npm - @cyanheads/pubchem-mcp-server - Versions diffs - 0.2.4 → 0.3.1 - Mend

@cyanheads/pubchem-mcp-server 0.2.4 → 0.3.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (30) hide show

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![Version](https://img.shields.io/badge/Version-0.2.4-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-^6.0.3-3178C6.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-0.3.1-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-^6.0.3-3178C6.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/index.js CHANGED Viewed

@@ -13,7 +13,7 @@ await createApp({
     title: 'pubchem-mcp-server',
     tools: allToolDefinitions,
     resources: allResourceDefinitions,
-    instructions: "Use the pubchem_* tools to query PubChem's chemical database. Compounds are addressed by CID, assays by AID. Most flows start at `pubchem_search_compounds` (name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity → CIDs), then call per-CID tools for details, safety, image, cross-references, bioactivity, interactions (drug-drug/drug-food/target), or 3D structure. For bioassays by biological target, chain `pubchem_search_assays` (gene/protein → AIDs) into `pubchem_get_bioactivity`. `pubchem_get_summary` covers assay/gene/protein/taxonomy entity lookups. Compound and assay records are also exposed as URI-addressable resources (e.g. `pubchem://compound/{cid}`, `pubchem://assay/{aid}`).",
+    instructions: "Use the pubchem_* tools to query PubChem's chemical database. Compounds are addressed by CID, assays by AID. Most flows start at `pubchem_search_compounds` (name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity → CIDs), then call per-CID tools for details, safety, image, cross-references, bioactivity, interactions (drug-drug/drug-food/target), or 3D structure. To find assays for a biological target, chain `pubchem_search_assays` (gene/protein → AIDs) into `pubchem_get_summary` (`entityType: assay`) per AID; to check whether a compound is active against a target, call `pubchem_get_bioactivity` with a `cid` plus `targetGeneId`/`targetAccession`. `pubchem_get_summary` covers assay/gene/protein/taxonomy entity lookups. Compound and assay records are also exposed as URI-addressable resources (e.g. `pubchem://compound/{cid}`, `pubchem://assay/{aid}`).",
     landing: {
         tagline: 'Search PubChem for chemical compounds, properties, safety, bioactivity, and cross-references.',
         repoRoot: 'https://github.com/cyanheads/pubchem-mcp-server',

package/dist/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;GAIG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,sBAAsB,EAAE,MAAM,6CAA6C,CAAC;AACrF,OAAO,EAAE,kBAAkB,EAAE,MAAM,yCAAyC,CAAC;AAC7E,OAAO,EAAE,iBAAiB,EAAE,MAAM,sCAAsC,CAAC;AAEzE,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,oBAAoB;IAC1B,KAAK,EAAE,oBAAoB;IAC3B,KAAK,EAAE,kBAAkB;IACzB,SAAS,EAAE,sBAAsB;IACjC,YAAY,EACV,q3BAAq3B;IACv3B,OAAO,EAAE;QACP,OAAO,EACL,+FAA+F;QACjG,QAAQ,EAAE,iDAAiD;QAC3D,KAAK,EAAE;YACL,EAAE,KAAK,EAAE,SAAS,EAAE,IAAI,EAAE,mCAAmC,EAAE,QAAQ,EAAE,IAAI,EAAE;YAC/E;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;YACD;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;SACF;KACF;IACD,KAAK;QACH,iBAAiB,EAAE,CAAC;IACtB,CAAC;CACF,CAAC,CAAC"}

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

@@ -12,6 +12,7 @@ export declare const getCompoundDetails: import("@cyanheads/mcp-ts-core").ToolDe
     includeDescription: z.ZodDefault<z.ZodBoolean>;
     maxDescriptions: z.ZodDefault<z.ZodNumber>;
     includeSynonyms: z.ZodDefault<z.ZodBoolean>;
+    maxSynonyms: z.ZodDefault<z.ZodNumber>;
     includeDrugLikeness: z.ZodDefault<z.ZodBoolean>;
     includeClassification: z.ZodDefault<z.ZodBoolean>;
 }, z.core.$strip>, z.ZodObject<{
@@ -25,6 +26,7 @@ export declare const getCompoundDetails: import("@cyanheads/mcp-ts-core").ToolDe
         }, z.core.$strip>>>;
         descriptionsTotal: z.ZodOptional<z.ZodNumber>;
         synonyms: z.ZodOptional<z.ZodArray<z.ZodString>>;
+        synonymsTotal: z.ZodOptional<z.ZodNumber>;
         drugLikeness: z.ZodOptional<z.ZodObject<{
             lipinski: z.ZodObject<{
                 hba: z.ZodObject<{

