npm - @cyanheads/pubchem-mcp-server - Versions diffs - 0.6.2 → 0.6.4 - Mend

@cyanheads/pubchem-mcp-server 0.6.2 → 0.6.4

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 (79) hide show

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

	@@ -1 +1 @@
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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EAyJvB~~,CAAC"}
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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4JvB,CAAC"}

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

@@ -35,6 +35,9 @@ export const searchAssays = tool('pubchem_search_assays', {
             .default(50)
             .describe('Max AIDs to return per page (1-200). Popular targets may have thousands of assays; use offset to reach the ones past this page. Default: 50.'),
     }),
+    // `targetQuery` is the only search term this tool takes, so the bare nouns a caller
+    // reaches for resolve to it with nothing to disambiguate against.
+    inputAliases: { query: 'targetQuery', target: 'targetQuery' },
     output: z.object({
         aids: z.array(z.number()).describe('PubChem Assay IDs.'),
     }),

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

	@@ -1 +1 @@
1	- {"version":3,"file":"search-assays.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-assays.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,YAAY,GAAG,IAAI,CAAC,uBAAuB,EAAE;IACxD,KAAK,EAAE,eAAe;IACtB,WAAW,EACT,oRAAoR;IACtR,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,UAAU,EAAE,CAAC;aACV,IAAI,CAAC,CAAC,YAAY,EAAE,aAAa,EAAE,QAAQ,EAAE,kBAAkB,CAAC,CAAC;aACjE,QAAQ,CACP,0JAA0J,CAC3J;QACH,WAAW,EAAE,CAAC;aACX,MAAM,EAAE;aACR,QAAQ,CACP,mJAAmJ,CACpJ;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,+HAA+H,CAChI;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,8IAA8I,CAC/I;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,IAAI,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;KACzD,CAAC;IACF,2FAA2F;IAC3F,+DAA+D;IAC/D,mFAAmF;IACnF,UAAU,EAAE;QACV,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,CACP,oFAAoF,CACrF;QACH,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;QAC/D,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qDAAqD,CAAC;QACtF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;QAC1E,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,iGAAiG,CAClG;QACH,SAAS,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QAC5F,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;QACpE,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QAC3E,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,oKAAoK,CACrK;KACJ;IACD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,oBAAoB;YAC5B,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,yCAAyC;YAC/C,QAAQ,EACN,yFAAyF;SAC5F;QACD;YACE,MAAM,EAAE,sBAAsB;YAC9B,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,kEAAkE;YACxE,QAAQ,EACN,6GAA6G;SAChH;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAElC,sFAAsF;QACtF,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,EAAE,CAAC;QAC7C,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,MAAM,GAAG,CAAC,IAAI,CAAC,oBAAoB,EAAE,SAAS,EAAE;gBAC9C,GAAG,GAAG,CAAC,WAAW,CAAC,oBAAoB,CAAC;aACzC,CAAC,CAAC;QACL,CAAC;QACD,sFAAsF;QACtF,6DAA6D;QAC7D,IAAI,KAAK,CAAC,UAAU,KAAK,QAAQ,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,WAAW,CAAC,EAAE,CAAC;YAChE,MAAM,GAAG,CAAC,IAAI,CACZ,sBAAsB,EACtB,2CAA2C,KAAK,CAAC,WAAW,sCAAsC,EAClG,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,sBAAsB,CAAC,EAAE,CAC/C,CAAC;QACJ,CAAC;QAED,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,oBAAoB,CAAC,KAAK,CAAC,UAAU,EAAE,WAAW,CAAC,CAAC;QAEjF,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAC;QAClC,wFAAwF;QACxF,2EAA2E;QAC3E,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,MAAM,GAAG,KAAK,CAAC,UAAU,CAAC,CAAC;QAC1E,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC;QAC9C,MAAM,OAAO,GAAG,UAAU,GAAG,UAAU,CAAC;QAExC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,wBAAwB,EAAE;YACrC,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,WAAW;YACX,UAAU;YACV,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,QAAQ,EAAE,IAAI,CAAC,MAAM;SACtB,CAAC,CAAC;QAEH,iFAAiF;QACjF,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,KAAK,CAAC,UAAU,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;QAC5F,IAAI,OAAO;YAAE,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,CAAC,CAAC;QACxC,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;YACrB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,wBAAwB,WAAW,MAAM,KAAK,CAAC,UAAU,yKAAyK,CACnO,CAAC;QACJ,CAAC;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,UAAU,KAAK,CAAC,MAAM,gBAAgB,UAAU,sBAAsB,WAAW,2BAA2B,UAAU,GAAG,CAC1H,CAAC;QACJ,CAAC;aAAM,IAAI,OAAO,EAAE,CAAC;YACnB,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC;gBACnB,KAAK,EAAE,IAAI,CAAC,MAAM;gBAClB,GAAG,EAAE,KAAK,CAAC,UAAU;gBACrB,QAAQ,EAAE,gBAAgB,KAAK,CAAC,MAAM,GAAG,CAAC,IAAI,UAAU,OAAO,UAAU,iBAAiB,UAAU,qBAAqB;aAC1H,CAAC,CAAC;QACL,CAAC;QAED,OAAO,EAAE,IAAI,EAAE,CAAC;IAClB,CAAC;IAED,MAAM,CAAC,MAAM;QACX,IAAI,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC3B,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,SAAS,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,EAAE,CAAC,CAAC;QACrE,CAAC;QACD,qFAAqF;QACrF,0CAA0C;QAC1C,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,qBAAqB,EAAE,CAAC,CAAC;IACzD,CAAC;CACF,CAAC,CAAC"}
