npm - @cyanheads/pubchem-mcp-server - Versions diffs - 0.1.14 → 0.1.16 - Mend

@cyanheads/pubchem-mcp-server 0.1.14 → 0.1.16

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 (27) hide show

package/README.md CHANGED Viewed

@@ -6,7 +6,7 @@
 <div align="center">
-[![Version](https://img.shields.io/badge/Version-0.1.14-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![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-^1.2.0-f472b6.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-0.1.16-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![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-^1.2.0-f472b6.svg?style=flat-square)](https://bun.sh/)
 </div>

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

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

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

@@ -35,7 +35,8 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
         activeCount: z.number().describe('Assays with "Active" outcome.'),
         inactiveCount: z.number().describe('Assays with "Inactive" outcome.'),
         results: z
-            .array(z.object({
+            .array(z
+            .object({
             aid: z.number().describe('PubChem Assay ID.'),
             assayName: z.string().describe('Assay name/title.'),
             outcome: z
@@ -47,7 +48,8 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
                 .describe('Target protein accession (UniProt/GenBank).'),
             targetGeneId: z.number().optional().describe('Target NCBI Gene ID.'),
             activityValues: z
-                .array(z.object({
+                .array(z
+                .object({
                 name: z
                     .string()
                     .optional()
@@ -57,9 +59,11 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
                     .string()
                     .optional()
                     .describe('Unit of measurement (e.g. uM, nM). Omitted when not reported.'),
-            }))
+            })
+                .describe('Quantitative activity measurement entry.'))
                 .describe('Quantitative activity measurements.'),
-        }))
+        })
+            .describe('Assay result entry.'))
             .describe('Assay results matching the filter.'),
     }),
     async handler(input, ctx) {

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

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

	@@ -1 +1 @@
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;~~AAyGjD~~,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~kBAmX7B~~,CAAC"}
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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA4X7B,CAAC"}

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

@@ -36,10 +36,12 @@ const drugLikenessSchema = z.object({
 });
 const classificationSchema = z.object({
     atcCodes: z
-        .array(z.object({
+        .array(z
+        .object({
         code: z.string().describe('ATC code.'),
         description: z.string().describe('ATC code description.'),
-    }))
+    })
+        .describe('ATC code entry with hierarchical description.'))
         .describe('ATC codes with hierarchical descriptions.'),
     fdaClasses: z.array(z.string()).describe('FDA Established Pharmacologic Classes.'),
     fdaMechanisms: z.array(z.string()).describe('FDA Mechanisms of Action.'),
@@ -147,7 +149,8 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
     }),
     output: z.object({
         compounds: z
-            .array(z.object({
+            .array(z
+            .object({
             cid: z.number().describe('PubChem Compound ID.'),
             found: z
                 .boolean()
@@ -156,13 +159,15 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 .record(z.string(), z.unknown())
                 .describe('Requested physicochemical properties.'),
             descriptions: z
-                .array(z.object({
+                .array(z
+                .object({
                 source: z
                     .string()
                     .optional()
                     .describe('Depositor source (e.g. "DrugBank", "Wikipedia", "ChEBI").'),
                 text: z.string().describe('Description text.'),
-            }))
+            })
+                .describe('Description entry with optional source attribution.'))
                 .optional()
                 .describe('Textual descriptions, deduplicated and capped at maxDescriptions. Each entry carries ' +
                 'optional source attribution.'),
@@ -178,7 +183,8 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
             classification: classificationSchema
                 .optional()
                 .describe('Pharmacological classification (FDA, MeSH, ATC).'),
-        }))
+        })
+            .describe('Per-CID compound detail record.'))
             .describe('Compound detail records.'),
     }),
     async handler(input, ctx) {
@@ -273,9 +279,9 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
             }
             const p = c.properties;
             const name = p.IUPACName ?? p.Title ?? '';
-            const header = name ? `## CID ${c.cid} — ${name}` : `## CID ${c.cid}`;
+            const header = name ? `## CID ${c.cid} — ${name} (found)` : `## CID ${c.cid} (found)`;
             blocks.push(header);
-            const lines = [];
+            const lines = ['**Properties:**'];
             // Key identifiers
             if (p.MolecularFormula)
                 lines.push(`**Formula:** ${p.MolecularFormula}`);
@@ -298,7 +304,7 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
             if (p.Complexity != null)
                 drugProps.push(`Complexity: ${p.Complexity}`);
             if (drugProps.length > 0)
-                lines.push(`**Properties:** ${drugProps.join(' | ')}`);
+                lines.push(`**Descriptors:** ${drugProps.join(' | ')}`);
             // Atom/bond counts
             const counts = [];
             if (p.HBondDonorCount != null)
@@ -381,13 +387,17 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
             }
             // Descriptions (with source attribution; truncated to maxDescriptions)
             if (c.descriptions && c.descriptions.length > 0) {
-                const descLines = [''];
+                const total = c.descriptionsTotal ?? c.descriptions.length;
+                const shown = c.descriptions.length;
+                const header = total > shown
+                    ? `\n**Descriptions** (showing ${shown} of ${total} total)`
+                    : `\n**Descriptions** (${total} total)`;
+                const descLines = [header];
                 for (const d of c.descriptions) {
                     const label = d.source ? `**Description (${d.source}):**` : '**Description:**';
                     descLines.push(`${label} ${d.text}`);
                 }
-                const total = c.descriptionsTotal ?? c.descriptions.length;
-                const more = total - c.descriptions.length;
+                const more = total - shown;
                 if (more > 0) {
                     descLines.push(`_+${more} more description${more === 1 ? '' : 's'} from other sources — increase maxDescriptions to see them._`);
                 }