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;AA2GjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;wCAoY7B,CAAC"}

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

@@ -126,6 +126,13 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
             .boolean()
             .default(false)
             .describe('Fetch all known names and synonyms (trade names, systematic names, registry numbers). One API call per CID — slower than the property batch for large CID lists.'),
+        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.'),
         includeDrugLikeness: z
             .boolean()
             .default(false)
@@ -163,6 +170,10 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 .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.'),
+            synonymsTotal: z
+                .number()
+                .optional()
+                .describe('Total synonyms available before truncation. Larger than synonyms.length when more exist — increase maxSynonyms to see them.'),
             drugLikeness: drugLikenessSchema
                 .optional()
                 .describe('Drug-likeness assessment. lipinski.violations ≤ 1 and veber.violations = 0 → pass.'),
@@ -243,8 +254,10 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 compound.descriptionsTotal = allDescs.length;
             }
             const syns = synMap?.get(cid);
-            if (syns)
-                compound.synonyms = syns;
+            if (syns) {
+                compound.synonyms = syns.slice(0, input.maxSynonyms);
+                compound.synonymsTotal = syns.length;
+            }
             if (input.includeDrugLikeness)
                 compound.drugLikeness = computeDrugLikeness(properties);
             const cls = classMap?.get(cid);
@@ -387,11 +400,12 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 }
                 blocks.push(descLines.join('\n\n'));
             }
-            // Synonyms
+            // Synonyms (capped at maxSynonyms in the handler; total reported)
             if (c.synonyms && c.synonyms.length > 0) {
-                const synShown = c.synonyms.slice(0, 20);
-                const more = c.synonyms.length > 20 ? ` (+${c.synonyms.length - 20} more)` : '';
-                blocks.push(`\n**Synonyms:** ${synShown.join(', ')}${more}`);
+                const total = c.synonymsTotal ?? c.synonyms.length;
+                const more = total - c.synonyms.length;
+                const suffix = more > 0 ? ` (+${more} more)` : '';
+                blocks.push(`\n**Synonyms** (${total} total): ${c.synonyms.join(', ')}${suffix}`);
             }
             blocks.push('');
         }

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-safety.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"get-compound-safety.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkCjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;~~EAiI5B~~,CAAC"}
1	+ {"version":3,"file":"get-compound-safety.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkCjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;EAmI5B,CAAC"}

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

@@ -128,8 +128,9 @@ export const getCompoundSafety = tool('pubchem_get_compound_safety', {
             }
             if (g.precautionaryStatements.length > 0) {
                 lines.push('', '**Precautionary Statements:**');
-                for (const p of g.precautionaryStatements)
-                    lines.push(`  ${p.code}: ${p.statement}`);
+                for (const p of g.precautionaryStatements) {
+                    lines.push(p.statement ? `  ${p.code}: ${p.statement}` : `  ${p.code}`);
+                }
             }
             if (r.source)
                 lines.push('', `*Source: ${r.source}*`);

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

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

@@ -17,5 +17,7 @@ export declare const getCompoundXrefs: import("@cyanheads/mcp-ts-core").ToolDefi
         totalAvailable: z.ZodNumber;
         truncated: z.ZodBoolean;
     }, z.core.$strip>>;
-}, z.core.$strip>, undefined, undefined>;
+}, z.core.$strip>, undefined, {
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
 //# sourceMappingURL=get-compound-xrefs.tool.d.ts.map

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"get-compound-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;EAsI3B,CAAC"}

