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

@@ -8,7 +8,7 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
 export const searchAssays = tool('pubchem_search_assays', {
     title: 'Search Assays',
-    description: 'Find PubChem bioassays associated with a biological target. Search by gene symbol (e.g. "EGFR"), protein name, NCBI Gene ID, or UniProt accession. Returns assay IDs (AIDs) which can be explored further with pubchem_get_summary.',
+    description: 'Find PubChem bioassays associated with a biological target. Search by gene symbol (e.g. "EGFR"), protein name, NCBI Gene ID, or UniProt accession. Returns a page of assay IDs (AIDs) — page past maxResults with offset — which can be explored further with pubchem_get_summary.',
     annotations: {
         readOnlyHint: true,
         idempotentHint: true,
@@ -21,34 +21,43 @@ export const searchAssays = tool('pubchem_search_assays', {
         targetQuery: z
             .string()
             .describe('Target identifier. Examples: "EGFR" (genesymbol), "Epidermal growth factor receptor" (proteinname), "1956" (geneid), "P00533" (proteinaccession).'),
+        offset: z
+            .number()
+            .int()
+            .min(0)
+            .default(0)
+            .describe('Zero-based index of the first AID to return. Pass the nextOffset from a previous call to read the following page. Default: 0.'),
         maxResults: z
             .number()
             .min(1)
             .max(200)
             .default(50)
-            .describe('Max AIDs to return (1-200). Popular targets may have thousands of assays. Default: 50.'),
+            .describe('Max AIDs to return per page (1-200). Popular targets may have thousands of assays; use offset to reach the ones past this page. Default: 50.'),
     }),
     output: z.object({
         aids: z.array(z.number()).describe('PubChem Assay IDs.'),
     }),
-    // Agent-facing context — target echo, total before cap, and an empty-result notice.
+    // Agent-facing context — target echo, the total across all pages, the page boundary, and a
+    // notice distinguishing "no match" from "offset past the end".
     // Reaches structuredContent and content[] automatically; not in the domain return.
     enrichment: {
         targetType: z
             .string()
             .describe('Target identifier type used: genesymbol, proteinname, geneid, or proteinaccession.'),
         targetQuery: z.string().describe('Target identifier searched.'),
-        totalFound: z.number().describe('Total AIDs found before the maxResults cap.'),
-        truncated: z
-            .boolean()
+        totalFound: z.number().describe('Total AIDs found for this target, across all pages.'),
+        offset: z.number().describe('Zero-based index of the first AID returned.'),
+        nextOffset: z
+            .number()
             .optional()
-            .describe('True when AIDs were capped at maxResults — more assays exist than returned.'),
-        shown: z.number().optional().describe('AIDs returned after the maxResults cap.'),
+            .describe('Offset to pass on the next call to continue past this page. Omitted when no further AIDs match.'),
+        truncated: z.boolean().optional().describe('True when matching AIDs remain past this page.'),
+        shown: z.number().optional().describe('AIDs returned on this page.'),
         cap: z.number().optional().describe('The maxResults cap that was applied.'),
         notice: z
             .string()
             .optional()
-            .describe('Recovery guidance when no assays matched — echoes the target and suggests alternative search types. Absent when assays were returned.'),
+            .describe('Recovery guidance when no assays matched, when the offset runs past the result set, or when further pages remain. Absent when this page is complete and non-empty.'),
     },
     errors: [
         {
@@ -80,20 +89,34 @@ export const searchAssays = tool('pubchem_search_assays', {
         }
         const allAids = await client.searchAssaysByTarget(input.targetType, targetQuery);
         const totalFound = allAids.length;
-        const aids = allAids.slice(0, input.maxResults);
+        // Offset is applied client-side: PubChem's target-to-AID endpoint returns the whole AID
+        // list in one response, so searchAssaysByTarget already holds every match.
+        const aids = allAids.slice(input.offset, input.offset + input.maxResults);
+        const nextOffset = input.offset + aids.length;
+        const hasMore = nextOffset < totalFound;
         ctx.log.info('Assay search completed', {
             targetType: input.targetType,
             targetQuery,
             totalFound,
+            offset: input.offset,
             returned: aids.length,
         });
-        // Agent-facing context: target echo, total, and empty-result notice.
-        ctx.enrich({ targetType: input.targetType, targetQuery, totalFound });
-        if (aids.length === 0) {
+        // Agent-facing context: target echo, total, page boundary, and recovery notices.
+        ctx.enrich({ targetType: input.targetType, targetQuery, totalFound, offset: input.offset });
+        if (hasMore)
+            ctx.enrich({ nextOffset });
+        if (totalFound === 0) {
             ctx.enrich.notice(`No assays found for "${targetQuery}" (${input.targetType}). Try a different targetType (e.g. switch from proteinname to genesymbol), verify the identifier spelling, or use pubchem_get_summary for gene/protein entity lookups.`);
         }
-        else if (totalFound > aids.length) {
-            ctx.enrich.truncated({ shown: aids.length, cap: input.maxResults });
+        else if (aids.length === 0) {
+            ctx.enrich.notice(`offset ${input.offset} is past the ${totalFound} AID(s) found for "${targetQuery}". Pass an offset below ${totalFound}.`);
+        }
+        else if (hasMore) {
+            ctx.enrich.truncated({
+                shown: aids.length,
+                cap: input.maxResults,
+                guidance: `Showing AIDs ${input.offset + 1}-${nextOffset} of ${totalFound}. Pass offset=${nextOffset} for the next page.`,
+            });
         }
         return { aids };
     },
@@ -101,7 +124,9 @@ export const searchAssays = tool('pubchem_search_assays', {
         if (result.aids.length > 0) {
             return [{ type: 'text', text: `AIDs: ${result.aids.join(', ')}` }];
         }
-        return [{ type: 'text', text: 'No assays found.' }];
+        // Neutral wording: an empty page is either "no match" or "offset past the end" — the
+        // enrichment trailer's notice says which.
+        return [{ type: 'text', text: 'No assays returned.' }];
     },
 });
 //# sourceMappingURL=search-assays.tool.js.map

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

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts CHANGED Viewed

@@ -27,6 +27,7 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
         smiles: "smiles";
     }>>;
     threshold: z.ZodDefault<z.ZodNumber>;
+    offset: z.ZodDefault<z.ZodNumber>;
     maxResults: z.ZodDefault<z.ZodNumber>;
     properties: z.ZodOptional<z.ZodArray<z.ZodEnum<{
         [x: string]: string;
@@ -62,6 +63,8 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
     readonly searchType: z.ZodString;
     readonly totalFound: z.ZodOptional<z.ZodNumber>;
     readonly totalFoundAtLeast: z.ZodOptional<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/search-compounds.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/search-compounds.tool.js CHANGED Viewed

@@ -19,7 +19,7 @@ const queryTypeEnum = z.enum(['smiles', 'cid']);
 const propertyEnum = z.enum(COMPOUND_PROPERTIES);
 export const searchCompounds = tool('pubchem_search_compounds', {
     title: 'Search Compounds',
-    description: 'Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, batched up to 25), molecular formula in Hill notation, substructure or superstructure containment, or 2D Tanimoto similarity. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.',
+    description: 'Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, batched up to 25), molecular formula in Hill notation, substructure or superstructure containment, or 2D Tanimoto similarity. Returns a page of CIDs — reach matches past maxResults with offset. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.',
     annotations: {
         readOnlyHint: true,
         idempotentHint: true,
@@ -60,12 +60,19 @@ export const searchCompounds = tool('pubchem_search_compounds', {
             .max(100)
             .default(90)
             .describe('Similarity search only. Minimum Tanimoto similarity (70-100). 90+ for close analogs, 70-80 for scaffold hops. Default: 90.'),
+        offset: z
+            .number()
+            .int()
+            .min(0)
+            .max(10000)
+            .default(0)
+            .describe('Zero-based index of the first CID to return. Pass the nextOffset from a previous call to read the following page. Identifier lookups resolve every match up front, so paging them is free; formula, substructure, superstructure, and similarity searches have to ask PubChem for offset + maxResults records to reach a page, so deep pages cost progressively more upstream — hence the 10000 ceiling. Default: 0.'),
         maxResults: z
             .number()
             .min(1)
             .max(200)
             .default(20)
-            .describe('Maximum CIDs to return (1-200). Default: 20.'),
+            .describe('Maximum CIDs to return per page (1-200). Use offset to reach matches past this page. Default: 20.'),
         properties: z
             .array(propertyEnum)
             .optional()
@@ -92,8 +99,9 @@ export const searchCompounds = tool('pubchem_search_compounds', {
             .optional()
             .describe('Identifier-mode only: input identifiers that resolved to no CID. Omitted when every identifier resolved and for non-identifier searches.'),
     }),
-    // Agent-facing context — search strategy echo, total before cap, and an empty-result
-    // notice. Reaches structuredContent and content[] automatically; not in the domain return.
+    // Agent-facing context — search strategy echo, total, the page boundary, and a notice
+    // covering unresolved identifiers, an empty page, and further pages. 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
@@ -108,21 +116,23 @@ export const searchCompounds = tool('pubchem_search_compounds', {
         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.'),
+            .describe('Exact number of matching CIDs across all pages. Omitted when a formula, substructure, superstructure, or similarity search saturated the records it requested — 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()
+            .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; page further with offset to observe more.'),
+        offset: z.number().describe('Zero-based index of the first CID returned.'),
+        nextOffset: z
+            .number()
             .optional()
-            .describe('True when CIDs were capped at maxResults — more matches exist than returned.'),
-        shown: z.number().optional().describe('CIDs returned after the maxResults cap.'),
+            .describe('Offset to pass on the next call to continue past this page. Omitted when no further matches remain.'),
+        truncated: z.boolean().optional().describe('True when matching CIDs remain past this page.'),
+        shown: z.number().optional().describe('CIDs returned on this page.'),
         cap: z.number().optional().describe('The maxResults cap that was applied.'),
         notice: z
             .string()
             .optional()
-            .describe('Recovery guidance when no compounds matched — echoes search strategy and suggests how to broaden. Absent when results were returned.'),
+            .describe('Recovery guidance when no compounds matched, when the offset runs past the matches observed, when identifiers failed to resolve, or when further pages remain. Absent when this page is complete and every identifier resolved.'),
     },
     errors: [
         {
@@ -153,10 +163,12 @@ 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;
+        // Formula and structure searches are bounded server-side. One record past the requested
+        // page 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. The window has to cover
+        // the offset too — these endpoints take a record count, not a start position, and their
+        // ordering is a stable prefix, so reaching page N means asking for everything up to it.
+        const recordCap = input.offset + input.maxResults + 1;
         let boundedSearch = false;
         const identifierMap = new Map();
         // Identifier-mode resolution tracking (#29): inputs that resolved to no CID, and
@@ -243,23 +255,33 @@ export const searchCompounds = tool('pubchem_search_compounds', {
                 break;
             }
         }
-        // Deduplicate and cap
+        // Deduplicate, then take the requested page.
         const uniqueCids = [...new Set(allCids)];
         const observedTotal = uniqueCids.length;
-        const cappedCids = uniqueCids.slice(0, input.maxResults);
+        const pagedCids = uniqueCids.slice(input.offset, input.offset + 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;
+        // The stride comes from the page that was returned, never from maxResults — that input
+        // accepts a fractional value, which would emit a nextOffset this tool's own integer
+        // offset validator then rejects.
+        const nextOffset = input.offset + pagedCids.length;
+        // A saturated bounded search proved a record beyond the window it asked for, so more
+        // remain even though observedTotal cannot say how many.
+        const hasMore = !totalIsExact || nextOffset < observedTotal;
         ctx.log.info('Search completed', {
             searchType: input.searchType,
             observedTotal,
             totalIsExact,
-            returned: cappedCids.length,
+            offset: input.offset,
+            returned: pagedCids.length,
         });
-        // Agent-facing context: search strategy echo, total, and empty-result notice.
+        // Agent-facing context: search strategy echo, total, page boundary, and notices.
         ctx.enrich(totalIsExact
-            ? { searchType: input.searchType, totalFound: observedTotal }
-            : { searchType: input.searchType, totalFoundAtLeast: observedTotal });
+            ? { searchType: input.searchType, totalFound: observedTotal, offset: input.offset }
+            : { searchType: input.searchType, totalFoundAtLeast: observedTotal, offset: input.offset });
+        if (hasMore)
+            ctx.enrich({ nextOffset });
         // 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 = [];
@@ -270,20 +292,30 @@ export const searchCompounds = tool('pubchem_search_compounds', {
         for (const c of collisions) {
             noticeParts.push(`Identifiers ${c.identifiers.join(', ')} all resolved to CID ${c.cid}; the result row echoes only "${identifierMap.get(c.cid)}" for it.`);
         }
-        if (cappedCids.length === 0) {
-            ctx.enrich.notice(noticeParts.length > 0
-                ? 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.`);
+        if (pagedCids.length === 0) {
+            // An empty page is either "nothing matched" or "the offset ran past the matches" —
+            // say which, and name the bound the caller can page back inside.
+            if (observedTotal === 0) {
+                if (noticeParts.length === 0) {
+                    noticeParts.push(`No compounds matched the ${input.searchType} search. Try a different identifier, broaden the formula, lower the similarity threshold, or verify the SMILES/CID.`);
+                }
+            }
+            else {
+                // Reachable only with an exact total: a saturated bounded search observed
+                // offset + maxResults + 1 records, so its page is never empty.
+                noticeParts.push(`offset ${input.offset} is past the ${observedTotal} match(es) found. Pass an offset below ${observedTotal}.`);
+            }
+            ctx.enrich.notice(noticeParts.join(' '));
         }
-        else if (observedTotal > cappedCids.length) {
+        else if (hasMore) {
             // Truncated: fold any identifier notice into the truncation guidance (notice is
             // last-wins, so compose rather than emit two). Without an exact total there is no
-            // "of N" to quote — say more exist and stop.
+            // "of N" to quote — say more exist, and still hand over the next offset.
             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.`;
+                ? `Showing matches ${input.offset + 1}-${nextOffset} of ${observedTotal}. Pass offset=${nextOffset} for the next page.`
+                : `Showing matches ${input.offset + 1}-${nextOffset}; more exist, but PubChem reports no match count for a ${input.searchType} search. Pass offset=${nextOffset} for the next page.`;
             ctx.enrich.truncated({
-                shown: cappedCids.length,
+                shown: pagedCids.length,
                 cap: input.maxResults,
                 guidance: noticeParts.length > 0
                     ? `${noticeParts.join(' ')} ${truncationGuidance}`
@@ -295,11 +327,11 @@ export const searchCompounds = tool('pubchem_search_compounds', {
         }
         // Optionally hydrate with properties
         let propsMap;
-        if (input.properties && input.properties.length > 0 && cappedCids.length > 0) {
-            const rows = await client.getProperties(cappedCids, input.properties);
+        if (input.properties && input.properties.length > 0 && pagedCids.length > 0) {
+            const rows = await client.getProperties(pagedCids, input.properties);
             propsMap = new Map(rows.map((r) => [r.CID, r]));
         }
-        const results = cappedCids.map((cid) => {
+        const results = pagedCids.map((cid) => {
             const result = { cid };
             const identifier = identifierMap.get(cid);
             if (identifier)

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

@@ -73,10 +73,11 @@ export declare class PubChemClient {
     searchAssaysByTarget(targetType: string, query: string): Promise<number[]>;
     getEntitySummary(entityType: string, identifier: string | number): Promise<Record<string, unknown> | null>;
     /** Fetch drug-drug, drug-food, and/or chemical-target interactions for a compound.
-     * Drug-drug and target data live in PubChem SDQ external tables (drugbankddi,
-     * consolidatedcompoundtarget); drug-food is inline PUG View text. Each kind is capped
-     * at maxEntries; absent data for a kind contributes nothing rather than erroring. */
-    getInteractions(cid: number, kinds: Array<'drug-drug' | 'drug-food' | 'target'>, maxEntries: number): Promise<InteractionsResult>;
+     * Drug-drug and target data live in PubChem SDQ external tables (drugbankddi, bioactivity);
+     * drug-food is inline PUG View text. Each kind reads a window of `maxEntries` entries
+     * starting at `offset` records into that kind's own stream; absent data for a kind
+     * contributes an empty page rather than erroring. */
+    getInteractions(cid: number, kinds: Array<'drug-drug' | 'drug-food' | 'target'>, maxEntries: number, offset: number): Promise<InteractionsResult>;
     private getInteractionsForKind;
     private getDrugDrugInteractions;
     /** Chemical-target binding/activity from PubChem's `bioactivity` SDQ collection (BindingDB,
@@ -84,15 +85,35 @@ export declare class PubChemClient {
      * compound; the `consolidatedcompoundtarget` collection used previously is gene-indexed, so
      * its `cid` filter was silently ignored — every CID returned the same default compound (#20).
      * Only rows naming a molecular target are returned; untargeted assay outcomes are the domain
-     * of pubchem_get_bioactivity. */
+     * of pubchem_get_bioactivity.
+     *
+     * Because most rows are dropped, the page position is an index into the activity records, not
+     * into the entries returned — the walk records exactly how many rows it read so the next page
+     * resumes at the first unread one. */
     private getTargetInteractions;
     private getDrugFoodInteractions;
     /** Query a PubChem SDQ external table for a single CID, projecting only the columns the
      * caller maps. Projection keeps payloads small and excludes the free-text `citations` column
-     * whose unescaped quotes make PubChem emit invalid JSON (#20). Returns [] on not-found; on an
-     * unparseable body throws a contextful error rather than the bare `Failed to parse JSON`, so
-     * the caller and per-kind isolation can report it cleanly. */
+     * whose unescaped quotes make PubChem emit invalid JSON (#20).
+     *
+     * Uses SDQ's `select` projection rather than `download`: the `SDQOutputSet` envelope it
+     * answers with carries `totalCount` — the records matching the query across all pages —
+     * beside the requested window, which is the only way to tell a full page from the last one.
+     * `start` is 1-based upstream; `offset` here is zero-based like every other paging input.
+     *
+     * Returns an empty page on not-found. A rejected query is reported, never read as "no data":
+     * SDQ answers a malformed query with a 5xx that the shared HTTP core already classifies and
+     * throws, and the `status.error` check covers the same rejection arriving inside a 2xx body.
+     * An unparseable body throws with the collection and a body snippet attached, so per-kind
+     * isolation can name what failed. */
     private fetchSdq;
+    /** Resolve a kind's record total for the page just fetched.
+     *
+     * SDQ reports `totalCount` alongside every non-empty page, but a `start` past the last record
+     * answers `totalCount` 0 — so an offset that overshoots would otherwise report "no records"
+     * for a compound that has thousands. A one-row probe from the top recovers the real bound,
+     * and only runs on that case. */
+    private resolveSdqTotal;
     /** Fetch the default 3D conformer as raw V2000 SDF text. Throws a typed not-found when
      * PubChem has no computed 3D coordinates (large molecules, mixtures, undefined salts). */
     getSdf3d(cid: number): Promise<string>;

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

	@@ -1 +1 @@
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