1	+ {"version":3,"file":"search-assays.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-assays.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,YAAY,GAAG,IAAI,CAAC,uBAAuB,EAAE;IACxD,KAAK,EAAE,eAAe;IACtB,WAAW,EACT,oRAAoR;IACtR,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,UAAU,EAAE,CAAC;aACV,IAAI,CAAC,CAAC,YAAY,EAAE,aAAa,EAAE,QAAQ,EAAE,kBAAkB,CAAC,CAAC;aACjE,QAAQ,CACP,0JAA0J,CAC3J;QACH,WAAW,EAAE,CAAC;aACX,MAAM,EAAE;aACR,QAAQ,CACP,mJAAmJ,CACpJ;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,+HAA+H,CAChI;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,8IAA8I,CAC/I;KACJ,CAAC;IACF,oFAAoF;IACpF,kEAAkE;IAClE,YAAY,EAAE,EAAE,KAAK,EAAE,aAAa,EAAE,MAAM,EAAE,aAAa,EAAE;IAC7D,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,IAAI,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;KACzD,CAAC;IACF,2FAA2F;IAC3F,+DAA+D;IAC/D,mFAAmF;IACnF,UAAU,EAAE;QACV,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,CACP,oFAAoF,CACrF;QACH,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;QAC/D,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qDAAqD,CAAC;QACtF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;QAC1E,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,iGAAiG,CAClG;QACH,SAAS,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QAC5F,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;QACpE,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QAC3E,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,oKAAoK,CACrK;KACJ;IACD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,oBAAoB;YAC5B,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,yCAAyC;YAC/C,QAAQ,EACN,yFAAyF;SAC5F;QACD;YACE,MAAM,EAAE,sBAAsB;YAC9B,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,kEAAkE;YACxE,QAAQ,EACN,6GAA6G;SAChH;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAElC,sFAAsF;QACtF,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,IAAI,EAAE,CAAC;QAC7C,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,MAAM,GAAG,CAAC,IAAI,CAAC,oBAAoB,EAAE,SAAS,EAAE;gBAC9C,GAAG,GAAG,CAAC,WAAW,CAAC,oBAAoB,CAAC;aACzC,CAAC,CAAC;QACL,CAAC;QACD,sFAAsF;QACtF,6DAA6D;QAC7D,IAAI,KAAK,CAAC,UAAU,KAAK,QAAQ,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,WAAW,CAAC,EAAE,CAAC;YAChE,MAAM,GAAG,CAAC,IAAI,CACZ,sBAAsB,EACtB,2CAA2C,KAAK,CAAC,WAAW,sCAAsC,EAClG,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,sBAAsB,CAAC,EAAE,CAC/C,CAAC;QACJ,CAAC;QAED,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,oBAAoB,CAAC,KAAK,CAAC,UAAU,EAAE,WAAW,CAAC,CAAC;QAEjF,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAC;QAClC,wFAAwF;QACxF,2EAA2E;QAC3E,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,MAAM,GAAG,KAAK,CAAC,UAAU,CAAC,CAAC;QAC1E,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC;QAC9C,MAAM,OAAO,GAAG,UAAU,GAAG,UAAU,CAAC;QAExC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,wBAAwB,EAAE;YACrC,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,WAAW;YACX,UAAU;YACV,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,QAAQ,EAAE,IAAI,CAAC,MAAM;SACtB,CAAC,CAAC;QAEH,iFAAiF;QACjF,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,KAAK,CAAC,UAAU,EAAE,WAAW,EAAE,UAAU,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;QAC5F,IAAI,OAAO;YAAE,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,CAAC,CAAC;QACxC,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;YACrB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,wBAAwB,WAAW,MAAM,KAAK,CAAC,UAAU,yKAAyK,CACnO,CAAC;QACJ,CAAC;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,UAAU,KAAK,CAAC,MAAM,gBAAgB,UAAU,sBAAsB,WAAW,2BAA2B,UAAU,GAAG,CAC1H,CAAC;QACJ,CAAC;aAAM,IAAI,OAAO,EAAE,CAAC;YACnB,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC;gBACnB,KAAK,EAAE,IAAI,CAAC,MAAM;gBAClB,GAAG,EAAE,KAAK,CAAC,UAAU;gBACrB,QAAQ,EAAE,gBAAgB,KAAK,CAAC,MAAM,GAAG,CAAC,IAAI,UAAU,OAAO,UAAU,iBAAiB,UAAU,qBAAqB;aAC1H,CAAC,CAAC;QACL,CAAC;QAED,OAAO,EAAE,IAAI,EAAE,CAAC;IAClB,CAAC;IAED,MAAM,CAAC,MAAM;QACX,IAAI,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC3B,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,SAAS,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,EAAE,CAAC,CAAC;QACrE,CAAC;QACD,qFAAqF;QACrF,0CAA0C;QAC1C,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,qBAAqB,EAAE,CAAC,CAAC;IACzD,CAAC;CACF,CAAC,CAAC"}

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

@@ -47,12 +47,12 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
 }, {
     readonly reason: "missing_formula";
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "searchType is \"formula\" but the formula field was omitted";
+    readonly when: "searchType is \"formula\" but the formula field was omitted or blank";
     readonly recovery: "Pass formula in Hill notation, for example \"C6H12O6\" or \"CaH2O2\".";
 }, {
     readonly reason: "missing_structure_args";
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "substructure/superstructure/similarity search missing query or queryType";
+    readonly when: "substructure/superstructure/similarity search with query or queryType omitted, or a blank query";
     readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
 }, {
     readonly reason: "invalid_cid_query";

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;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EAqb1B~~,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;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwb1B,CAAC"}

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

@@ -26,7 +26,7 @@ export const searchCompounds = tool('pubchem_search_compounds', {
         openWorldHint: true,
     },
     input: z.object({
-        searchType: searchTypeEnum.describe('Search strategy. "identifier": name/SMILES/InChIKey lookup. "formula": molecular formula. "substructure": find compounds containing the query as a substructure. "superstructure": find compounds that are themselves substructures of the query. "similarity": 2D Tanimoto similarity to the query.'),
+        searchType: searchTypeEnum.describe('Search strategy; each mode needs its own fields. "identifier": name/SMILES/InChIKey lookup — requires identifierType and identifiers. "formula": molecular formula — requires formula. "substructure": find compounds containing the query as a substructure. "superstructure": find compounds that are themselves substructures of the query. "similarity": 2D Tanimoto similarity to the query. substructure, superstructure, and similarity require query and queryType.'),
         identifierType: identifierTypeEnum
             .optional()
             .describe('Required for identifier search. Type of chemical identifier: "name", "smiles", or "inchikey".'),
@@ -145,13 +145,13 @@ export const searchCompounds = tool('pubchem_search_compounds', {
         {
             reason: 'missing_formula',
             code: JsonRpcErrorCode.ValidationError,
-            when: 'searchType is "formula" but the formula field was omitted',
+            when: 'searchType is "formula" but the formula field was omitted or blank',
             recovery: 'Pass formula in Hill notation, for example "C6H12O6" or "CaH2O2".',
         },
         {
             reason: 'missing_structure_args',
             code: JsonRpcErrorCode.ValidationError,
-            when: 'substructure/superstructure/similarity search missing query or queryType',
+            when: 'substructure/superstructure/similarity search with query or queryType omitted, or a blank query',
             recovery: 'Provide both query (SMILES string or CID as string) and queryType ("smiles" or "cid").',
         },
         {
@@ -229,7 +229,9 @@ export const searchCompounds = tool('pubchem_search_compounds', {
                 break;
             }
             case 'formula': {
-                if (!input.formula) {
+                // Blank means missing: PubChem answers a whitespace-only formula with unrelated
+                // compounds. A padded formula passes through — PubChem trims it.
+                if (!input.formula?.trim()) {
                     throw ctx.fail('missing_formula', undefined, {
                         ...ctx.recoveryFor('missing_formula'),
                     });
@@ -241,7 +243,8 @@ export const searchCompounds = tool('pubchem_search_compounds', {
             case 'substructure':
             case 'superstructure':
             case 'similarity': {
-                if (!input.query || !input.queryType) {
+                // A whitespace-only SMILES query otherwise surfaces as an upstream HTTP 500.
+                if (!input.query?.trim() || !input.queryType) {
                     throw ctx.fail('missing_structure_args', undefined, {
                         ...ctx.recoveryFor('missing_structure_args'),
                     });

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

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/untrusted-text.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"untrusted-text.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/untrusted-text.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;~~AAaH~~;;;;;GAKG;AACH,wBAAgB,UAAU,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAKhD;AAED;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAW9C;AAED;;;;;GAKG;AACH,wBAAgB,UAAU,CAAC,OAAO,EAAE,MAAM,EAAE,QAAQ,SAAK,GAAG,MAAM,CAIjE"}
1	+ {"version":3,"file":"untrusted-text.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/untrusted-text.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAoBH;;;;;GAKG;AACH,wBAAgB,UAAU,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAKhD;AAED;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAW9C;AAED;;;;;GAKG;AACH,wBAAgB,UAAU,CAAC,OAAO,EAAE,MAAM,EAAE,QAAQ,SAAK,GAAG,MAAM,CAIjE"}

package/dist/mcp-server/tools/definitions/untrusted-text.js CHANGED Viewed

@@ -17,8 +17,15 @@
  * Underscore is intentionally excluded: CommonMark treats intraword `_` as
  * literal, so it is a far weaker vector than `*`, and escaping it collides with
  * the format-parity linter's underscored sentinels.
+ *
+ * The backslash is in the class because escaping is not idempotent against one
+ * the payload already carries: `\*` escaped to `\\*` reads as a literal
+ * backslash followed by a LIVE `*`, re-arming the delimiter the escape was meant
+ * to defuse. Escaping it to `\\` first keeps the following `\*` inert. It also
+ * matters on its own — a SMILES stereo bond (`C/C=C\C`) ends a line with a
+ * backslash, which CommonMark reads as a hard line break.
  */
-const INLINE_MARKDOWN = /[`*~]/g;
+const INLINE_MARKDOWN = /[\\`*~]/g;
 /**
  * Frame a single upstream value for safe inline interpolation into `content[]`
  * markdown. Collapses embedded newlines (so the value cannot start a new

package/dist/mcp-server/tools/definitions/untrusted-text.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"untrusted-text.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/untrusted-text.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH~~;;;;;;;;GAQG~~;AACH,MAAM,eAAe,GAAG,~~QAAQ~~,CAAC;~~AAEjC~~;;;;;GAKG;AACH,MAAM,UAAU,UAAU,CAAC,KAAa;IACtC,OAAO,KAAK;SACT,OAAO,CAAC,gBAAgB,EAAE,GAAG,CAAC;SAC9B,OAAO,CAAC,eAAe,EAAE,MAAM,CAAC;SAChC,IAAI,EAAE,CAAC;AACZ,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,SAAS,CAAC,IAAY;IACpC,OAAO,IAAI;SACR,KAAK,CAAC,UAAU,CAAC;SACjB,GAAG,CAAC,CAAC,OAAO,EAAE,EAAE;QACf,MAAM,IAAI,GAAG,OAAO;aACjB,OAAO,CAAC,eAAe,EAAE,MAAM,CAAC;aAChC,OAAO,CAAC,gBAAgB,EAAE,QAAQ,CAAC;aACnC,OAAO,CAAC,qBAAqB,EAAE,QAAQ,CAAC,CAAC;QAC5C,OAAO,IAAI,CAAC,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;IACpD,CAAC,CAAC;SACD,IAAI,CAAC,IAAI,CAAC,CAAC;AAChB,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,UAAU,CAAC,OAAe,EAAE,QAAQ,GAAG,EAAE;IACvD,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,GAAG,CAAC,GAAG,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC;IACxF,MAAM,KAAK,GAAG,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,UAAU,GAAG,CAAC,CAAC,CAAC,CAAC;IACtD,OAAO,GAAG,KAAK,GAAG,QAAQ,KAAK,OAAO,KAAK,KAAK,EAAE,CAAC;AACrD,CAAC"}
1	+ {"version":3,"file":"untrusted-text.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/untrusted-text.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH;;;;;;;;;;;;;;;GAeG;AACH,MAAM,eAAe,GAAG,UAAU,CAAC;AAEnC;;;;;GAKG;AACH,MAAM,UAAU,UAAU,CAAC,KAAa;IACtC,OAAO,KAAK;SACT,OAAO,CAAC,gBAAgB,EAAE,GAAG,CAAC;SAC9B,OAAO,CAAC,eAAe,EAAE,MAAM,CAAC;SAChC,IAAI,EAAE,CAAC;AACZ,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,SAAS,CAAC,IAAY;IACpC,OAAO,IAAI;SACR,KAAK,CAAC,UAAU,CAAC;SACjB,GAAG,CAAC,CAAC,OAAO,EAAE,EAAE;QACf,MAAM,IAAI,GAAG,OAAO;aACjB,OAAO,CAAC,eAAe,EAAE,MAAM,CAAC;aAChC,OAAO,CAAC,gBAAgB,EAAE,QAAQ,CAAC;aACnC,OAAO,CAAC,qBAAqB,EAAE,QAAQ,CAAC,CAAC;QAC5C,OAAO,IAAI,CAAC,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;IACpD,CAAC,CAAC;SACD,IAAI,CAAC,IAAI,CAAC,CAAC;AAChB,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,UAAU,CAAC,OAAe,EAAE,QAAQ,GAAG,EAAE;IACvD,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,GAAG,CAAC,GAAG,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC;IACxF,MAAM,KAAK,GAAG,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,UAAU,GAAG,CAAC,CAAC,CAAC,CAAC;IACtD,OAAO,GAAG,KAAK,GAAG,QAAQ,KAAK,OAAO,KAAK,KAAK,EAAE,CAAC;AACrD,CAAC"}

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

@@ -4,7 +4,7 @@
  * @module services/pubchem/pubchem-client
  */
 import { JsonRpcErrorCode, McpError, notFound, serviceUnavailable, } from '@cyanheads/mcp-ts-core/errors';
-import { httpErrorFromResponse } from '@cyanheads/mcp-ts-core/utils';
+import { httpErrorFromResponse, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 const isNotFound = (error) => error instanceof McpError && error.code === JsonRpcErrorCode.NotFound;
 /** Distinguishes the two outcomes PUG View hides behind a single HTTP 404.
  *
@@ -63,6 +63,17 @@ class RateLimiter {
 }
 // ── Helpers ──────────────────────────────────────────────────────────
 const sleep = (ms) => new Promise((r) => setTimeout(r, ms));
+/** Records a failed PubChem request, with its URL, in the server's own log. The error the
+ * caller receives deliberately omits the URL, so this line is the only place an operator can
+ * see which route failed. The module `logger` writes server-side only — `ctx.log` would also
+ * forward the line to the client as `notifications/message`. */
+function logFailedRequest(level, url, method, detail) {
+    const summary = 'status' in detail ? `HTTP ${detail.status}` : detail.error;
+    logger[level](`PubChem request failed: ${summary}`, requestContextService.createRequestContext({
+        operation: 'PubChemClient.fetch',
+        additionalContext: { url, method, ...detail },
+    }));
+}
 /** PubChem returns different field names than the request parameter names for some properties.
  * Request IsomericSMILES → response key "SMILES" (includes stereochemistry).
  * Request CanonicalSMILES → response key "ConnectivitySMILES" (connectivity only). */
@@ -189,9 +200,15 @@ function extractGHSInfo(section) {
  * H361f/H361fd — naming a narrower classification than its base code, and on some records it
  * is the only form deposited. Allowing up to two trailing letters keeps those as their own
  * entries instead of dropping the statement; a suffixed code is deliberately distinct from
- * its base, so both survive the later dedup-by-code. */
+ * its base, so both survive the later dedup-by-code.
+ *
+ * The annotation group consumes exactly one annotation per iteration, with its leading
+ * whitespace attached and the trailing whitespace taken once after the loop. Writing it as
+ * `(?:(?:\([^)]*\)|\*+)\s*)*` instead nests `\*+` inside a `*` loop, so a code followed by a
+ * run of asterisks and no separator makes the engine try every partition of that run — the
+ * same statements match either way, but only this form matches them in linear time. */
 function parseCodedStatement(text) {
-    const match = text.match(/^([HP]\d{3}[A-Za-z]{0,2}(?:\+[HP]\d{3}[A-Za-z]{0,2})*)\s*(?:(?:\([^)]*\)|\*+)\s*)*[:\-–]\s*(.+)/);
+    const match = text.match(/^([HP]\d{3}[A-Za-z]{0,2}(?:\+[HP]\d{3}[A-Za-z]{0,2})*)(?:\s*(?:\([^)]*\)|\*))*\s*[:\-–]\s*(.+)/);
     if (match?.[1] && match[2])
         return { code: match[1], statement: match[2].trim() };
     const codeOnly = text.match(/^([HP]\d{3}[A-Za-z]{0,2}(?:\+[HP]\d{3}[A-Za-z]{0,2})*)$/);
@@ -401,6 +418,7 @@ export class PubChemClient {
      * one resilience contract — the divergence that left fetchBinary without retry or a clean
      * timeout message (#16) cannot recur. */
     async fetchResponse(url, init) {
+        const method = init?.method ?? 'GET';
         for (let attempt = 0;; attempt++) {
             await this.rateLimiter.acquire();
             const controller = new AbortController();
@@ -411,20 +429,30 @@ export class PubChemClient {
                     return response;
                 const text = await response.text();
                 const fault = parseFaultMessage(text) ?? text.slice(0, 300);
+                /** `data` reaches the client as `structuredContent.error.data`, and a PubChem
+                 * request URL carries the caller's own query — a compound name, a SMILES string,
+                 * an SDQ query blob. Only the parsed fault travels; the framework omits the URL
+                 * by default and names the host in the message, which is enough to place the
+                 * failure without echoing the request back. */
                 const error = await httpErrorFromResponse(response, {
                     captureBody: false,
                     service: 'PubChem',
-                    data: { fault, url },
+                    data: { fault },
                 });
                 // Retry once on 5xx unless the framework marks the failure as permanent.
                 if (response.status >= 500 && error.data?.retryable !== false && attempt < 1) {
                     await sleep(1000 * 2 ** attempt);
                     continue;
                 }
+                // A 404 is routine — most callers read it as "no data" — so it logs below warning.
+                logFailedRequest(response.status === 404 ? 'debug' : 'warning', url, method, {
+                    status: response.status,
+                    fault,
+                });
                 throw error;
             }
             catch (error) {
-                // HTTP errors are already classified — surface them, don't retry.
+                // HTTP errors are already classified and logged — surface them, don't retry.
                 if (error instanceof McpError)
                     throw error;
                 // Retry once on network errors
@@ -432,10 +460,13 @@ export class PubChemClient {
                     await sleep(1000 * 2 ** attempt);
                     continue;
                 }
-                if (error instanceof Error && error.name === 'AbortError') {
-                    throw new Error('PubChem request timed out (30s)');
-                }
-                throw error;
+                const failure = error instanceof Error && error.name === 'AbortError'
+                    ? new Error('PubChem request timed out (30s)')
+                    : error;
+                logFailedRequest('warning', url, method, {
+                    error: failure instanceof Error ? failure.message : String(failure),
+                });
+                throw failure;
             }
             finally {
                 clearTimeout(timeoutId);
@@ -1087,18 +1118,27 @@ export class PubChemClient {
                 return empty;
             throw error;
         }
+        // Both rejections below arrive inside a 2xx, past fetchResponse's failure logging.
+        const reject = (message, data) => {
+            logFailedRequest('warning', url, 'GET', { error: message });
+            throw serviceUnavailable(message, data);
+        };
         let parsed;
         try {
             parsed = JSON.parse(body);
         }
         catch {
-            throw serviceUnavailable(`PubChem SDQ returned unparseable JSON for collection "${collection}"`, { collection, cid, snippet: body.slice(0, 200) });
+            return reject(`PubChem SDQ returned unparseable JSON for collection "${collection}"`, {
+                collection,
+                cid,
+                snippet: body.slice(0, 200),
+            });
         }
         const set = parsed.SDQOutputSet?.[0];
         if (!set)
             return empty;
         if (set.status?.error) {
-            throw serviceUnavailable(`PubChem SDQ rejected the query for collection "${collection}": ${set.status.error}`, { collection, cid, sdqError: set.status.error });
+            return reject(`PubChem SDQ rejected the query for collection "${collection}": ${set.status.error}`, { collection, cid, sdqError: set.status.error });
         }
         return { rows: set.rows ?? [], totalCount: set.totalCount ?? 0 };
     }

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

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

@@ -1,7 +1,7 @@
 {
   "manifest_version": "0.3",
   "name": "pubchem-mcp-server",
-  "version": "0.6.2",
+  "version": "0.6.4",
   "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": "0.6.2",
+  "version": "0.6.4",
   "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",
@@ -9,7 +9,17 @@
   "bin": {
     "pubchem-mcp-server": "dist/index.js"
   },
-  "files": ["dist/", "README.md", "LICENSE", "server.json", "manifest.json", "Dockerfile"],
+  "files": [
+    "changelog/",
+    "dist/",
+    "README.md",
+    "LICENSE",
+    "CLAUDE.md",
+    "AGENTS.md",
+    "Dockerfile",
+    "server.json",
+    "manifest.json"
+  ],
   "scripts": {
     "build": "bun scripts/build.ts",
     "rebuild": "bun scripts/clean.ts && bun scripts/build.ts",
@@ -74,18 +84,18 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.13.0",
+    "@cyanheads/mcp-ts-core": "^0.13.6",
     "pino-pretty": "^13.1.3",
-    "zod": "^4.6.1"
+    "zod": "^4.6.5"
   },
   "devDependencies": {
-    "@biomejs/biome": "2.5.13",
-    "@socketsecurity/bun-security-scanner": "^1.1.2",
-    "@types/node": "26.5.1",
+    "@biomejs/biome": "2.5.14",
+    "@socketsecurity/bun-security-scanner": "^1.1.3",
+    "@types/node": "26.6.2",
     "depcheck": "^1.4.7",
     "ignore": "^7.0.9",
-    "tsc-alias": "^1.9.4",
+    "tsc-alias": "^1.9.5",
     "typescript": "^7.0.2",
-    "vitest": "^5.0.0"
+    "vitest": "^5.0.1"
   }
 }