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

@@ -55,6 +55,15 @@ export const getCompoundXrefs = tool('pubchem_get_compound_xrefs', {
             .describe('Cross-reference group for one type.'))
             .describe('Cross-references grouped by type.'),
     }),
+    // Agent-facing context — an empty-result notice distinguishing a nonexistent CID from a
+    // real compound that simply has none of the requested xref types. Reaches structuredContent
+    // and content[]; keys disjoint from output (cid/xrefs live there).
+    enrichment: {
+        notice: z
+            .string()
+            .optional()
+            .describe('Recovery guidance when every requested xref type returned zero IDs — hints to verify the CID. Absent when any cross-references were found.'),
+    },
     async handler(input, ctx) {
         const client = getPubChemClient();
         // Sequential per type to avoid rate limit spikes
@@ -75,6 +84,11 @@ export const getCompoundXrefs = tool('pubchem_get_compound_xrefs', {
             types: input.xrefTypes,
             totalIds: xrefs.reduce((sum, x) => sum + x.ids.length, 0),
         });
+        // Empty-result signal (#30): every requested type came back empty — either the CID
+        // doesn't exist or it genuinely has none of these xref types. Point at CID verification.
+        if (xrefs.every((x) => x.totalAvailable === 0)) {
+            ctx.enrich.notice(`No cross-references found for CID ${input.cid} across the requested type(s): ${input.xrefTypes.join(', ')}. The compound may have none of these xref types, or verify the CID with pubchem_search_compounds.`);
+        }
         return { cid: input.cid, xrefs };
     },
     format(result) {

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"get-compound-xrefs.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAEzD,MAAM,YAAY,GAAG,CAAC,CAAC,IAAI,CAAC,UAA8C,CAAC,CAAC;AAE5E,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IACjE,KAAK,EAAE,+BAA+B;IACtC,WAAW,EACT,6MAA6M;IAC/M,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,SAAS,EAAE,CAAC;aACT,KAAK,CAAC,YAAY,CAAC;aACnB,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,iNAAiN,CAClN;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,wIAAwI,CACzI;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,IAAI,EAAE,CAAC;iBACJ,MAAM,EAAE;iBACR,QAAQ,CACP,6FAA6F,CAC9F;YACH,GAAG,EAAE,CAAC;iBACH,KAAK,CACJ,CAAC;iBACE,KAAK,CAAC;gBACL,CAAC;qBACE,MAAM,EAAE;qBACR,QAAQ,CAAC,2DAA2D,CAAC;gBACxE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uDAAuD,CAAC;aAC7E,CAAC;iBACD,QAAQ,CAAC,kEAAkE,CAAC,CAChF;iBACA,QAAQ,CAAC,6CAA6C,CAAC;YAC1D,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;YAC7E,SAAS,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;SACnE,CAAC;aACD,QAAQ,CAAC,qCAAqC,CAAC,CACnD;aACA,QAAQ,CAAC,mCAAmC,CAAC;KACjD,CAAC;IACF,wFAAwF;IACxF,4FAA4F;IAC5F,mEAAmE;IACnE,UAAU,EAAE;QACV,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,4IAA4I,CAC7I;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAElC,iDAAiD;QACjD,MAAM,KAAK,GAKN,EAAE,CAAC;QAER,KAAK,MAAM,QAAQ,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;YACvC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC;YAC1D,MAAM,cAAc,GAAG,MAAM,CAAC,MAAM,CAAC;YACrC,MAAM,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,UAAU,CAAC,CAAC;YAE9C,KAAK,CAAC,IAAI,CAAC;gBACT,IAAI,EAAE,QAAQ;gBACd,GAAG;gBACH,cAAc;gBACd,SAAS,EAAE,cAAc,GAAG,KAAK,CAAC,UAAU;aAC7C,CAAC,CAAC;QACL,CAAC;QAED,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE;YAC5B,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,KAAK,EAAE,KAAK,CAAC,SAAS;YACtB,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;SAC1D,CAAC,CAAC;QAEH,mFAAmF;QACnF,yFAAyF;QACzF,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,KAAK,CAAC,CAAC,EAAE,CAAC;YAC/C,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,qCAAqC,KAAK,CAAC,GAAG,kCAAkC,KAAK,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,oGAAoG,CAC/M,CAAC;QACJ,CAAC;QAED,OAAO,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,KAAK,EAAE,CAAC;IACnC,CAAC;IAED,MAAM,CAAC,MAAM;QACX,MAAM,KAAK,GAAa,CAAC,4BAA4B,MAAM,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,CAAC;QAEvE,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;YAChC,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS;gBAC9B,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,OAAO,IAAI,CAAC,cAAc,oBAAoB;gBAClE,CAAC,CAAC,GAAG,IAAI,CAAC,cAAc,QAAQ,CAAC;YACnC,KAAK,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,IAAI,OAAO,SAAS,GAAG,CAAC,CAAC;YAE9C,IAAI,IAAI,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxB,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBACtC,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,GAAG,EAAE,CAAC,CAAC,CAAC,WAAW,IAAI,CAAC,GAAG,CAAC,MAAM,GAAG,EAAE,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC;gBACjF,KAAK,CAAC,IAAI,CAAC,KAAK,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YAC/C,CAAC;iBAAM,CAAC;gBACN,KAAK,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;YAC7B,CAAC;YACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACjB,CAAC;QAED,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}

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

@@ -76,6 +76,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
     includeDescription: import("zod").ZodDefault<import("zod").ZodBoolean>;
     maxDescriptions: import("zod").ZodDefault<import("zod").ZodNumber>;
     includeSynonyms: import("zod").ZodDefault<import("zod").ZodBoolean>;
+    maxSynonyms: import("zod").ZodDefault<import("zod").ZodNumber>;
     includeDrugLikeness: import("zod").ZodDefault<import("zod").ZodBoolean>;
     includeClassification: import("zod").ZodDefault<import("zod").ZodBoolean>;
 }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
@@ -89,6 +90,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
         }, import("zod/v4/core").$strip>>>;
         descriptionsTotal: import("zod").ZodOptional<import("zod").ZodNumber>;
         synonyms: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
+        synonymsTotal: import("zod").ZodOptional<import("zod").ZodNumber>;
         drugLikeness: import("zod").ZodOptional<import("zod").ZodObject<{
             lipinski: import("zod").ZodObject<{
                 hba: import("zod").ZodObject<{
@@ -219,7 +221,9 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
         totalAvailable: import("zod").ZodNumber;
         truncated: import("zod").ZodBoolean;
     }, import("zod/v4/core").$strip>>;
-}, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+}, import("zod/v4/core").$strip>, undefined, {
+    readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
+}> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     entityType: import("zod").ZodEnum<{
         assay: "assay";
         gene: "gene";
@@ -266,7 +270,17 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
     maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
 }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
     aids: import("zod").ZodArray<import("zod").ZodNumber>;
-}, import("zod/v4/core").$strip>, undefined, {
+}, import("zod/v4/core").$strip>, readonly [{
+    readonly reason: "blank_target_query";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
+    readonly when: "targetQuery is empty or whitespace-only";
+    readonly recovery: "Provide a non-empty target identifier, e.g. \"EGFR\" for genesymbol or \"1956\" for geneid.";
+}, {
+    readonly reason: "invalid_geneid_query";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
+    readonly when: "targetType is \"geneid\" but targetQuery is not a positive integer";
+    readonly recovery: "Pass a numeric NCBI Gene ID (e.g. \"1956\"), or switch targetType to genesymbol/proteinname for text queries.";
+}], {
     readonly targetType: import("zod").ZodString;
     readonly targetQuery: import("zod").ZodString;
     readonly totalFound: import("zod").ZodNumber;
@@ -306,6 +320,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
         identifier: import("zod").ZodOptional<import("zod").ZodString>;
         properties: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>>;
     }, import("zod/v4/core").$strip>>;
+    unresolvedIdentifiers: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
 }, import("zod/v4/core").$strip>, readonly [{
     readonly reason: "missing_identifier_args";
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
@@ -321,6 +336,11 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
     readonly when: "substructure/superstructure/similarity search missing query or queryType";
     readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
+}, {
+    readonly reason: "invalid_cid_query";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
+    readonly when: "structure/similarity search with queryType \"cid\" but query is not a positive integer CID";
+    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;

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-assays.tool.d.ts CHANGED Viewed