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

	@@ -1 +1 @@
1	- {"version":3,"file":"get-compound-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAQjD~~,eAAO,MAAM,gBAAgB;;;;;;;;;;;;kBAgD3B,CAAC"}
1	+ {"version":3,"file":"get-compound-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,gBAAgB;;;;;;;;;;;;kBAgD3B,CAAC"}

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

@@ -4,10 +4,6 @@
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
-/** Convert ArrayBuffer to base64 string */
-function arrayBufferToBase64(buffer) {
-    return Buffer.from(buffer).toString('base64');
-}
 export const getCompoundImage = tool('pubchem_get_compound_image', {
     title: 'Get Compound Image',
     description: 'Fetch a 2D structure diagram (PNG image) for a compound by CID.',
@@ -37,7 +33,7 @@ export const getCompoundImage = tool('pubchem_get_compound_image', {
         ctx.log.info('Image fetched', { cid: input.cid, size: input.size, bytes: buffer.byteLength });
         return {
             cid: input.cid,
-            imageBase64: arrayBufferToBase64(buffer),
+            imageBase64: Buffer.from(buffer).toString('base64'),
             mimeType: 'image/png',
             width: dim,
             height: dim,

package/dist/mcp-server/tools/definitions/get-compound-image.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;AAGjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;~~kBAmG5B~~,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;AAGjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;kBAuG5B,CAAC"}

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

@@ -27,16 +27,20 @@ export const getCompoundSafety = tool('pubchem_get_compound_safety', {
                 .array(z.string())
                 .describe('GHS pictogram labels (e.g. "Flammable", "Toxic").'),
             hazardStatements: z
-                .array(z.object({
+                .array(z
+                .object({
                 code: z.string().describe('H-code (e.g. "H225").'),
                 statement: z.string().describe('Hazard statement text.'),
-            }))
+            })
+                .describe('GHS hazard statement entry.'))
                 .describe('GHS hazard statements.'),
             precautionaryStatements: z
-                .array(z.object({
+                .array(z
+                .object({
                 code: z.string().describe('P-code (e.g. "P210").'),
                 statement: z.string().describe('Precautionary statement text.'),
-            }))
+            })
+                .describe('GHS precautionary statement entry.'))
                 .describe('GHS precautionary statements.'),
         })
             .optional()
@@ -66,7 +70,7 @@ export const getCompoundSafety = tool('pubchem_get_compound_safety', {
         if (!result.hasData || !result.ghs) {
             return [{ type: 'text', text: `No GHS safety data available for CID ${result.cid}.` }];
         }
-        const lines = [`## GHS Safety — CID ${result.cid}`, ''];
+        const lines = [`## GHS Safety Data — CID ${result.cid}`, ''];
         const g = result.ghs;
         if (g.signalWord)
             lines.push(`**Signal Word:** ${g.signalWord}`);

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

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

	@@ -1 +1 @@
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;;;;;;;;;;;;;;~~kBAoG3B~~,CAAC"}
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;;;;;;;;;;;;;;kBA+G3B,CAAC"}

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

@@ -34,14 +34,23 @@ export const getCompoundXrefs = tool('pubchem_get_compound_xrefs', {
     output: z.object({
         cid: z.number().describe('PubChem Compound ID.'),
         xrefs: z
-            .array(z.object({
+            .array(z
+            .object({
             type: z.string().describe('Cross-reference type.'),
             ids: z
-                .array(z.union([z.string(), z.number()]))
+                .array(z
+                .union([
+                z
+                    .string()
+                    .describe('String-form cross-reference ID (e.g. CAS number, patent).'),
+                z.number().describe('Numeric cross-reference ID (e.g. PubMed ID, Gene ID).'),
+            ])
+                .describe('Cross-reference identifier — string or number depending on type.'))
                 .describe('Cross-reference IDs (capped by maxPerType).'),
             totalAvailable: z.number().describe('Total IDs available before truncation.'),
             truncated: z.boolean().describe('Whether results were truncated.'),
-        }))
+        })
+            .describe('Cross-reference group for one type.'))
             .describe('Cross-references grouped by type.'),
     }),
     async handler(input, ctx) {
@@ -70,7 +79,7 @@ export const getCompoundXrefs = tool('pubchem_get_compound_xrefs', {
         const lines = [`Cross-references for CID ${result.cid}`, ''];
         for (const xref of result.xrefs) {
             const countInfo = xref.truncated
-                ? `${xref.ids.length} of ${xref.totalAvailable} total`
+                ? `${xref.ids.length} of ${xref.totalAvailable} total — truncated`
                 : `${xref.totalAvailable} total`;
             lines.push(`**${xref.type}** (${countInfo})`);
             if (xref.ids.length > 0) {

