npm - @cyanheads/pubchem-mcp-server - Versions diffs - 0.5.1 → 0.5.2 - Mend

@cyanheads/pubchem-mcp-server 0.5.1 → 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 (21) hide show

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

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

@@ -908,19 +908,25 @@ export class PubChemClient {
     }
     // ── Interactions ────────────────────────────────────────────────
     /** 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. */
-    async getInteractions(cid, kinds, maxEntries) {
+     * 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. */
+    async getInteractions(cid, kinds, maxEntries, offset) {
         // Per-kind isolation: a failure in one source (upstream parse error, timeout, network)
         // must not discard the kinds that succeeded. Failures are reported, not thrown (#21).
-        const settled = await Promise.allSettled(kinds.map((kind) => this.getInteractionsForKind(cid, kind, maxEntries)));
+        // Page state is recorded per kind from that kind's own result, so a failing kind leaves
+        // the others' continuation signals untouched rather than zeroing them.
+        const settled = await Promise.allSettled(kinds.map((kind) => this.getInteractionsForKind(cid, kind, maxEntries, offset)));
         const entries = [];
+        const pages = [];
         const failedKinds = [];
         kinds.forEach((kind, i) => {
             const result = settled[i];
             if (result?.status === 'fulfilled') {
-                entries.push(...result.value);
+                const { entries: kindEntries, totalRecords, recordsConsumed } = result.value;
+                entries.push(...kindEntries);
+                pages.push({ kind, returnedCount: kindEntries.length, totalRecords, recordsConsumed });
             }
             else if (result?.status === 'rejected') {
                 const reason = result.reason;
@@ -930,20 +936,20 @@ export class PubChemClient {
                 });
             }
         });
-        return { entries, failedKinds };
+        return { entries, pages, failedKinds };
     }
-    getInteractionsForKind(cid, kind, maxEntries) {
+    getInteractionsForKind(cid, kind, maxEntries, offset) {
         switch (kind) {
             case 'drug-drug':
-                return this.getDrugDrugInteractions(cid, maxEntries);
+                return this.getDrugDrugInteractions(cid, maxEntries, offset);
             case 'drug-food':
-                return this.getDrugFoodInteractions(cid, maxEntries);
+                return this.getDrugFoodInteractions(cid, maxEntries, offset);
             case 'target':
-                return this.getTargetInteractions(cid, maxEntries);
+                return this.getTargetInteractions(cid, maxEntries, offset);
         }
     }
-    async getDrugDrugInteractions(cid, maxEntries) {
-        const rows = await this.fetchSdq('drugbankddi', cid, ['cid', 'name2', 'descr'], maxEntries);
+    async getDrugDrugInteractions(cid, maxEntries, offset) {
+        const { rows, totalCount } = await this.fetchSdq('drugbankddi', cid, ['cid', 'name2', 'descr'], maxEntries, offset);
         const entries = [];
         for (const row of rows) {
             const text = typeof row.descr === 'string' ? row.descr : '';
@@ -954,21 +960,35 @@ export class PubChemClient {
                 entry.partner = row.name2;
             entries.push(entry);
         }
-        return entries;
+        return {
+            entries,
+            totalRecords: await this.resolveSdqTotal('drugbankddi', cid, rows.length, totalCount, offset),
+            recordsConsumed: rows.length,
+        };
     }
     /** Chemical-target binding/activity from PubChem's `bioactivity` SDQ collection (BindingDB,
      * ChEMBL, and others). That collection is cid-keyed and scopes correctly to the requested
      * 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. */
-    async getTargetInteractions(cid, maxEntries) {
+     * 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. */
+    async getTargetInteractions(cid, maxEntries, offset) {
         // `targetname` is sparse (most rows are untargeted assay outcomes), so oversample and keep
         // the target-bearing rows, most-potent-first.
         const window = Math.min(Math.max(maxEntries * 4, 20), 100);
-        const rows = await this.fetchSdq('bioactivity', cid, ['cid', 'targetname', 'acname', 'acqualifier', 'acvalue', 'aidsrcname'], window, ['acvalue,asc']);
+        const { rows, totalCount } = await this.fetchSdq('bioactivity', cid, ['cid', 'targetname', 'acname', 'acqualifier', 'acvalue', 'aidsrcname'], window, offset, ['acvalue,asc']);
         const entries = [];
+        // Collapse duplicate measurements of the same target/value reported across assays.
+        const seen = new Set();
+        let recordsConsumed = 0;
         for (const row of rows) {
+            if (entries.length === maxEntries)
+                break;
+            recordsConsumed++;
             const target = typeof row.targetname === 'string' ? row.targetname.trim() : '';
             if (!target)
                 continue;
@@ -981,53 +1001,79 @@ export class PubChemClient {
             // assaysummary endpoint's "Activity Value [uM]" column. We assert that documented µM
             // convention here — it is not a per-row unit fetched from SDQ (none exists to fetch).
             const activity = acname && acvalue ? `${acname} ${qualifier} ${acvalue} uM`.replace(/\s+/g, ' ').trim() : '';
+            const text = activity || 'Activity reported';
+            const key = `${target}|${text}`;
+            if (seen.has(key))
+                continue;
+            seen.add(key);
             entries.push({
                 kind: 'target',
                 source: typeof row.aidsrcname === 'string' && row.aidsrcname ? row.aidsrcname : 'PubChem',
                 partner: target,
-                text: activity || 'Activity reported',
+                text,
             });
         }
-        // Collapse duplicate measurements of the same target/value reported across assays.
-        return dedupByKey(entries, (e) => `${e.partner ?? ''}|${e.text}`).slice(0, maxEntries);
+        return {
+            entries,
+            totalRecords: await this.resolveSdqTotal('bioactivity', cid, rows.length, totalCount, offset),
+            recordsConsumed,
+        };
     }
-    async getDrugFoodInteractions(cid, maxEntries) {
+    async getDrugFoodInteractions(cid, maxEntries, offset) {
+        const empty = { entries: [], totalRecords: 0, recordsConsumed: 0 };
         try {
             const data = await this.fetchJson(`${this.viewBase}/data/compound/${cid}/JSON?heading=Drug-Food+Interactions`);
             const sections = data.Record.Section;
             if (!sections)
-                return [];
+                return empty;
             const section = findSection(sections, 'Drug-Food Interactions');
             if (!section)
-                return [];
+                return empty;
             const refToSource = new Map();
             for (const ref of data.Record.Reference ?? []) {
                 refToSource.set(ref.ReferenceNumber, ref.SourceName);
             }
+            // PUG View returns the whole section inline, so the deduped item list is the complete
+            // record stream and the page is a plain slice of it.
             const items = dedupByKey(extractDescriptionItems(section), descriptionKey);
-            return items.slice(0, maxEntries).map((item) => {
-                const source = item.refNum != null ? refToSource.get(item.refNum) : undefined;
-                return { kind: 'drug-food', source: source ?? 'PubChem', text: item.text };
-            });
+            const page = items.slice(offset, offset + maxEntries);
+            return {
+                entries: page.map((item) => {
+                    const source = item.refNum != null ? refToSource.get(item.refNum) : undefined;
+                    return { kind: 'drug-food', source: source ?? 'PubChem', text: item.text };
+                }),
+                totalRecords: items.length,
+                recordsConsumed: page.length,
+            };
         }
         catch (error) {
             if (isNotFound(error))
-                return [];
+                return empty;
             throw error;
         }
     }
     /** 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. */
-    async fetchSdq(collection, cid, columns, limit, order) {
+     * 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. */
+    async fetchSdq(collection, cid, columns, limit, offset = 0, order) {
+        const empty = { rows: [], totalCount: 0 };
         const query = JSON.stringify({
-            download: columns,
+            select: columns,
             collection,
             where: { ands: [{ cid: String(cid) }] },
             ...(order ? { order } : {}),
-            start: 1,
+            start: offset + 1,
             limit,
         });
         const url = `${this.sdqBase}?infmt=json&outfmt=json&query=${encodeURIComponent(query)}`;
@@ -1037,16 +1083,35 @@ export class PubChemClient {
         }
         catch (error) {
             if (isNotFound(error))
-                return [];
+                return empty;
             throw error;
         }
+        let parsed;
         try {
-            const data = JSON.parse(body);
-            return Array.isArray(data) ? data : [];
+            parsed = JSON.parse(body);
         }
         catch {
             throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `PubChem SDQ returned unparseable JSON for collection "${collection}"`, { collection, cid, snippet: body.slice(0, 200) });
         }
+        const set = parsed.SDQOutputSet?.[0];
+        if (!set)
+            return empty;
+        if (set.status?.error) {
+            throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `PubChem SDQ rejected the query for collection "${collection}": ${set.status.error}`, { collection, cid, sdqError: set.status.error });
+        }
+        return { rows: set.rows ?? [], totalCount: set.totalCount ?? 0 };
+    }
+    /** 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. */
+    async resolveSdqTotal(collection, cid, rowsReturned, reportedTotal, offset) {
+        if (rowsReturned > 0 || offset === 0)
+            return reportedTotal;
+        const { totalCount } = await this.fetchSdq(collection, cid, ['cid'], 1);
+        return totalCount;
     }
     // ── 3D Structure ────────────────────────────────────────────────
     /** Fetch the default 3D conformer as raw V2000 SDF text. Throws a typed not-found when

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

	@@ -1 +1 @@
1	- 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package/dist/services/pubchem/types.d.ts CHANGED Viewed

@@ -102,6 +102,27 @@ export interface PugViewInformation {
         Boolean?: boolean[];
     };
 }
+/** Envelope returned by the SDQ agent for a `select` projection.
+ *
+ * `totalCount` is the number of records matching the query across all pages, independent of
+ * the `limit` window — with one exception: a `start` past the last record reports `totalCount`
+ * 0 alongside an `eNoHitsFound` warning, so an empty page cannot be read as a total.
+ *
+ * `status` separates a rejection from an absence. SDQ reports a malformed query as a 5xx
+ * carrying `status.error`, so an empty `rows` beside a populated `status.error` is a failure
+ * whatever the HTTP status was — while an empty `rows` under `status.code` 0 is a real absence. */
+export interface SdqResponse {
+    SDQOutputSet?: Array<{
+        status?: {
+            code?: number;
+            error?: string;
+            warning?: string[];
+        };
+        totalCount?: number;
+        collection?: string;
+        rows?: Array<Record<string, unknown>>;
+    }>;
+}
 /** Parsed GHS hazard classification */
 export interface GHSClassification {
     hazardStatements: Array<{
@@ -162,6 +183,33 @@ export interface InteractionEntry {
     /** The interaction statement. */
     text: string;
 }
+/** Where one interaction kind's page landed in that kind's source-record stream.
+ *
+ * Every kind is backed by an ordered stream of source records, and entries are derived from
+ * them: an SDQ row whose `targetname` is blank or whose `descr` is empty produces no entry, and
+ * duplicate measurements collapse within a page. So `returnedCount` counts entries while
+ * `totalRecords` and `recordsConsumed` count records, and the two are not interchangeable —
+ * paging divides the records, so a duplicate split across two pages survives on both. */
+export interface InteractionKindPage {
+    /** Interaction category this page covers. */
+    kind: 'drug-drug' | 'drug-food' | 'target';
+    /** Source records this page read, starting at the requested offset. The next page resumes
+     * at the first record it did not read. */
+    recordsConsumed: number;
+    /** Interaction entries this page produced. */
+    returnedCount: number;
+    /** Source records available for this kind, across all pages. */
+    totalRecords: number;
+}
+/** One kind's page: the entries it produced, plus where it landed in that kind's record
+ * stream. `getInteractions` turns this into an {@link InteractionKindPage} per kind. */
+export interface InteractionKindFetch {
+    entries: InteractionEntry[];
+    /** Source records this page read, starting at the requested offset. */
+    recordsConsumed: number;
+    /** Source records available for this kind, across all pages. */
+    totalRecords: number;
+}
 /** Result of a multi-kind interaction fetch. Kinds are fetched independently so a failure in
  * one (upstream parse error, timeout, network) never discards the kinds that succeeded. */
 export interface InteractionsResult {
@@ -172,6 +220,9 @@ export interface InteractionsResult {
         kind: string;
         message: string;
     }>;
+    /** Page state for each kind that resolved successfully, in the order requested. A kind
+     * present in `failedKinds` is absent here — its page state is unknown, not zero. */
+    pages: InteractionKindPage[];
 }
 /** A single atom in a 3D conformer (Cartesian coordinates, Angstroms). */
 export interface Sdf3DAtom {

package/dist/services/pubchem/types.d.ts.map CHANGED Viewed

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

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 {
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   "name": "pubchem-mcp-server",
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   "author": {
     "name": "cyanheads"

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
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+  "version": "0.5.2",
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