@@ -4,6 +4,7 @@
  * @module mcp-server/tools/definitions/search-assays
  */
 import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const searchAssays: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     targetType: z.ZodEnum<{
         proteinaccession: "proteinaccession";
@@ -15,7 +16,17 @@ export declare const searchAssays: import("@cyanheads/mcp-ts-core").ToolDefiniti
     maxResults: z.ZodDefault<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     aids: z.ZodArray<z.ZodNumber>;
-}, z.core.$strip>, undefined, {
+}, z.core.$strip>, readonly [{
+    readonly reason: "blank_target_query";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "targetQuery is empty or whitespace-only";
+    readonly recovery: "Provide a non-empty target identifier, e.g. \"EGFR\" for genesymbol or \"1956\" for geneid.";
+}, {
+    readonly reason: "invalid_geneid_query";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "targetType is \"geneid\" but targetQuery is not a positive integer";
+    readonly recovery: "Pass a numeric NCBI Gene ID (e.g. \"1956\"), or switch targetType to genesymbol/proteinname for text queries.";
+}], {
     readonly targetType: z.ZodString;
     readonly targetQuery: z.ZodString;
     readonly totalFound: z.ZodNumber;

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"search-assays.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-assays.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2HvB,CAAC"}

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

@@ -4,6 +4,7 @@
  * @module mcp-server/tools/definitions/search-assays
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
+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',
@@ -49,21 +50,47 @@ export const searchAssays = tool('pubchem_search_assays', {
             .optional()
             .describe('Recovery guidance when no assays matched — echoes the target and suggests alternative search types. Absent when assays were returned.'),
     },
+    errors: [
+        {
+            reason: 'blank_target_query',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'targetQuery is empty or whitespace-only',
+            recovery: 'Provide a non-empty target identifier, e.g. "EGFR" for genesymbol or "1956" for geneid.',
+        },
+        {
+            reason: 'invalid_geneid_query',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'targetType is "geneid" but targetQuery is not a positive integer',
+            recovery: 'Pass a numeric NCBI Gene ID (e.g. "1956"), or switch targetType to genesymbol/proteinname for text queries.',
+        },
+    ],
     async handler(input, ctx) {
         const client = getPubChemClient();
-        const allAids = await client.searchAssaysByTarget(input.targetType, input.targetQuery);
+        // Reject inputs that cannot represent a useful target before the upstream call (#26).
+        const targetQuery = input.targetQuery.trim();
+        if (targetQuery.length === 0) {
+            throw ctx.fail('blank_target_query', undefined, {
+                ...ctx.recoveryFor('blank_target_query'),
+            });
+        }
+        // geneid targets are numeric NCBI Gene IDs — a non-numeric value otherwise hits a raw
+        // PubChem 400 (searchAssaysByTarget only special-cases 404).
+        if (input.targetType === 'geneid' && !/^\d+$/.test(targetQuery)) {
+            throw ctx.fail('invalid_geneid_query', `targetType is "geneid" but targetQuery "${input.targetQuery}" is not a positive integer Gene ID.`, { ...ctx.recoveryFor('invalid_geneid_query') });
+        }
+        const allAids = await client.searchAssaysByTarget(input.targetType, targetQuery);
         const totalFound = allAids.length;
         const aids = allAids.slice(0, input.maxResults);
         ctx.log.info('Assay search completed', {
             targetType: input.targetType,
-            targetQuery: input.targetQuery,
+            targetQuery,
             totalFound,
             returned: aids.length,
         });
         // Agent-facing context: target echo, total, and empty-result notice.
-        ctx.enrich({ targetType: input.targetType, targetQuery: input.targetQuery, totalFound });
+        ctx.enrich({ targetType: input.targetType, targetQuery, totalFound });
         if (aids.length === 0) {
-            ctx.enrich.notice(`No assays found for "${input.targetQuery}" (${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.`);
+            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 });

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

@@ -37,6 +37,7 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
         identifier: z.ZodOptional<z.ZodString>;
         properties: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
     }, z.core.$strip>>;
+    unresolvedIdentifiers: z.ZodOptional<z.ZodArray<z.ZodString>>;
 }, z.core.$strip>, readonly [{
     readonly reason: "missing_identifier_args";
     readonly code: JsonRpcErrorCode.ValidationError;
@@ -52,6 +53,11 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "substructure/superstructure/similarity search missing query or queryType";
     readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
+}, {
+    readonly reason: "invalid_cid_query";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "structure/similarity search with queryType \"cid\" but query is not a positive integer CID";
+    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;

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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwW1B,CAAC"}

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

@@ -87,6 +87,10 @@ export const searchCompounds = tool('pubchem_search_compounds', {
         })
             .describe('Matching compound entry.'))
             .describe('Matching compounds.'),
+        unresolvedIdentifiers: z
+            .array(z.string())
+            .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.
@@ -125,11 +129,21 @@ export const searchCompounds = tool('pubchem_search_compounds', {
             when: 'substructure/superstructure/similarity search missing query or queryType',
             recovery: 'Provide both query (SMILES string or CID as string) and queryType ("smiles" or "cid").',
         },
+        {
+            reason: 'invalid_cid_query',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'structure/similarity search with queryType "cid" but query is not a positive integer CID',
+            recovery: 'Pass a positive integer CID string (e.g. "2244"), or set queryType "smiles" with a SMILES query.',
+        },
     ],
     async handler(input, ctx) {
         const client = getPubChemClient();
         let allCids = [];
         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).
+        const unresolvedIdentifiers = [];
+        const collisions = [];
         switch (input.searchType) {
             case 'identifier': {
                 const { identifierType, identifiers } = input;
@@ -151,12 +165,35 @@ export const searchCompounds = tool('pubchem_search_compounds', {
                             cids = await client.searchByInchiKey(id);
                             break;
                     }
-                    for (const cid of cids)
-                        identifierMap.set(cid, id);
-                    return cids;
+                    return { id, cids };
                 });
-                const results = await Promise.all(lookups);
-                allCids = results.flat();
+                const resolutions = await Promise.all(lookups);
+                // Track resolution per input in request order: a CID's echo goes to its first
+                // requester (deterministic, unlike the prior last-write-wins), unresolved inputs
+                // are collected, and any CID with multiple distinct requesters is a collision.
+                const cidToIdentifiers = new Map();
+                for (const { id, cids } of resolutions) {
+                    if (cids.length === 0) {
+                        unresolvedIdentifiers.push(id);
+                        continue;
+                    }
+                    for (const cid of cids) {
+                        const owners = cidToIdentifiers.get(cid);
+                        if (owners) {
+                            if (!owners.includes(id))
+                                owners.push(id);
+                        }
+                        else {
+                            cidToIdentifiers.set(cid, [id]);
+                            identifierMap.set(cid, id);
+                        }
+                    }
+                }
+                for (const [cid, owners] of cidToIdentifiers) {
+                    if (owners.length > 1)
+                        collisions.push({ cid, identifiers: owners });
+                }
+                allCids = resolutions.flatMap((r) => r.cids);
                 break;
             }
             case 'formula': {
@@ -176,6 +213,11 @@ export const searchCompounds = tool('pubchem_search_compounds', {
                         ...ctx.recoveryFor('missing_structure_args'),
                     });
                 }
+                // A "cid" query must be a positive integer string — catch it here instead of
+                // forwarding a malformed value into a raw PubChem 400 (#26).
+                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);
                 break;
             }
@@ -191,11 +233,37 @@ export const searchCompounds = tool('pubchem_search_compounds', {
         });
         // Agent-facing context: search strategy echo, total, and empty-result notice.
         ctx.enrich({ searchType: input.searchType, totalFound });
+        // 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 = [];
+        if (unresolvedIdentifiers.length > 0) {
+            const requested = input.identifiers?.length ?? unresolvedIdentifiers.length;
+            noticeParts.push(`${unresolvedIdentifiers.length} of ${requested} identifier(s) did not resolve to a CID: ${unresolvedIdentifiers.join(', ')}. Verify spelling and that identifierType="${input.identifierType}" matches the identifier form (name/smiles/inchikey).`);
+        }
+        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(`No compounds matched the ${input.searchType} search. Try a different identifier, broaden the formula, lower the similarity threshold, or verify the SMILES/CID.`);
+            ctx.enrich.notice(noticeParts.length > 0
+                ? noticeParts.join(' ')
+                : `No compounds matched the ${input.searchType} search. Try a different identifier, broaden the formula, lower the similarity threshold, or verify the SMILES/CID.`);
         }
         else if (totalFound > cappedCids.length) {
-            ctx.enrich.truncated({ shown: cappedCids.length, cap: input.maxResults });
+            // Truncated: fold any identifier notice into the truncation guidance (notice is
+            // last-wins, so compose rather than emit two; restate the cap when overriding).
+            if (noticeParts.length > 0) {
+                ctx.enrich.truncated({
+                    shown: cappedCids.length,
+                    cap: input.maxResults,
+                    guidance: `${noticeParts.join(' ')} Showing ${cappedCids.length} of ${totalFound} matches — raise maxResults (max 200) for more.`,
+                });
+            }
+            else {
+                ctx.enrich.truncated({ shown: cappedCids.length, cap: input.maxResults });
+            }
+        }
+        else if (noticeParts.length > 0) {
+            ctx.enrich.notice(noticeParts.join(' '));
         }
         // Optionally hydrate with properties
         let propsMap;
@@ -215,30 +283,34 @@ export const searchCompounds = tool('pubchem_search_compounds', {
             }
             return result;
         });
-        return { results };
+        return unresolvedIdentifiers.length > 0 ? { results, unresolvedIdentifiers } : { results };
     },
     format(result) {
         const lines = [];
         if (result.results.length === 0) {
             lines.push('No results.');
-            return [{ type: 'text', text: lines.join('\n') }];
         }
-        const hasProps = result.results.some((r) => r.properties);
-        if (hasProps) {
-            for (const r of result.results) {
-                const label = r.identifier ? `CID ${r.cid} — ${r.identifier}` : `CID ${r.cid}`;
-                lines.push(`**${label}**`);
-                if (r.properties) {
-                    const entries = Object.entries(r.properties);
-                    lines.push('  **Properties:**');
-                    lines.push(entries.map(([k, v]) => `    ${k}: ${v}`).join('\n'));
+        else {
+            const hasProps = result.results.some((r) => r.properties);
+            if (hasProps) {
+                for (const r of result.results) {
+                    const label = r.identifier ? `CID ${r.cid} — ${r.identifier}` : `CID ${r.cid}`;
+                    lines.push(`**${label}**`);
+                    if (r.properties) {
+                        const entries = Object.entries(r.properties);
+                        lines.push('  **Properties:**');
+                        lines.push(entries.map(([k, v]) => `    ${k}: ${v}`).join('\n'));
+                    }
+                    lines.push('');
                 }
-                lines.push('');
+            }
+            else {
+                const items = result.results.map((r) => r.identifier ? `${r.cid} (${r.identifier})` : String(r.cid));
+                lines.push(`CIDs: ${items.join(', ')}`);
             }
         }
-        else {
-            const items = result.results.map((r) => r.identifier ? `${r.cid} (${r.identifier})` : String(r.cid));
-            lines.push(`CIDs: ${items.join(', ')}`);
+        if (result.unresolvedIdentifiers && result.unresolvedIdentifiers.length > 0) {
+            lines.push(`Unresolved identifiers (${result.unresolvedIdentifiers.length}): ${result.unresolvedIdentifiers.join(', ')}`);
         }
         return [{ type: 'text', text: lines.join('\n') }];
     },

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

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

	@@ -1 +1 @@
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package/dist/services/pubchem/pubchem-client.js CHANGED Viewed

@@ -169,6 +169,21 @@ function parseCodedStatement(text) {
         return { code: codeOnly[1], statement: '' };
     return;
 }
+/** Parse PubChem's comma-separated precautionary code list — e.g.
+ * "P261, P264+P265, P305+P351+P338, P405, and P501" — into code-only entries.
+ * PubChem deposits precautionary statements as codes without descriptive text, so
+ * `statement` is always empty; we don't fabricate the standard P-statement text.
+ * Handles the terminal Oxford "and", combined (`Pxxx+Pyyy`) and triple codes, and
+ * skips any token that isn't a P-code. */
+function parsePrecautionaryCodes(text) {
+    const entries = [];
+    for (const token of text.split(',')) {
+        const code = token.trim().replace(/^and\s+/i, '');
+        if (/^P\d{3}(?:\+P\d{3})*$/.test(code))
+            entries.push({ code, statement: '' });
+    }
+    return entries;
+}
 /** Map PubChem pictogram markup strings to human labels */
 const PICTOGRAM_LABELS = {
     GHS01: 'Explosive',
@@ -448,10 +463,11 @@ export class PubChemClient {
                     }
                 }
                 else if (name.includes('precautionary') && name.includes('statement')) {
+                    // PubChem deposits precautionary statements as a single comma-separated code
+                    // list (codes only, no text) — not the "Pxxx: text" shape parseCodedStatement
+                    // expects. Split each list into individual code entries.
                     for (const s of strings) {
-                        const parsed = parseCodedStatement(s);
-                        if (parsed)
-                            result.precautionaryStatements.push(parsed);
+                        result.precautionaryStatements.push(...parsePrecautionaryCodes(s));
                     }
                 }
             }
@@ -486,26 +502,28 @@ export class PubChemClient {
                 fdaMechanisms: [],
                 meshClasses: [],
             };
-            // FDA Pharmacological Classification
+            // FDA Pharmacological Classification — PubChem emits two redundant shapes
+            // (either alone covers all classes):
+            //   individual: "<Type> [TAG] - <Name>"        (name after the dash)
+            //   combined:   "<Name> [TAG]; <Name> [TAG]; …" (name before the tag)
+            // Bucket EPC → fdaClasses, MoA → fdaMechanisms; CS/PE have no output field.
             const fdaSection = findSection(sections, 'FDA Pharmacological Classification');
             if (fdaSection) {
-                const strings = extractStrings(fdaSection);
-                for (const s of strings) {
-                    if (!s.startsWith('Pharmacological Classes:'))
-                        continue;
-                    const classes = s.slice('Pharmacological Classes:'.length).trim();
-                    for (const entry of classes.split(';')) {
+                for (const s of extractStrings(fdaSection)) {
+                    for (const entry of s.split(';')) {
                         const trimmed = entry.trim();
-                        const tagMatch = trimmed.match(/^(.+?)\s*\[(\w+)\]$/);
-                        if (!tagMatch)
+                        if (!trimmed)
                             continue;
-                        const [, name, tag] = tagMatch;
-                        if (!name)
+                        const individual = trimmed.match(/^.+\[(\w+)\]\s*-\s*(.+)$/);
+                        const tagAtEnd = individual ? null : trimmed.match(/^(.+?)\s*\[(\w+)\]$/);
+                        const tag = individual?.[1] ?? tagAtEnd?.[2];
+                        const name = (individual?.[2] ?? tagAtEnd?.[1])?.trim();
+                        if (!tag || !name)
                             continue;
-                        if (tag === 'EPC' || tag === 'CS')
-                            result.fdaClasses.push(name.trim());
+                        if (tag === 'EPC')
+                            result.fdaClasses.push(name);
                         else if (tag === 'MoA')
-                            result.fdaMechanisms.push(name.trim());
+                            result.fdaMechanisms.push(name);
                     }
                 }
                 result.fdaClasses = [...new Set(result.fdaClasses)];

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package/manifest.json CHANGED Viewed

@@ -1,7 +1,7 @@
 {
   "manifest_version": "0.3",
   "name": "pubchem-mcp-server",
-  "version": "0.2.4",
+  "version": "0.3.1",
   "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": "0.2.4",
+  "version": "0.3.1",
   "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",
@@ -73,13 +73,13 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.10.9",
+    "@cyanheads/mcp-ts-core": "^0.10.10",
     "pino-pretty": "^13.1.3",
     "zod": "^4.4.3"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.5.0",
-    "@types/node": "^26.0.0",
+    "@biomejs/biome": "^2.5.2",
+    "@types/node": "^26.1.0",
     "depcheck": "^1.4.7",
     "ignore": "^7.0.5",
     "tsc-alias": "^1.8.17",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubchem-mcp-server",
     "source": "github"
   },
-  "version": "0.2.4",
+  "version": "0.3.1",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubchem-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.2.4",
+      "version": "0.3.1",
       "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": "0.2.4",
+      "version": "0.3.1",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }