@cyanheads/pubchem-mcp-server 0.6.3 → 0.6.5
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.
- package/AGENTS.md +1 -1
- package/CLAUDE.md +1 -1
- package/README.md +6 -3
- package/changelog/0.6.x/0.6.4.md +23 -0
- package/changelog/0.6.x/0.6.5.md +22 -0
- package/dist/mcp-server/resources/definitions/assay.resource.js +3 -3
- package/dist/mcp-server/resources/definitions/assay.resource.js.map +1 -1
- package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js +3 -3
- package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js.map +1 -1
- package/dist/mcp-server/resources/definitions/compound-image.resource.js +3 -3
- package/dist/mcp-server/resources/definitions/compound-image.resource.js.map +1 -1
- package/dist/mcp-server/resources/definitions/compound-safety.resource.js +3 -3
- package/dist/mcp-server/resources/definitions/compound-safety.resource.js.map +1 -1
- package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js +3 -3
- package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js.map +1 -1
- package/dist/mcp-server/resources/definitions/compound.resource.js +3 -3
- package/dist/mcp-server/resources/definitions/compound.resource.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js +3 -3
- package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js +5 -5
- package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-details.tool.js +5 -5
- package/dist/mcp-server/tools/definitions/get-compound-details.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-image.tool.js +2 -2
- package/dist/mcp-server/tools/definitions/get-compound-image.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js +2 -2
- package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js +2 -2
- package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js +2 -2
- package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-summary.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/get-summary.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/index.d.ts +13 -2
- package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-assays.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/search-assays.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts +13 -2
- package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-compounds.tool.js +93 -42
- package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map +1 -1
- package/dist/services/pubchem/pubchem-client.d.ts +40 -26
- package/dist/services/pubchem/pubchem-client.d.ts.map +1 -1
- package/dist/services/pubchem/pubchem-client.js +242 -106
- package/dist/services/pubchem/pubchem-client.js.map +1 -1
- package/manifest.json +1 -1
- package/package.json +4 -4
- package/server.json +3 -3
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-
{"version":3,"file":"get-compound-image.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;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,gBAAgB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IACjE,KAAK,EAAE,oBAAoB;IAC3B,WAAW,EAAE,iEAAiE;IAC9E,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,
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1
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+
{"version":3,"file":"get-compound-image.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-image.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;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,gBAAgB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IACjE,KAAK,EAAE,oBAAoB;IAC3B,WAAW,EAAE,iEAAiE;IAC9E,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,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,CAAC,OAAO,EAAE,OAAO,CAAC,CAAC;aACxB,OAAO,CAAC,OAAO,CAAC;aAChB,QAAQ,CAAC,uEAAuE,CAAC;KACrF,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;QAClE,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QAChE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QACpD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;KACvD,CAAC;IACF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,iFAAiF;YACjF,mFAAmF;YACnF,QAAQ,EAAE,SAAS;YACnB,IAAI,EAAE,4CAA4C;YAClD,QAAQ,EAAE,+DAA+D;SAC1E;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;QACxE,MAAM,GAAG,GAAG,KAAK,CAAC,IAAI,KAAK,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC;QAE/C,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,EAAE,MAAM,CAAC,UAAU,EAAE,CAAC,CAAC;QAE9F,OAAO;YACL,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,WAAW,EAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,QAAQ,CAAC;YACnD,QAAQ,EAAE,WAAW;YACrB,KAAK,EAAE,GAAG;YACV,MAAM,EAAE,GAAG;SACZ,CAAC;IACJ,CAAC;IAED,MAAM,CAAC,MAAM;QACX,OAAO;YACL,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,MAAM,CAAC,WAAW,EAAE,QAAQ,EAAE,MAAM,CAAC,QAAQ,EAAE;YACtE;gBACE,IAAI,EAAE,MAAM;gBACZ,IAAI,EAAE,wBAAwB,MAAM,CAAC,GAAG,KAAK,MAAM,CAAC,KAAK,IAAI,MAAM,CAAC,MAAM,GAAG;aAC9E;SACF,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
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{"version":3,"file":"get-compound-interactions.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-interactions.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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{"version":3,"file":"get-compound-interactions.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-interactions.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA0PlC,CAAC"}
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@@ -17,7 +17,7 @@ export const getCompoundInteractions = tool('pubchem_get_compound_interactions',
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cid: z
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.number()
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.int()
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-
.
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.min(1)
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.describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
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kinds: z
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.array(z.enum(['drug-drug', 'drug-food', 'target']))
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@@ -106,7 +106,7 @@ export const getCompoundInteractions = tool('pubchem_get_compound_interactions',
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},
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async handler(input, ctx) {
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const client = getPubChemClient();
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const { entries, pages, failedKinds } = await client.getInteractions(input.cid, input.kinds, input.maxEntries, input.offset);
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const { entries, pages, failedKinds } = await client.getInteractions(input.cid, input.kinds, input.maxEntries, input.offset, ctx.signal);
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for (const f of failedKinds) {
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ctx.log.warning('Interaction kind failed', {
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cid: input.cid,
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+
{"version":3,"file":"get-compound-interactions.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-interactions.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,SAAS,EAAE,MAAM,qBAAqB,CAAC;AAE5D,MAAM,CAAC,MAAM,uBAAuB,GAAG,IAAI,CAAC,mCAAmC,EAAE;IAC/E,KAAK,EAAE,2BAA2B;IAClC,WAAW,EACT,oZAAoZ;IACtZ,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,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,KAAK,EAAE,CAAC;aACL,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAC,CAAC;aACnD,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,WAAW,CAAC,CAAC;aACtB,QAAQ,CACP,6LAA6L,CAC9L;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;YACP,wFAAwF;YACxF,yFAAyF;YACzF,oDAAoD;aACnD,GAAG,CAAC,UAAU,CAAC;aACf,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,qTAAqT,CACtT;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,sJAAsJ,CACvJ;KACJ,CAAC;IACF,gFAAgF;IAChF,kEAAkE;IAClE,YAAY,EAAE,EAAE,UAAU,EAAE,YAAY,EAAE;IAC1C,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,uBAAuB,CAAC;YACpF,OAAO,EAAE,CAAC;iBACP,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,sEAAsE,CAAC;YACnF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oDAAoD,CAAC;YACjF,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4BAA4B,CAAC;SACxD,CAAC;aACD,QAAQ,CAAC,6BAA6B,CAAC,CAC3C;aACA,QAAQ,CAAC,iDAAiD,CAAC;QAC9D,MAAM,EAAE,CAAC;aACN,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,IAAI,EAAE,CAAC;iBACJ,IAAI,CAAC,CAAC,WAAW,EAAE,WAAW,EAAE,QAAQ,CAAC,CAAC;iBAC1C,QAAQ,CAAC,wCAAwC,CAAC;YACrD,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;YACjF,YAAY,EAAE,CAAC;iBACZ,MAAM,EAAE;iBACR,QAAQ,CACP,6XAA6X,CAC9X;YACH,UAAU,EAAE,CAAC;iBACV,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,8GAA8G,CAC/G;YACH,SAAS,EAAE,CAAC;iBACT,OAAO,EAAE;iBACT,QAAQ,CAAC,sEAAsE,CAAC;SACpF,CAAC;aACD,QAAQ,CAAC,yCAAyC,CAAC,CACvD;aACA,QAAQ,CACP,2JAA2J,CAC5J;KACJ,CAAC;IACF,yFAAyF;IACzF,sFAAsF;IACtF,+BAA+B;IAC/B,UAAU,EAAE;QACV,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QACrF,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;QAC1F,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,CACP,oLAAoL,CACrL;QACH,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4DAA4D,CAAC;QACzF,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,yNAAyN,CAC1N;QACH,WAAW,EAAE,CAAC;aACX,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,4JAA4J,CAC7J;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,2MAA2M,CAC5M;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,MAAM,MAAM,CAAC,eAAe,CAClE,KAAK,CAAC,GAAG,EACT,KAAK,CAAC,KAAK,EACX,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,MAAM,EACZ,GAAG,CAAC,MAAM,CACX,CAAC;QAEF,KAAK,MAAM,CAAC,IAAI,WAAW,EAAE,CAAC;YAC5B,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,yBAAyB,EAAE;gBACzC,GAAG,EAAE,KAAK,CAAC,GAAG;gBACd,IAAI,EAAE,CAAC,CAAC,IAAI;gBACZ,KAAK,EAAE,CAAC,CAAC,OAAO;aACjB,CAAC,CAAC;QACL,CAAC;QACD,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,sBAAsB,EAAE;YACnC,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