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

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"get-summary.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-summary.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAkCjD,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA2GrB,CAAC"}

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

@@ -42,7 +42,12 @@ export const getSummary = tool('pubchem_get_summary', {
     input: z.object({
         entityType: entityTypeEnum.describe('Entity type. Determines ID format and returned fields.'),
         identifiers: z
-            .array(z.union([z.string(), z.number()]))
+            .array(z
+            .union([
+            z.string().describe('String identifier (e.g. UniProt accession).'),
+            z.number().describe('Numeric identifier (e.g. AID, Gene ID, Tax ID).'),
+        ])
+            .describe('Entity identifier — string or number depending on entityType.'))
             .min(1)
             .max(10)
             .describe('Entity identifiers (1-10). Type depends on entityType:\n' +
@@ -54,13 +59,20 @@ export const getSummary = tool('pubchem_get_summary', {
     output: z.object({
         entityType: z.string().describe('Entity type queried.'),
         summaries: z
-            .array(z.object({
-            identifier: z.union([z.string(), z.number()]).describe('Queried identifier.'),
+            .array(z
+            .object({
+            identifier: z
+                .union([
+                z.string().describe('String identifier (e.g. UniProt accession).'),
+                z.number().describe('Numeric identifier (e.g. AID, Gene ID, Tax ID).'),
+            ])
+                .describe('Queried identifier.'),
             found: z.boolean().describe('Whether the entity was found.'),
             data: entitySummaryDataSchema
                 .optional()
                 .describe('Entity summary data. Populated fields depend on entityType.'),
-        }))
+        })
+            .describe('Per-identifier summary result.'))
             .describe('Summary results.'),
     }),
     async handler(input, ctx) {
@@ -83,14 +95,15 @@ export const getSummary = tool('pubchem_get_summary', {
         const lines = [`## ${capitalize(result.entityType)} Summaries`, ''];
         for (const s of result.summaries) {
             if (!s.found || !s.data) {
-                lines.push(`**${s.identifier}** — not found`);
+                lines.push(`**Identifier ${s.identifier}** — not found`);
                 lines.push('');
                 continue;
             }
             const d = s.data;
-            lines.push(`**${d.name ?? d.symbol ?? s.identifier}**`);
+            const displayName = d.name ?? d.symbol ?? String(s.identifier);
+            lines.push(`**${displayName}** (identifier: ${s.identifier}, found)`);
             for (const [key, value] of Object.entries(d)) {
-                if (value == null || key === 'name' || key === 'symbol')
+                if (value == null || key === 'name')
                     continue;
                 if (Array.isArray(value)) {
                     if (value.length === 0)

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

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

	@@ -1 +1 @@
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;AAgBjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~kBAsO1B~~,CAAC"}
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;AAgBjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAyO1B,CAAC"}

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

@@ -84,7 +84,8 @@ export const searchCompounds = tool('pubchem_search_compounds', {
         searchType: z.string().describe('The search strategy used.'),
         totalFound: z.number().describe('Total CIDs found (before maxResults cap).'),
         results: z
-            .array(z.object({
+            .array(z
+            .object({
             cid: z.number().describe('PubChem Compound ID.'),
             identifier: z
                 .string()
@@ -94,7 +95,8 @@ export const searchCompounds = tool('pubchem_search_compounds', {
                 .record(z.string(), z.unknown())
                 .optional()
                 .describe('Compound properties when requested.'),
-        }))
+        })
+            .describe('Matching compound entry.'))
             .describe('Matching compounds.'),
     }),
     async handler(input, ctx) {
@@ -191,7 +193,8 @@ export const searchCompounds = tool('pubchem_search_compounds', {
                 lines.push(`**${label}**`);
                 if (r.properties) {
                     const entries = Object.entries(r.properties);
-                    lines.push(entries.map(([k, v]) => `  ${k}: ${v}`).join('\n'));
+                    lines.push('  **Properties:**');
+                    lines.push(entries.map(([k, v]) => `    ${k}: ${v}`).join('\n'));
                 }
                 lines.push('');
             }

