.includeClassification) && skippedViewCids.length > 0;
+        if (viewCapEngaged) {
+            ctx.log.info('PUG View fetch capped', {
+                cap: PUG_VIEW_CID_CAP,
                 requested: foundCids.length,
                 fetching: viewCids.length,
             });
@@ -251,12 +322,12 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 return compound;
             const allDescs = descMap?.get(cid);
             if (allDescs && allDescs.length > 0) {
-                compound.descriptions = allDescs.slice(0, input.maxDescriptions);
+                compound.descriptions = allDescs.slice(input.descriptionOffset, input.descriptionOffset + input.maxDescriptions);
                 compound.descriptionsTotal = allDescs.length;
             }
             const syns = synMap?.get(cid);
             if (syns) {
-                compound.synonyms = syns.slice(0, input.maxSynonyms);
+                compound.synonyms = syns.slice(input.synonymOffset, input.synonymOffset + input.maxSynonyms);
                 compound.synonymsTotal = syns.length;
             }
             if (input.includeDrugLikeness)
@@ -266,6 +337,40 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 compound.classification = cls;
             return compound;
         });
+        const notices = [];
+        // #40 — the PUG View fan-out cap is otherwise invisible: a capped-out CID looks exactly
+        // like a compound PubChem has no description for.
+        if (viewCapEngaged) {
+            ctx.enrich({ enrichedCids: viewCids, skippedCids: skippedViewCids });
+            notices.push(`Descriptions and classification were fetched for the first ${viewCids.length} of ${foundCids.length} found CIDs (limit: ${PUG_VIEW_CID_CAP} per call). CID ${skippedViewCids.join(', ')} returned without them — re-request those CIDs in a follow-up call.`);
+        }
+        if (input.includeSynonyms) {
+            const page = listPage([...(synMap?.values() ?? [])].map((s) => s.length), input.synonymOffset, input.maxSynonyms);
+            ctx.enrich({ synonymOffset: input.synonymOffset });
+            if (page.hasMore)
+                ctx.enrich({ nextSynonymOffset: page.nextOffset });
+            if (page.allEmpty) {
+                notices.push(`synonymOffset ${input.synonymOffset} is past every compound in this batch — the longest synonym list has ${page.largestTotal} entries. Pass a synonymOffset below ${page.largestTotal}.`);
+            }
+            else if (page.hasMore) {
+                notices.push(`More synonyms remain — pass synonymOffset=${page.nextOffset} to continue.`);
+            }
+        }
+        if (input.includeDescription) {
+            const page = listPage([...(descMap?.values() ?? [])].map((d) => d.length), input.descriptionOffset, input.maxDescriptions);
+            ctx.enrich({ descriptionOffset: input.descriptionOffset });
+            if (page.hasMore)
+                ctx.enrich({ nextDescriptionOffset: page.nextOffset });
+            if (page.allEmpty) {
+                notices.push(`descriptionOffset ${input.descriptionOffset} is past every compound in this batch — the longest description list has ${page.largestTotal} entries. Pass a descriptionOffset below ${page.largestTotal}.`);
+            }
+            else if (page.hasMore) {
+                notices.push(`More descriptions remain — pass descriptionOffset=${page.nextOffset} to continue.`);
+            }
+        }
+        // One notice field, so the sources are composed rather than overwriting one another.
+        if (notices.length > 0)
+            ctx.enrich.notice(notices.join(' '));
         return { compounds };
     },
     format(result) {
@@ -391,7 +496,12 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 }
                 blocks.push(lines.join('\n'));
             }
-            // Descriptions (with source attribution; truncated to maxDescriptions)
+            // An empty list with a non-zero total means the offset ran past this compound —
+            // distinct from having no descriptions at all, which omits the field entirely.
+            if (c.descriptions?.length === 0) {
+                blocks.push(`\n**Descriptions** (${c.descriptionsTotal ?? 0} total): none at this descriptionOffset`);
+            }
+            // Descriptions (with source attribution; windowed by descriptionOffset/maxDescriptions)
             if (c.descriptions && c.descriptions.length > 0) {
                 const total = c.descriptionsTotal ?? c.descriptions.length;
                 const shown = c.descriptions.length;
@@ -409,15 +519,18 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 }
                 const more = total - shown;
                 if (more > 0) {
-                    descLines.push(`_+${more} more description${more === 1 ? '' : 's'} from other sources — increase maxDescriptions to see them._`);
+                    descLines.push(`_+${more} more description${more === 1 ? '' : 's'} from other sources — raise maxDescriptions or page with descriptionOffset to see them._`);
                 }
                 blocks.push(descLines.join('\n\n'));
             }
-            // Synonyms (capped at maxSynonyms in the handler; total reported)
+            if (c.synonyms?.length === 0) {
+                blocks.push(`\n**Synonyms** (${c.synonymsTotal ?? 0} total): none at this synonymOffset`);
+            }
+            // Synonyms (windowed by synonymOffset/maxSynonyms in the handler; total reported)
             if (c.synonyms && c.synonyms.length > 0) {
                 const total = c.synonymsTotal ?? c.synonyms.length;
                 const more = total - c.synonyms.length;
-                const suffix = more > 0 ? ` (+${more} more)` : '';
+                const suffix = more > 0 ? ` (+${more} more not on this page)` : '';
                 /**
                  * Pipe-separated: CAS-style inverted names ("Benzoic acid, 2-(acetyloxy)-") carry
                  * their own ", ", which would split one synonym into two. " | " is this formatter's
@@ -434,6 +547,19 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
         return [{ type: 'text', text: blocks.join('\n') }];
     },
 });
+/**
+ * Batch-wide page state for one of the per-compound lists. `totals` holds each compound's
+ * full list length; a page is windowed at the same offset and cap for every compound.
+ */
+function listPage(totals, offset, cap) {
+    const largestTotal = totals.reduce((max, t) => Math.max(max, t), 0);
+    return {
+        allEmpty: largestTotal > 0 && totals.every((t) => t <= offset),
+        hasMore: totals.some((t) => t > offset + cap),
+        largestTotal,
+        nextOffset: offset + cap,
+    };
+}
 function formatRules(rules) {
     return rules
         .map(([label, r]) => {

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

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts CHANGED Viewed

@@ -10,6 +10,7 @@ export declare const getCompoundInteractions: import("@cyanheads/mcp-ts-core").T
         "drug-food": "drug-food";
         target: "target";
     }>>>;
+    offset: z.ZodDefault<z.ZodNumber>;
     maxEntries: z.ZodDefault<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     cid: z.ZodNumber;
@@ -23,9 +24,22 @@ export declare const getCompoundInteractions: import("@cyanheads/mcp-ts-core").T
         source: z.ZodString;
         text: z.ZodString;
     }, z.core.$strip>>;
+    paging: z.ZodArray<z.ZodObject<{
+        kind: z.ZodEnum<{
+            "drug-drug": "drug-drug";
+            "drug-food": "drug-food";
+            target: "target";
+        }>;
+        returnedCount: z.ZodNumber;
+        totalRecords: z.ZodNumber;
+        nextOffset: z.ZodOptional<z.ZodNumber>;
+        truncated: z.ZodBoolean;
+    }, z.core.$strip>>;
 }, z.core.$strip>, undefined, {
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     readonly returnedCount: z.ZodNumber;
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+    readonly nextOffset: z.ZodOptional<z.ZodNumber>;
     readonly failedKinds: z.ZodOptional<z.ZodString>;
     readonly notice: z.ZodOptional<z.ZodString>;
 }>;

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

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