,QAAQ,EAAE,OAAO,CAAC,MAAM;YACxB,MAAM,EAAE,WAAW,CAAC,MAAM;SAC3B,CAAC,CAAC;QAEH,wFAAwF;QACxF,0FAA0F;QAC1F,2EAA2E;QAC3E,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;YAC7B,MAAM,IAAI,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,eAAe,CAAC;YAC9C,MAAM,SAAS,GAAG,IAAI,GAAG,CAAC,CAAC,YAAY,CAAC;YACxC,OAAO;gBACL,IAAI,EAAE,CAAC,CAAC,IAAI;gBACZ,aAAa,EAAE,CAAC,CAAC,aAAa;gBAC9B,YAAY,EAAE,CAAC,CAAC,YAAY;gBAC5B,SAAS;gBACT,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,UAAU,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;aAC3C,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;QAEpD,GAAG,CAAC,MAAM,CAAC;YACT,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC;YACtC,aAAa,EAAE,OAAO,CAAC,MAAM;YAC7B,SAAS,EAAE,SAAS,CAAC,MAAM,GAAG,CAAC;YAC/B,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QAEH,yFAAyF;QACzF,mEAAmE;QACnE,MAAM,cAAc,GAAG,SAAS,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC;QACrF,IAAI,cAAc,KAAK,SAAS;YAAE,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,cAAc,EAAE,CAAC,CAAC;QAE7E,4EAA4E;QAC5E,MAAM,WAAW,GAAa,EAAE,CAAC;QAEjC,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YACxD,MAAM,MAAM,GAAG,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACtC,GAAG,CAAC,MAAM,CAAC,EAAE,WAAW,EAAE,KAAK,EAAE,CAAC,CAAC;YACnC,WAAW,CAAC,IAAI,CACd,sBAAsB,KAAK,eAAe,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,YAAY,KAAK,CAAC,GAAG,IAC9E,OAAO,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,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@@ -44,7 +44,7 @@ export const getCompoundSafety = tool('pubchem_get_compound_safety', {
|
|
|
44
44
|
},
|
|
45
45
|
input: z.object({
|
|
46
46
|
cids: z
|
|
47
|
-
.array(z.number().int().
|
|
47
|
+
.array(z.number().int().min(1))
|
|
48
48
|
.min(1)
|
|
49
49
|
.max(25)
|
|
50
50
|
.describe('PubChem Compound IDs to fetch safety data for (1-25). Resolve from names/SMILES with pubchem_search_compounds.'),
|
|
@@ -83,7 +83,7 @@ export const getCompoundSafety = tool('pubchem_get_compound_safety', {
|
|
|
83
83
|
const lookupByCid = new Map();
|
|
84
84
|
for (let i = 0; i < input.cids.length; i += MAX_IN_FLIGHT) {
|
|
85
85
|
const chunk = input.cids.slice(i, i + MAX_IN_FLIGHT);
|
|
86
|
-
const chunkData = await Promise.all(chunk.map(async (cid) => [cid, await client.getSafetyData(cid)]));
|
|
86
|
+
const chunkData = await Promise.all(chunk.map(async (cid) => [cid, await client.getSafetyData(cid, ctx.signal)]));
|
|
87
87
|
for (const [cid, lookup] of chunkData)
|
|
88
88
|
lookupByCid.set(cid, lookup);
|
|
89
89
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-compound-safety.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-safety.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AAEjD,MAAM,SAAS,GAAG,CAAC;KAChB,MAAM,CAAC;IACN,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;IACrF,UAAU,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,mDAAmD,CAAC;IAC7F,gBAAgB,EAAE,CAAC;SAChB,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QAClD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;KACzD,CAAC;SACD,QAAQ,CAAC,6BAA6B,CAAC,CAC3C;SACA,QAAQ,CAAC,wBAAwB,CAAC;IACrC,uBAAuB,EAAE,CAAC;SACvB,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QAClD,SAAS,EAAE,CAAC;aACT,MAAM,EAAE;aACR,QAAQ,CACP,8OAA8O,CAC/O;QACH,OAAO,EAAE,CAAC;aACP,OAAO,EAAE;aACT,QAAQ,CACP,uQAAuQ,CACxQ;KACJ,CAAC;SACD,QAAQ,CAAC,oCAAoC,CAAC,CAClD;SACA,QAAQ,CAAC,+BAA+B,CAAC;CAC7C,CAAC;KACD,QAAQ,CAAC,0BAA0B,CAAC,CAAC;AAExC,sGAAsG;AACtG,MAAM,aAAa,GAAG,EAAE,CAAC;AAEzB,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,6BAA6B,EAAE;IACnE,KAAK,EAAE,qBAAqB;IAC5B,WAAW,EACT,qSAAqS;IACvS,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,IAAI,EAAE,CAAC;aACJ,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,
|
|
1
|
+
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@@ -18,7 +18,7 @@ export const getCompoundXrefs = tool('pubchem_get_compound_xrefs', {
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18
18
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cid: z
|
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19
19
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.number()
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20
20
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.int()
|
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21
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-
.
|
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21
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+
.min(1)
|
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22
22
|
.describe('PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.'),
|
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23
23
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xrefTypes: z
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24
24
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.array(xrefTypeEnum)
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@@ -93,7 +93,7 @@ export const getCompoundXrefs = tool('pubchem_get_compound_xrefs', {
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93
93
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// Sequential per type to avoid rate limit spikes
|
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94
94
|
const xrefs = [];
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95
95
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for (const xrefType of input.xrefTypes) {
|
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96
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-
const allIds = await client.getXrefs(input.cid, xrefType);
|
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96
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+
const allIds = await client.getXrefs(input.cid, xrefType, ctx.signal);
|
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97
97
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const totalAvailable = allIds.length;
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98
98
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// Offset is applied client-side: PubChem's xref endpoint returns the whole list for a
|
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99
99
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// type in one response, so getXrefs already holds every ID.
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@@ -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,6QAA6Q;IAC/Q,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,
|
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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,6QAA6Q;IAC/Q,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,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,SAAS,EAAE,CAAC;aACT,KAAK,CAAC,YAAY,CAAC;aACnB,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,iNAAiN,CAClN;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,wMAAwM,CACzM;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,8LAA8L,CAC/L;KACJ,CAAC;IACF,mFAAmF;IACnF,gFAAgF;IAChF,+EAA+E;IAC/E,YAAY,EAAE,EAAE,UAAU,EAAE,YAAY,EAAE;IAC1C,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,mEAAmE,CAAC;YAChF,cAAc,EAAE,CAAC;iBACd,MAAM,EAAE;iBACR,QAAQ,CAAC,sDAAsD,CAAC;YACnE,SAAS,EAAE,CAAC;iBACT,OAAO,EAAE;iBACT,QAAQ,CAAC,2DAA2D,CAAC;SACzE,CAAC;aACD,QAAQ,CAAC,qCAAqC,CAAC,CACnD;aACA,QAAQ,CAAC,mCAAmC,CAAC;KACjD,CAAC;IACF,yFAAyF;IACzF,oFAAoF;IACpF,2FAA2F;IAC3F,0BAA0B;IAC1B,UAAU,EAAE;QACV,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6DAA6D,CAAC;QAC1F,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,CACP,8KAA8K,CAC/K;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,6GAA6G,CAC9G;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,0LAA0L,CAC3L;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,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;YACtE,MAAM,cAAc,GAAG,MAAM,CAAC,MAAM,CAAC;YACrC,sFAAsF;YACtF,4DAA4D;YAC5D,MAAM,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,MAAM,GAAG,KAAK,CAAC,UAAU,CAAC,CAAC;YAExE,KAAK,CAAC,IAAI,CAAC;gBACT,IAAI,EAAE,QAAQ;gBACd,GAAG;gBACH,cAAc;gBACd,SAAS,EAAE,KAAK,CAAC,MAAM,GAAG,GAAG,CAAC,MAAM,GAAG,cAAc;aACtD,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,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,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,2FAA2F;QAC3F,4FAA4F;QAC5F,yFAAyF;QACzF,0EAA0E;QAC1E,MAAM,cAAc,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;QACxD,MAAM,OAAO,GAAG,cAAc,CAAC,MAAM,GAAG,CAAC,CAAC;QAC1C,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,MAAM,IAAI,CAAC,CAAC,CAAC;QACvE,MAAM,YAAY,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC;QAErE,GAAG,CAAC,MAAM,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,CAAC,CAAC;QACzD,IAAI,OAAO;YAAE,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,CAAC,CAAC;QAExC,mFAAmF;QACnF,yFAAyF;QACzF,IAAI,YAAY,KAAK,CAAC,EAAE,CAAC;YACvB,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;aAAM,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,KAAK,CAAC,CAAC,EAAE,CAAC;YAClD,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,UAAU,KAAK,CAAC,MAAM,mDAAmD,YAAY,gCAAgC,YAAY,GAAG,CACrI,CAAC;QACJ,CAAC;aAAM,IAAI,OAAO,EAAE,CAAC;YACnB,MAAM,SAAS,GAAG,cAAc;iBAC7B,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,cAAc,SAAS,CAAC;iBACnD,IAAI,CAAC,IAAI,CAAC,CAAC;YACd,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,wBAAwB,SAAS,iBAAiB,UAAU,qBAAqB,CAClF,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,mFAAmF;YACnF,6EAA6E;YAC7E,IAAI,SAAS,GAAG,GAAG,IAAI,CAAC,cAAc,QAAQ,CAAC;YAC/C,IAAI,IAAI,CAAC,GAAG,CAAC,MAAM,KAAK,IAAI,CAAC,cAAc,EAAE,CAAC;gBAC5C,SAAS,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,OAAO,IAAI,CAAC,cAAc,QAAQ,CAAC;gBACjE,IAAI,IAAI,CAAC,SAAS;oBAAE,SAAS,IAAI,cAAc,CAAC;YAClD,CAAC;YACD,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,gFAAgF;gBAChF,wFAAwF;gBACxF,KAAK,CAAC,IAAI,CAAC,K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|
|
@@ -86,7 +86,7 @@ export const getSummary = tool('pubchem_get_summary', {
|
|
|
86
86
|
async handler(input, ctx) {
|
|
87
87
|
const client = getPubChemClient();
|
|
88
88
|
const summaries = await Promise.all(input.identifiers.map(async (id) => {
|
|
89
|
-
const raw = await client.getEntitySummary(input.entityType, id);
|
|
89
|
+
const raw = await client.getEntitySummary(input.entityType, id, ctx.signal);
|
|
90
90
|
if (!raw)
|
|
91
91
|
return { identifier: id, found: false };
|
|
92
92
|
const data = extractSummary(input.entityType, raw);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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+
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@@ -147,18 +147,29 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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147
147
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}, {
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148
148
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readonly reason: "missing_formula";
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149
149
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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150
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-
readonly when: "searchType is \"formula\" but the formula field was omitted";
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150
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+
readonly when: "searchType is \"formula\" but the formula field was omitted or blank";
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151
151
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readonly recovery: "Pass formula in Hill notation, for example \"C6H12O6\" or \"CaH2O2\".";
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152
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}, {
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153
153
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readonly reason: "missing_structure_args";
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154
154
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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155
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-
readonly when: "substructure/superstructure/similarity search
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155
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+
readonly when: "substructure/superstructure/similarity search with query or queryType omitted, or a blank query";
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156
156
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readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
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157
157
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}, {
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|
158
158
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readonly reason: "invalid_cid_query";
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|
159
159
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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|
160
160
|
readonly when: "structure/similarity search with queryType \"cid\" but query is not a positive integer CID";
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161
161
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readonly recovery: "Pass a positive integer CID string (e.g. \"2244\"), or set queryType \"smiles\" with a SMILES query.";
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|
162
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+
}, {
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|
163
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+
readonly reason: "identifier_rejected";
|
|
164
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+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
165
|
+
readonly when: "identifier search where PubChem rejected every identifier in the batch as unreadable (HTTP 400) — for SMILES, a string it could not standardize into a structure. A batch with any other outcome lists rejected inputs in unresolvedIdentifiers instead";
|
|
166
|
+
readonly recovery: "Check each identifier against identifierType: for SMILES, balanced ring closures and parentheses, valid element symbols, and no \"*\" wildcard atoms; otherwise set identifierType to the form the identifiers are in.";
|
|
167
|
+
}, {
|
|
168
|
+
readonly reason: "search_query_rejected";
|
|
169
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
170
|
+
readonly thrownBy: "service";
|
|
171
|
+
readonly when: "PubChem failed a formula, substructure, superstructure, or similarity search with HTTP 500 \"Search status indicates failure\" — its answer for a malformed SMILES or formula, a SMILES with a \"*\" wildcard atom, or a CID with no record";
|
|
172
|
+
readonly recovery: "Fix the SMILES syntax or remove \"*\" atoms, write the formula in Hill notation (e.g. \"C6H12O6\"), or confirm the CID exists with pubchem_get_compound_details.";
|
|
162
173
|
}], {
|
|
163
174
|
readonly searchType: import("zod").ZodString;
|
|
164
175
|
readonly totalFound: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
@@ -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
|
|
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"}
|
|
@@ -91,7 +91,7 @@ export const searchAssays = tool('pubchem_search_assays', {
|
|
|
91
91
|
if (input.targetType === 'geneid' && !/^\d+$/.test(targetQuery)) {
|
|
92
92
|
throw ctx.fail('invalid_geneid_query', `targetType is "geneid" but targetQuery "${input.targetQuery}" is not a positive integer Gene ID.`, { ...ctx.recoveryFor('invalid_geneid_query') });
|
|
93
93
|
}
|
|
94
|
-
const allAids = await client.searchAssaysByTarget(input.targetType, targetQuery);
|
|
94
|
+
const allAids = await client.searchAssaysByTarget(input.targetType, targetQuery, ctx.signal);
|
|
95
95
|
const totalFound = allAids.length;
|
|
96
96
|
// Offset is applied client-side: PubChem's target-to-AID endpoint returns the whole AID
|
|
97
97
|
// list in one response, so searchAssaysByTarget already holds every match.
|
|
@@ -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,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;
|
|
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,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;QAE7F,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"}
|
|
@@ -47,18 +47,29 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
|
|
|
47
47
|
}, {
|
|
48
48
|
readonly reason: "missing_formula";
|
|
49
49
|
readonly code: JsonRpcErrorCode.ValidationError;
|
|
50
|
-
readonly when: "searchType is \"formula\" but the formula field was omitted";
|
|
50
|
+
readonly when: "searchType is \"formula\" but the formula field was omitted or blank";
|
|
51
51
|
readonly recovery: "Pass formula in Hill notation, for example \"C6H12O6\" or \"CaH2O2\".";
|
|
52
52
|
}, {
|
|
53
53
|
readonly reason: "missing_structure_args";
|
|
54
54
|
readonly code: JsonRpcErrorCode.ValidationError;
|
|
55
|
-
readonly when: "substructure/superstructure/similarity search
|
|
55
|
+
readonly when: "substructure/superstructure/similarity search with query or queryType omitted, or a blank query";
|
|
56
56
|
readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
|
|
57
57
|
}, {
|
|
58
58
|
readonly reason: "invalid_cid_query";
|
|
59
59
|
readonly code: JsonRpcErrorCode.ValidationError;
|
|
60
60
|
readonly when: "structure/similarity search with queryType \"cid\" but query is not a positive integer CID";
|
|
61
61
|
readonly recovery: "Pass a positive integer CID string (e.g. \"2244\"), or set queryType \"smiles\" with a SMILES query.";
|
|
62
|
+
}, {
|
|
63
|
+
readonly reason: "identifier_rejected";
|
|
64
|
+
readonly code: JsonRpcErrorCode.ValidationError;
|
|
65
|
+
readonly when: "identifier search where PubChem rejected every identifier in the batch as unreadable (HTTP 400) — for SMILES, a string it could not standardize into a structure. A batch with any other outcome lists rejected inputs in unresolvedIdentifiers instead";
|
|
66
|
+
readonly recovery: "Check each identifier against identifierType: for SMILES, balanced ring closures and parentheses, valid element symbols, and no \"*\" wildcard atoms; otherwise set identifierType to the form the identifiers are in.";
|
|
67
|
+
}, {
|
|
68
|
+
readonly reason: "search_query_rejected";
|
|
69
|
+
readonly code: JsonRpcErrorCode.ValidationError;
|
|
70
|
+
readonly thrownBy: "service";
|
|
71
|
+
readonly when: "PubChem failed a formula, substructure, superstructure, or similarity search with HTTP 500 \"Search status indicates failure\" — its answer for a malformed SMILES or formula, a SMILES with a \"*\" wildcard atom, or a CID with no record";
|
|
72
|
+
readonly recovery: "Fix the SMILES syntax or remove \"*\" atoms, write the formula in Hill notation (e.g. \"C6H12O6\"), or confirm the CID exists with pubchem_get_compound_details.";
|
|
62
73
|
}], {
|
|
63
74
|
readonly searchType: z.ZodString;
|
|
64
75
|
readonly totalFound: z.ZodOptional<z.ZodNumber>;
|
|
@@ -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,
|
|
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,EAAY,MAAM,+BAA+B,CAAC;AAqC3E,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwe1B,CAAC"}
|