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

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"pubchem-client.d.ts","sourceRoot":"","sources":["../../../src/services/pubchem/pubchem-client.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAGV,cAAc,EAEd,sBAAsB,EACtB,iBAAiB,EAQlB,MAAM,YAAY,CAAC;AA2MpB,qBAAa,aAAa;IACxB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAA+C;IACvE,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAoD;IAC7E,OAAO,CAAC,QAAQ,CAAC,WAAW,CAAsB;YAIpC,SAAS;YAgDT,WAAW;IAwBzB,wEAAwE;YAC1D,SAAS;IAWvB,qDAAqD;YACvC,WAAW;IAgBzB,YAAY,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAI7C,cAAc,CAAC,MAAM,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAQjD,gBAAgB,CAAC,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAMrD,eAAe,CAAC,OAAO,EAAE,MAAM,EAAE,UAAU,UAAQ,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAOvE,iBAAiB,CACf,IAAI,EAAE,cAAc,GAAG,gBAAgB,GAAG,YAAY,EACtD,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,QAAQ,GAAG,KAAK,EAC3B,SAAS,CAAC,EAAE,MAAM,GACjB,OAAO,CAAC,MAAM,EAAE,CAAC;IA2Bd,aAAa,CACjB,IAAI,EAAE,MAAM,EAAE,EACd,UAAU,EAAE,MAAM,EAAE,GACnB,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG;QAAE,GAAG,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IA+BtD,WAAW,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAYjD,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,GAAE,OAAO,GAAG,OAAiB,GAAG,OAAO,CAAC,WAAW,CAAC;IAKxE,QAAQ,CAAC,GAAG,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAAC,CAAC,MAAM,GAAG,MAAM,CAAC,EAAE,CAAC;IAiBrE,cAAc,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,KAAK,CAAC;QAAE,MAAM,CAAC,EAAE,MAAM,CAAC;QAAC,IAAI,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IA8B9E,aAAa,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,iBAAiB,GAAG,IAAI,CAAC;IA0E7D,iBAAiB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,sBAAsB,GAAG,IAAI,CAAC;IA8EtE,eAAe,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAAC,cAAc,EAAE,CAAC;IAY7D,OAAO,CAAC,eAAe;IA0EjB,oBAAoB,CAAC,UAAU,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC;IAgB1E,gBAAgB,CACpB,UAAU,EAAE,MAAM,EAClB,UAAU,EAAE,MAAM,GAAG,MAAM,GAC1B,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC;CA+B3C;AAMD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC;AAED,wBAAgB,gBAAgB,IAAI,aAAa,CAIhD"}

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

@@ -187,6 +187,8 @@ function parsePictogram(text) {
     }
     return text.replace(/.*\//, '').replace(/\..*/, '');
 }
+/** Identity key for bioactivity entry dedup within an AID. */
+const activityKey = (v) => `${v.name ?? ''}|${v.value}|${v.unit ?? ''}`;
 // ── Client ───────────────────────────────────────────────────────────
 export class PubChemClient {
     pugBase = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug';
@@ -623,7 +625,6 @@ export class PubChemClient {
             }
             if (actValueUnit)
                 entry.unit = actValueUnit;
-            const activityKey = (v) => `${v.name ?? ''}|${v.value}|${v.unit ?? ''}`;
             const key = activityKey(entry);
             if (!bucket.activityValues.some((v) => activityKey(v) === key)) {
                 bucket.activityValues.push(entry);

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

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

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubchem-mcp-server",
-  "version": "0.1.14",
+  "version": "0.1.16",
   "description": "MCP server for the PubChem chemical database. Search compounds, fetch properties, safety data, bioactivity, cross-references, and entity summaries. STDIO & Streamable HTTP.",
   "mcpName": "io.github.cyanheads/pubchem-mcp-server",
   "type": "module",
@@ -62,21 +62,16 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.3.7",
+    "@cyanheads/mcp-ts-core": "^0.7.0",
     "pino-pretty": "^13.1.3"
   },
-  "overrides": {
-    "brace-expansion": ">=2.0.3",
-    "path-to-regexp": ">=8.4.0",
-    "picomatch": ">=4.0.4"
-  },
   "devDependencies": {
-    "@biomejs/biome": "^2.4.12",
+    "@biomejs/biome": "^2.4.13",
     "@types/node": "^25.6.0",
     "depcheck": "^1.4.7",
     "ignore": "^7.0.5",
     "tsc-alias": "^1.8.16",
     "typescript": "^6.0.3",
-    "vitest": "^4.1.4"
+    "vitest": "^4.1.5"
   }
 }

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubchem-mcp-server",
     "source": "github"
   },
-  "version": "0.1.14",
+  "version": "0.1.16",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubchem-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.1.14",
+      "version": "0.1.16",
       "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": "0.1.14",
+      "version": "0.1.16",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }