@cyanheads/pubchem-mcp-server 0.3.0 → 0.4.0
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/README.md +2 -1
- package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js +2 -1
- package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.d.ts +12 -1
- package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js +106 -4
- 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 +12 -4
- package/dist/mcp-server/tools/definitions/get-compound-details.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 +8 -3
- package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-safety.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js +4 -3
- package/dist/mcp-server/tools/definitions/get-compound-safety.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.d.ts +3 -1
- package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js +14 -0
- package/dist/mcp-server/tools/definitions/get-compound-xrefs.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-summary.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-summary.tool.js +17 -4
- package/dist/mcp-server/tools/definitions/get-summary.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/index.d.ts +32 -3
- package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts +12 -1
- package/dist/mcp-server/tools/definitions/search-assays.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-assays.tool.js +31 -4
- package/dist/mcp-server/tools/definitions/search-assays.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts +6 -0
- package/dist/mcp-server/tools/definitions/search-compounds.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-compounds.tool.js +94 -22
- package/dist/mcp-server/tools/definitions/search-compounds.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/untrusted-text.d.ts +35 -0
- package/dist/mcp-server/tools/definitions/untrusted-text.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/untrusted-text.js +65 -0
- package/dist/mcp-server/tools/definitions/untrusted-text.js.map +1 -0
- package/manifest.json +1 -1
- package/package.json +3 -3
- package/server.json +3 -3
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-
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{"version":3,"file":"get-compound-xrefs.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,UAAU,EAAE,MAAM,6BAA6B,CAAC;AAEzD,MAAM,YAAY,GAAG,CAAC,CAAC,IAAI,CAAC,UAA8C,CAAC,CAAC;AAE5E,MAAM,CAAC,MAAM,gBAAgB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IACjE,KAAK,EAAE,+BAA+B;IACtC,WAAW,EACT,6MAA6M;IAC/M,WAAW,EAAE;QACX,YAAY,EAAE,IAAI;QAClB,cAAc,EAAE,IAAI;QACpB,aAAa,EAAE,IAAI;KACpB;IACD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,GAAG,EAAE;aACL,QAAQ,EAAE;aACV,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,SAAS,EAAE,CAAC;aACT,KAAK,CAAC,YAAY,CAAC;aACnB,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,iNAAiN,CAClN;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,wIAAwI,CACzI;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAChD,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,IAAI,EAAE,CAAC;iBACJ,MAAM,EAAE;iBACR,QAAQ,CACP,6FAA6F,CAC9F;YACH,GAAG,EAAE,CAAC;iBACH,KAAK,CACJ,CAAC;iBACE,KAAK,CAAC;gBACL,CAAC;qBACE,MAAM,EAAE;qBACR,QAAQ,CAAC,2DAA2D,CAAC;gBACxE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uDAAuD,CAAC;aAC7E,CAAC;iBACD,QAAQ,CAAC,kEAAkE,CAAC,CAChF;iBACA,QAAQ,CAAC,6CAA6C,CAAC;YAC1D,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;YAC7E,SAAS,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;SACnE,CAAC;aACD,QAAQ,CAAC,qCAAqC,CAAC,CACnD;aACA,QAAQ,CAAC,mCAAmC,CAAC;KACjD,CAAC;IACF,wFAAwF;IACxF,4FAA4F;IAC5F,mEAAmE;IACnE,UAAU,EAAE;QACV,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,4IAA4I,CAC7I;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAElC,iDAAiD;QACjD,MAAM,KAAK,GAKN,EAAE,CAAC;QAER,KAAK,MAAM,QAAQ,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;YACvC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAC;YAC1D,MAAM,cAAc,GAAG,MAAM,CAAC,MAAM,CAAC;YACrC,MAAM,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,UAAU,CAAC,CAAC;YAE9C,KAAK,CAAC,IAAI,CAAC;gBACT,IAAI,EAAE,QAAQ;gBACd,GAAG;gBACH,cAAc;gBACd,SAAS,EAAE,cAAc,GAAG,KAAK,CAAC,UAAU;aAC7C,CAAC,CAAC;QACL,CAAC;QAED,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE;YAC5B,GAAG,EAAE,KAAK,CAAC,GAAG;YACd,KAAK,EAAE,KAAK,CAAC,SAAS;YACtB,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;SAC1D,CAAC,CAAC;QAEH,mFAAmF;QACnF,yFAAyF;QACzF,IAAI,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,KAAK,CAAC,CAAC,EAAE,CAAC;YAC/C,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,qCAAqC,KAAK,CAAC,GAAG,kCAAkC,KAAK,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,oGAAoG,CAC/M,CAAC;QACJ,CAAC;QAED,OAAO,EAAE,GAAG,EAAE,KAAK,CAAC,GAAG,EAAE,KAAK,EAAE,CAAC;IACnC,CAAC;IAED,MAAM,CAAC,MAAM;QACX,MAAM,KAAK,GAAa,CAAC,4BAA4B,MAAM,CAAC,GAAG,EAAE,EAAE,EAAE,CAAC,CAAC;QAEvE,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;YAChC,MAAM,SAAS,GAAG,IAAI,CAAC,SAAS;gBAC9B,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,OAAO,IAAI,CAAC,cAAc,oBAAoB;gBAClE,CAAC,CAAC,GAAG,IAAI,CAAC,cAAc,QAAQ,CAAC;YACnC,KAAK,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,IAAI,OAAO,SAAS,GAAG,CAAC,CAAC;YAE9C,IAAI,IAAI,CAAC,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxB,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBACtC,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,GAAG,EAAE,CAAC,CAAC,CAAC,WAAW,IAAI,CAAC,GAAG,CAAC,MAAM,GAAG,EAAE,QAAQ,CAAC,CAAC,CAAC,EAAE,CAAC;gBACjF,KAAK,CAAC,IAAI,CAAC,KAAK,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;YAC/C,CAAC;iBAAM,CAAC;gBACN,KAAK,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;YAC7B,CAAC;YACD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACjB,CAAC;QAED,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
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{"version":3,"file":"get-summary.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-summary.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;
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{"version":3,"file":"get-summary.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-summary.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAmCjD,eAAO,MAAM,UAAU;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmIrB,CAAC"}
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*/
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import { tool, z } from '@cyanheads/mcp-ts-core';
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import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
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import { inlineData, quoteData } from './untrusted-text.js';
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const entityTypeEnum = z.enum(['assay', 'gene', 'protein', 'taxonomy']);
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/**
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* Union-of-shapes schema for entity summaries. All fields are optional because the
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@@ -110,18 +111,30 @@ export const getSummary = tool('pubchem_get_summary', {
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}
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const d = s.data;
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const displayName = d.name ?? d.symbol ?? String(s.identifier);
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lines.push(`**${displayName}** (identifier: ${s.identifier}, found)`);
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lines.push(`**${inlineData(displayName)}** (identifier: ${s.identifier}, found)`);
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for (const [key, value] of Object.entries(d)) {
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if (value == null || key === 'name')
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continue;
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// description is upstream prose — frame it as a blockquote data block.
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if (key === 'description' && typeof value === 'string') {
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lines.push(` ${formatKey(key)}:`);
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for (const q of quoteData(value).split('\n'))
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lines.push(` ${q}`);
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continue;
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}
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if (Array.isArray(value)) {
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if (value.length === 0)
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continue;
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// synonyms / lineage — upstream free text; escape each element inline.
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const items = value.map((v) => inlineData(String(v)));
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const display = items.length > 10
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? `${items.slice(0, 10).join(', ')} (+${items.length - 10} more)`
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: items.join(', ');
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lines.push(` ${formatKey(key)}: ${display}`);
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}
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else if (typeof value === 'string') {
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lines.push(` ${formatKey(key)}: ${inlineData(value)}`);
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}
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else {
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lines.push(` ${formatKey(key)}: ${value}`);
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}
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+
{"version":3,"file":"get-summary.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-summary.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,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,UAAU,CAAC,CAAC,CAAC;AAIxE;;;;;GAKG;AACH,MAAM,uBAAuB,GAAG,CAAC,CAAC,MAAM,CAAC;IACvC,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;IAC7E,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;IAC7D,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;IAC/E,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,4CAA4C,CAAC;IACxF,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;IACrF,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;IACxF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;IACxE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;IACvE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qDAAqD,CAAC;IACjG,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oDAAoD,CAAC;IAC9F,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;IAClF,gBAAgB,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;IAC1F,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;IACvF,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;IAC/E,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;IAC5E,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+CAA+C,CAAC;CAClG,CAAC,CAAC;AAIH,MAAM,CAAC,MAAM,UAAU,GAAG,IAAI,CAAC,qBAAqB,EAAE;IACpD,KAAK,EAAE,oBAAoB;IAC3B,WAAW,EACT,uKAAuK;IACzK,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,CAAC,QAAQ,CAAC,wDAAwD,CAAC;QAC7F,WAAW,EAAE,CAAC;aACX,KAAK,CACJ,CAAC;aACE,KAAK,CAAC;YACL,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;YAClE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iDAAiD,CAAC;SACvE,CAAC;aACD,QAAQ,CAAC,+DAA+D,CAAC,CAC7E;aACA,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CACP,qOAAqO,CACtO;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QACvD,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,UAAU,EAAE,CAAC;iBACV,KAAK,CAAC;gBACL,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;gBAClE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iDAAiD,CAAC;aACvE,CAAC;iBACD,QAAQ,CAAC,qBAAqB,CAAC;YAClC,KAAK,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;YAC5D,IAAI,EAAE,uBAAuB;iBAC1B,QAAQ,EAAE;iBACV,QAAQ,CAAC,6DAA6D,CAAC;SAC3E,CAAC;aACD,QAAQ,CAAC,gCAAgC,CAAC,CAC9C;aACA,QAAQ,CAAC,kBAAkB,CAAC;KAChC,CAAC;IACF,yFAAyF;IACzF,sEAAsE;IACtE,UAAU,EAAE;QACV,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QAC7D,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oCAAoC,CAAC;QACrE,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,gEAAgE,CAAC;KAC9E;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAElC,MAAM,SAAS,GAAG,MAAM,OAAO,CAAC,GAAG,CACjC,KAAK,CAAC,WAAW,CAAC,GAAG,CAAC,KAAK,EAAE,EAAE,EAAE,EAAE;YACjC,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,KAAK,CAAC,UAAU,EAAE,EAAE,CAAC,CAAC;YAChE,IAAI,CAAC,GAAG;gBAAE,OAAO,EAAE,UAAU,EAAE,EAAE,EAAE,KAAK,EAAE,KAAc,EAAE,CAAC;YAE3D,MAAM,IAAI,GAAG,cAAc,CAAC,KAAK,CAAC,UAAU,EAAE,GAAG,CAAC,CAAC;YACnD,OAAO,EAAE,UAAU,EAAE,EAAE,EAAE,KAAK,EAAE,IAAa,EAAE,IAAI,EAAE,CAAC;QACxD,CAAC,CAAC,CACH,CAAC;QAEF,MAAM,UAAU,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,MAAM,CAAC;QAE3D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,mBAAmB,EAAE;YAChC,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,SAAS,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM;YACnC,KAAK,EAAE,UAAU;SAClB,CAAC,CAAC;QAEH,GAAG,CAAC,MAAM,CAAC,EAAE,cAAc,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,EAAE,UAAU,EAAE,CAAC,CAAC;QACrE,IAAI,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,EAAE,CAAC;YAC1C,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,UAAU,OAAO,KAAK,CAAC,WAAW,CAAC,MAAM,IAAI,KAAK,CAAC,UAAU,oEAAoE,KAAK,CAAC,UAAU,8EAA8E,CAC9P,CAAC;QACJ,CAAC;QAED,OAAO,EAAE,UAAU,EAAE,KAAK,CAAC,UAAU,EAAE,SAAS,EAAE,CAAC;IACrD,CAAC;IAED,MAAM,CAAC,MAAM;QACX,MAAM,KAAK,GAAa,CAAC,MAAM,UAAU,CAAC,MAAM,CAAC,UAAU,CAAC,YAAY,EAAE,EAAE,CAAC,CAAC;QAE9E,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;YACjC,IAAI,CAAC,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;gBACxB,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,UAAU,gBAAgB,CAAC,CAAC;gBACzD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;gBACf,SAAS;YACX,CAAC;YAED,MAAM,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC;YACjB,MAAM,WAAW,GAAG,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,MAAM,IAAI,MAAM,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC;YAC/D,KAAK,CAAC,IAAI,CAAC,KAAK,UAAU,CAAC,WAAW,CAAC,mBAAmB,CAAC,CAAC,UAAU,UAAU,CAAC,CAAC;YAElF,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC;gBAC7C,IAAI,KAAK,IAAI,IAAI,IAAI,GAA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D,SAAS,UAAU,CAAC,CAAS;IAC3B,OAAO,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;AAChD,CAAC;AAED,SAAS,SAAS,CAAC,GAAW;IAC5B,OAAO,GAAG;SACP,OAAO,CAAC,UAAU,EAAE,KAAK,CAAC;SAC1B,OAAO,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,WAAW,EAAE,CAAC;SACrC,IAAI,EAAE,CAAC;AACZ,CAAC"}
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@@ -45,6 +45,9 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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|
|
45
45
|
json: "json";
|
|
46
46
|
}>>;
|
|
47
47
|
includeAlternateConformerIds: import("zod").ZodDefault<import("zod").ZodBoolean>;
|
|
48
|
+
maxAtoms: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
49
|
+
maxBonds: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
50
|
+
includeRawSdf: import("zod").ZodDefault<import("zod").ZodBoolean>;
|
|
48
51
|
}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
|
|
49
52
|
cid: import("zod").ZodNumber;
|
|
50
53
|
conformerId: import("zod").ZodOptional<import("zod").ZodString>;
|
|
@@ -68,7 +71,15 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
|
|
|
68
71
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
69
72
|
readonly when: "PubChem has no computed 3D conformer for the requested CID";
|
|
70
73
|
readonly recovery: "Use pubchem_get_compound_image for the 2D structure, or verify the CID with pubchem_search_compounds.";
|
|
71
|
-
}],
|
|
74
|
+
}], {
|
|
75
|
+
readonly truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
|
|
76
|
+
readonly shownAtoms: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
77
|
+
readonly shownBonds: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
78
|
+
readonly atomCap: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
79
|
+
readonly bondCap: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
80
|
+
readonly shownSdfLines: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
81
|
+
readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
|
|
82
|
+
}> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
72
83
|
cids: import("zod").ZodArray<import("zod").ZodNumber>;
|
|
73
84
|
properties: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodEnum<{
|
|
74
85
|
[x: string]: string;
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@@ -221,7 +232,9 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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totalAvailable: import("zod").ZodNumber;
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truncated: import("zod").ZodBoolean;
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}, import("zod/v4/core").$strip>>;
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}, import("zod/v4/core").$strip>, undefined,
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}, import("zod/v4/core").$strip>, undefined, {
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readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
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}> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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entityType: import("zod").ZodEnum<{
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assay: "assay";
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gene: "gene";
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@@ -268,7 +281,17 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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maxResults: import("zod").ZodDefault<import("zod").ZodNumber>;
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}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
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aids: import("zod").ZodArray<import("zod").ZodNumber>;
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}, import("zod/v4/core").$strip>,
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}, import("zod/v4/core").$strip>, readonly [{
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readonly reason: "blank_target_query";
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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readonly when: "targetQuery is empty or whitespace-only";
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readonly recovery: "Provide a non-empty target identifier, e.g. \"EGFR\" for genesymbol or \"1956\" for geneid.";
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}, {
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readonly reason: "invalid_geneid_query";
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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readonly when: "targetType is \"geneid\" but targetQuery is not a positive integer";
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readonly recovery: "Pass a numeric NCBI Gene ID (e.g. \"1956\"), or switch targetType to genesymbol/proteinname for text queries.";
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}], {
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readonly targetType: import("zod").ZodString;
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readonly targetQuery: import("zod").ZodString;
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readonly totalFound: import("zod").ZodNumber;
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@@ -308,6 +331,7 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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identifier: import("zod").ZodOptional<import("zod").ZodString>;
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properties: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>>;
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}, import("zod/v4/core").$strip>>;
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unresolvedIdentifiers: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
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}, import("zod/v4/core").$strip>, readonly [{
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readonly reason: "missing_identifier_args";
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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@@ -323,6 +347,11 @@ export declare const allToolDefinitions: (import("@cyanheads/mcp-ts-core").ToolD
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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readonly when: "substructure/superstructure/similarity search missing query or queryType";
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readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
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}, {
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readonly reason: "invalid_cid_query";
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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readonly when: "structure/similarity search with queryType \"cid\" but query is not a positive integer CID";
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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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}], {
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readonly searchType: import("zod").ZodString;
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readonly totalFound: import("zod").ZodNumber;
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAaH,eAAO,MAAM,kBAAkB
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{"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"}
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@@ -4,6 +4,7 @@
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* @module mcp-server/tools/definitions/search-assays
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*/
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import { z } from '@cyanheads/mcp-ts-core';
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import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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export declare const searchAssays: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
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targetType: z.ZodEnum<{
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proteinaccession: "proteinaccession";
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@@ -15,7 +16,17 @@ export declare const searchAssays: import("@cyanheads/mcp-ts-core").ToolDefiniti
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maxResults: z.ZodDefault<z.ZodNumber>;
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}, z.core.$strip>, z.ZodObject<{
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aids: z.ZodArray<z.ZodNumber>;
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}, z.core.$strip>,
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}, z.core.$strip>, readonly [{
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readonly reason: "blank_target_query";
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readonly code: JsonRpcErrorCode.ValidationError;
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readonly when: "targetQuery is empty or whitespace-only";
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readonly recovery: "Provide a non-empty target identifier, e.g. \"EGFR\" for genesymbol or \"1956\" for geneid.";
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}, {
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readonly reason: "invalid_geneid_query";
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readonly code: JsonRpcErrorCode.ValidationError;
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readonly when: "targetType is \"geneid\" but targetQuery is not a positive integer";
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readonly recovery: "Pass a numeric NCBI Gene ID (e.g. \"1956\"), or switch targetType to genesymbol/proteinname for text queries.";
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}], {
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readonly targetType: z.ZodString;
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readonly targetQuery: z.ZodString;
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readonly totalFound: z.ZodNumber;
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@@ -1 +1 @@
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1
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-
{"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;
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{"version":3,"file":"search-assays.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-assays.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2HvB,CAAC"}
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@@ -4,6 +4,7 @@
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* @module mcp-server/tools/definitions/search-assays
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*/
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import { tool, z } from '@cyanheads/mcp-ts-core';
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import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
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export const searchAssays = tool('pubchem_search_assays', {
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title: 'Search Assays',
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@@ -49,21 +50,47 @@ export const searchAssays = tool('pubchem_search_assays', {
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.optional()
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.describe('Recovery guidance when no assays matched — echoes the target and suggests alternative search types. Absent when assays were returned.'),
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},
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errors: [
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{
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reason: 'blank_target_query',
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code: JsonRpcErrorCode.ValidationError,
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when: 'targetQuery is empty or whitespace-only',
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recovery: 'Provide a non-empty target identifier, e.g. "EGFR" for genesymbol or "1956" for geneid.',
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},
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{
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reason: 'invalid_geneid_query',
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code: JsonRpcErrorCode.ValidationError,
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when: 'targetType is "geneid" but targetQuery is not a positive integer',
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recovery: 'Pass a numeric NCBI Gene ID (e.g. "1956"), or switch targetType to genesymbol/proteinname for text queries.',
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},
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],
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async handler(input, ctx) {
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const client = getPubChemClient();
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// Reject inputs that cannot represent a useful target before the upstream call (#26).
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const targetQuery = input.targetQuery.trim();
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if (targetQuery.length === 0) {
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throw ctx.fail('blank_target_query', undefined, {
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...ctx.recoveryFor('blank_target_query'),
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});
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}
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// geneid targets are numeric NCBI Gene IDs — a non-numeric value otherwise hits a raw
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// PubChem 400 (searchAssaysByTarget only special-cases 404).
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if (input.targetType === 'geneid' && !/^\d+$/.test(targetQuery)) {
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throw ctx.fail('invalid_geneid_query', `targetType is "geneid" but targetQuery "${input.targetQuery}" is not a positive integer Gene ID.`, { ...ctx.recoveryFor('invalid_geneid_query') });
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}
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const allAids = await client.searchAssaysByTarget(input.targetType, targetQuery);
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const totalFound = allAids.length;
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const aids = allAids.slice(0, input.maxResults);
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ctx.log.info('Assay search completed', {
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targetType: input.targetType,
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targetQuery
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targetQuery,
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totalFound,
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returned: aids.length,
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});
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// Agent-facing context: target echo, total, and empty-result notice.
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ctx.enrich({ targetType: input.targetType, targetQuery
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ctx.enrich({ targetType: input.targetType, targetQuery, totalFound });
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if (aids.length === 0) {
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ctx.enrich.notice(`No assays found for "${
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ctx.enrich.notice(`No assays found for "${targetQuery}" (${input.targetType}). Try a different targetType (e.g. switch from proteinname to genesymbol), verify the identifier spelling, or use pubchem_get_summary for gene/protein entity lookups.`);
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}
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else if (totalFound > aids.length) {
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ctx.enrich.truncated({ shown: aids.length, cap: input.maxResults });
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@@ -1 +1 @@
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{"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,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,YAAY,GAAG,IAAI,CAAC,uBAAuB,EAAE;IACxD,KAAK,EAAE,eAAe;IACtB,WAAW,EACT,qOAAqO;IACvO,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,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,wFAAwF,CACzF;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,oFAAoF;IACpF,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,6CAA6C,CAAC;QAC9E,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,EAAE;aACV,QAAQ,CAAC,6EAA6E,CAAC;QAC1F,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;QAChF,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,uIAAuI,CACxI;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;
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+
{"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,qOAAqO;IACvO,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,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,wFAAwF,CACzF;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,oFAAoF;IACpF,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,6CAA6C,CAAC;QAC9E,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,EAAE;aACV,QAAQ,CAAC,6EAA6E,CAAC;QAC1F,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;QAChF,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,uIAAuI,CACxI;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,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,UAAU,CAAC,CAAC;QAEhD,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,wBAAwB,EAAE;YACrC,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,WAAW;YACX,UAAU;YACV,QAAQ,EAAE,IAAI,CAAC,MAAM;SACtB,CAAC,CAAC;QAEH,qEAAqE;QACrE,GAAG,CAAC,MAAM,CAAC,EAAE,UAAU,EAAE,KAAK,CAAC,UAAU,EAAE,WAAW,EAAE,UAAU,EAAE,CAAC,CAAC;QACtE,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACtB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,wBAAwB,WAAW,MAAM,KAAK,CAAC,UAAU,yKAAyK,CACnO,CAAC;QACJ,CAAC;aAAM,IAAI,UAAU,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC;YACpC,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,IAAI,CAAC,MAAM,EAAE,GAAG,EAAE,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC;QACtE,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,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,kBAAkB,EAAE,CAAC,CAAC;IACtD,CAAC;CACF,CAAC,CAAC"}
|
|
@@ -37,6 +37,7 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
|
|
|
37
37
|
identifier: z.ZodOptional<z.ZodString>;
|
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38
38
|
properties: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
|
|
39
39
|
}, z.core.$strip>>;
|
|
40
|
+
unresolvedIdentifiers: z.ZodOptional<z.ZodArray<z.ZodString>>;
|
|
40
41
|
}, z.core.$strip>, readonly [{
|
|
41
42
|
readonly reason: "missing_identifier_args";
|
|
42
43
|
readonly code: JsonRpcErrorCode.ValidationError;
|
|
@@ -52,6 +53,11 @@ export declare const searchCompounds: import("@cyanheads/mcp-ts-core").ToolDefin
|
|
|
52
53
|
readonly code: JsonRpcErrorCode.ValidationError;
|
|
53
54
|
readonly when: "substructure/superstructure/similarity search missing query or queryType";
|
|
54
55
|
readonly recovery: "Provide both query (SMILES string or CID as string) and queryType (\"smiles\" or \"cid\").";
|
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56
|
+
}, {
|
|
57
|
+
readonly reason: "invalid_cid_query";
|
|
58
|
+
readonly code: JsonRpcErrorCode.ValidationError;
|
|
59
|
+
readonly when: "structure/similarity search with queryType \"cid\" but query is not a positive integer CID";
|
|
60
|
+
readonly recovery: "Pass a positive integer CID string (e.g. \"2244\"), or set queryType \"smiles\" with a SMILES query.";
|
|
55
61
|
}], {
|
|
56
62
|
readonly searchType: z.ZodString;
|
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57
63
|
readonly totalFound: 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,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,eAAe
|
|
1
|
+
{"version":3,"file":"search-compounds.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-compounds.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwW1B,CAAC"}
|
|
@@ -87,6 +87,10 @@ export const searchCompounds = tool('pubchem_search_compounds', {
|
|
|
87
87
|
})
|
|
88
88
|
.describe('Matching compound entry.'))
|
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89
89
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.describe('Matching compounds.'),
|
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90
|
+
unresolvedIdentifiers: z
|
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91
|
+
.array(z.string())
|
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92
|
+
.optional()
|
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93
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+
.describe('Identifier-mode only: input identifiers that resolved to no CID. Omitted when every identifier resolved and for non-identifier searches.'),
|
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90
94
|
}),
|
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91
95
|
// Agent-facing context — search strategy echo, total before cap, and an empty-result
|
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92
96
|
// notice. Reaches structuredContent and content[] automatically; not in the domain return.
|
|
@@ -125,11 +129,21 @@ export const searchCompounds = tool('pubchem_search_compounds', {
|
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|
125
129
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when: 'substructure/superstructure/similarity search missing query or queryType',
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126
130
|
recovery: 'Provide both query (SMILES string or CID as string) and queryType ("smiles" or "cid").',
|
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127
131
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},
|
|
132
|
+
{
|
|
133
|
+
reason: 'invalid_cid_query',
|
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134
|
+
code: JsonRpcErrorCode.ValidationError,
|
|
135
|
+
when: 'structure/similarity search with queryType "cid" but query is not a positive integer CID',
|
|
136
|
+
recovery: 'Pass a positive integer CID string (e.g. "2244"), or set queryType "smiles" with a SMILES query.',
|
|
137
|
+
},
|
|
128
138
|
],
|
|
129
139
|
async handler(input, ctx) {
|
|
130
140
|
const client = getPubChemClient();
|
|
131
141
|
let allCids = [];
|
|
132
142
|
const identifierMap = new Map();
|
|
143
|
+
// Identifier-mode resolution tracking (#29): inputs that resolved to no CID, and
|
|
144
|
+
// CIDs claimed by more than one distinct input (the output row can echo only one).
|
|
145
|
+
const unresolvedIdentifiers = [];
|
|
146
|
+
const collisions = [];
|
|
133
147
|
switch (input.searchType) {
|
|
134
148
|
case 'identifier': {
|
|
135
149
|
const { identifierType, identifiers } = input;
|
|
@@ -151,12 +165,35 @@ export const searchCompounds = tool('pubchem_search_compounds', {
|
|
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151
165
|
cids = await client.searchByInchiKey(id);
|
|
152
166
|
break;
|
|
153
167
|
}
|
|
154
|
-
|
|
155
|
-
identifierMap.set(cid, id);
|
|
156
|
-
return cids;
|
|
168
|
+
return { id, cids };
|
|
157
169
|
});
|
|
158
|
-
const
|
|
159
|
-
|
|
170
|
+
const resolutions = await Promise.all(lookups);
|
|
171
|
+
// Track resolution per input in request order: a CID's echo goes to its first
|
|
172
|
+
// requester (deterministic, unlike the prior last-write-wins), unresolved inputs
|
|
173
|
+
// are collected, and any CID with multiple distinct requesters is a collision.
|
|
174
|
+
const cidToIdentifiers = new Map();
|
|
175
|
+
for (const { id, cids } of resolutions) {
|
|
176
|
+
if (cids.length === 0) {
|
|
177
|
+
unresolvedIdentifiers.push(id);
|
|
178
|
+
continue;
|
|
179
|
+
}
|
|
180
|
+
for (const cid of cids) {
|
|
181
|
+
const owners = cidToIdentifiers.get(cid);
|
|
182
|
+
if (owners) {
|
|
183
|
+
if (!owners.includes(id))
|
|
184
|
+
owners.push(id);
|
|
185
|
+
}
|
|
186
|
+
else {
|
|
187
|
+
cidToIdentifiers.set(cid, [id]);
|
|
188
|
+
identifierMap.set(cid, id);
|
|
189
|
+
}
|
|
190
|
+
}
|
|
191
|
+
}
|
|
192
|
+
for (const [cid, owners] of cidToIdentifiers) {
|
|
193
|
+
if (owners.length > 1)
|
|
194
|
+
collisions.push({ cid, identifiers: owners });
|
|
195
|
+
}
|
|
196
|
+
allCids = resolutions.flatMap((r) => r.cids);
|
|
160
197
|
break;
|
|
161
198
|
}
|
|
162
199
|
case 'formula': {
|
|
@@ -176,6 +213,11 @@ export const searchCompounds = tool('pubchem_search_compounds', {
|
|
|
176
213
|
...ctx.recoveryFor('missing_structure_args'),
|
|
177
214
|
});
|
|
178
215
|
}
|
|
216
|
+
// A "cid" query must be a positive integer string — catch it here instead of
|
|
217
|
+
// forwarding a malformed value into a raw PubChem 400 (#26).
|
|
218
|
+
if (input.queryType === 'cid' && !(/^\d+$/.test(input.query) && Number(input.query) > 0)) {
|
|
219
|
+
throw ctx.fail('invalid_cid_query', `queryType is "cid" but query "${input.query}" is not a positive integer CID.`, { ...ctx.recoveryFor('invalid_cid_query') });
|
|
220
|
+
}
|
|
179
221
|
allCids = await client.searchByStructure(input.searchType, input.query, input.queryType, input.threshold);
|
|
180
222
|
break;
|
|
181
223
|
}
|
|
@@ -191,11 +233,37 @@ export const searchCompounds = tool('pubchem_search_compounds', {
|
|
|
191
233
|
});
|
|
192
234
|
// Agent-facing context: search strategy echo, total, and empty-result notice.
|
|
193
235
|
ctx.enrich({ searchType: input.searchType, totalFound });
|
|
236
|
+
// Identifier-mode signals (#29): name inputs that did not resolve and flag CID
|
|
237
|
+
// collisions, so a partial miss is never silent. Empty for other search types.
|
|
238
|
+
const noticeParts = [];
|
|
239
|
+
if (unresolvedIdentifiers.length > 0) {
|
|
240
|
+
const requested = input.identifiers?.length ?? unresolvedIdentifiers.length;
|
|
241
|
+
noticeParts.push(`${unresolvedIdentifiers.length} of ${requested} identifier(s) did not resolve to a CID: ${unresolvedIdentifiers.join(', ')}. Verify spelling and that identifierType="${input.identifierType}" matches the identifier form (name/smiles/inchikey).`);
|
|
242
|
+
}
|
|
243
|
+
for (const c of collisions) {
|
|
244
|
+
noticeParts.push(`Identifiers ${c.identifiers.join(', ')} all resolved to CID ${c.cid}; the result row echoes only "${identifierMap.get(c.cid)}" for it.`);
|
|
245
|
+
}
|
|
194
246
|
if (cappedCids.length === 0) {
|
|
195
|
-
ctx.enrich.notice(
|
|
247
|
+
ctx.enrich.notice(noticeParts.length > 0
|
|
248
|
+
? noticeParts.join(' ')
|
|
249
|
+
: `No compounds matched the ${input.searchType} search. Try a different identifier, broaden the formula, lower the similarity threshold, or verify the SMILES/CID.`);
|
|
196
250
|
}
|
|
197
251
|
else if (totalFound > cappedCids.length) {
|
|
198
|
-
|
|
252
|
+
// Truncated: fold any identifier notice into the truncation guidance (notice is
|
|
253
|
+
// last-wins, so compose rather than emit two; restate the cap when overriding).
|
|
254
|
+
if (noticeParts.length > 0) {
|
|
255
|
+
ctx.enrich.truncated({
|
|
256
|
+
shown: cappedCids.length,
|
|
257
|
+
cap: input.maxResults,
|
|
258
|
+
guidance: `${noticeParts.join(' ')} Showing ${cappedCids.length} of ${totalFound} matches — raise maxResults (max 200) for more.`,
|
|
259
|
+
});
|
|
260
|
+
}
|
|
261
|
+
else {
|
|
262
|
+
ctx.enrich.truncated({ shown: cappedCids.length, cap: input.maxResults });
|
|
263
|
+
}
|
|
264
|
+
}
|
|
265
|
+
else if (noticeParts.length > 0) {
|
|
266
|
+
ctx.enrich.notice(noticeParts.join(' '));
|
|
199
267
|
}
|
|
200
268
|
// Optionally hydrate with properties
|
|
201
269
|
let propsMap;
|
|
@@ -215,30 +283,34 @@ export const searchCompounds = tool('pubchem_search_compounds', {
|
|
|
215
283
|
}
|
|
216
284
|
return result;
|
|
217
285
|
});
|
|
218
|
-
return { results };
|
|
286
|
+
return unresolvedIdentifiers.length > 0 ? { results, unresolvedIdentifiers } : { results };
|
|
219
287
|
},
|
|
220
288
|
format(result) {
|
|
221
289
|
const lines = [];
|
|
222
290
|
if (result.results.length === 0) {
|
|
223
291
|
lines.push('No results.');
|
|
224
|
-
return [{ type: 'text', text: lines.join('\n') }];
|
|
225
292
|
}
|
|
226
|
-
|
|
227
|
-
|
|
228
|
-
|
|
229
|
-
const
|
|
230
|
-
|
|
231
|
-
|
|
232
|
-
|
|
233
|
-
|
|
234
|
-
|
|
293
|
+
else {
|
|
294
|
+
const hasProps = result.results.some((r) => r.properties);
|
|
295
|
+
if (hasProps) {
|
|
296
|
+
for (const r of result.results) {
|
|
297
|
+
const label = r.identifier ? `CID ${r.cid} — ${r.identifier}` : `CID ${r.cid}`;
|
|
298
|
+
lines.push(`**${label}**`);
|
|
299
|
+
if (r.properties) {
|
|
300
|
+
const entries = Object.entries(r.properties);
|
|
301
|
+
lines.push(' **Properties:**');
|
|
302
|
+
lines.push(entries.map(([k, v]) => ` ${k}: ${v}`).join('\n'));
|
|
303
|
+
}
|
|
304
|
+
lines.push('');
|
|
235
305
|
}
|
|
236
|
-
|
|
306
|
+
}
|
|
307
|
+
else {
|
|
308
|
+
const items = result.results.map((r) => r.identifier ? `${r.cid} (${r.identifier})` : String(r.cid));
|
|
309
|
+
lines.push(`CIDs: ${items.join(', ')}`);
|
|
237
310
|
}
|
|
238
311
|
}
|
|
239
|
-
|
|
240
|
-
|
|
241
|
-
lines.push(`CIDs: ${items.join(', ')}`);
|
|
312
|
+
if (result.unresolvedIdentifiers && result.unresolvedIdentifiers.length > 0) {
|
|
313
|
+
lines.push(`Unresolved identifiers (${result.unresolvedIdentifiers.length}): ${result.unresolvedIdentifiers.join(', ')}`);
|
|
242
314
|
}
|
|
243
315
|
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+
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@@ -0,0 +1,35 @@
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1
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+
/**
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2
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+
* @fileoverview Framing helpers that render upstream-controlled free text as
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3
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+
* clearly-delimited DATA in MCP `content[]` output. PubChem descriptions,
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4
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+
* summaries, interaction statements, synonyms, and assay/GHS text are relayed
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5
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+
* verbatim into the model's context; rendered as bare prose they blur the
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6
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+
* boundary between server-authored instructions and retrieved data and can
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7
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+
* inject markdown structure. These helpers keep that boundary explicit and
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8
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+
* neutralize markdown-structure injection. `structuredContent` always carries
|
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9
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+
* the raw value — this only shapes the human/LLM text-rendering surface.
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10
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+
* @module mcp-server/tools/definitions/untrusted-text
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11
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+
*/
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12
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+
/**
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13
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+
* Frame a single upstream value for safe inline interpolation into `content[]`
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14
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+
* markdown. Collapses embedded newlines (so the value cannot start a new
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15
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+
* markdown block) and escapes emphasis / inline-code delimiters. Proportionate
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16
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+
* by design: the goal is a data boundary, not heavy escaping.
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17
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+
*/
|
|
18
|
+
export declare function inlineData(value: string): string;
|
|
19
|
+
/**
|
|
20
|
+
* Frame multi-line upstream prose as a markdown blockquote — an explicit
|
|
21
|
+
* "quoted data" boundary distinct from server-authored instructions. Every
|
|
22
|
+
* line (blank ones included) is prefixed with `>` so the payload cannot break
|
|
23
|
+
* out of the quote; inline emphasis/code is escaped and a leading block marker
|
|
24
|
+
* (heading, quote, bullet, ordered list) is defused so it cannot restructure
|
|
25
|
+
* the surrounding document.
|
|
26
|
+
*/
|
|
27
|
+
export declare function quoteData(text: string): string;
|
|
28
|
+
/**
|
|
29
|
+
* Wrap raw upstream text in a fenced code block whose fence is guaranteed
|
|
30
|
+
* longer than any backtick run inside the payload, so a stray ``` cannot close
|
|
31
|
+
* the fence early and let following lines render as markdown. Preserves the
|
|
32
|
+
* content verbatim (no character substitution) — used for raw V2000 SDF.
|
|
33
|
+
*/
|
|
34
|
+
export declare function fencedData(content: string, language?: string): string;
|
|
35
|
+
//# sourceMappingURL=untrusted-text.d.ts.map
|
|
@@ -0,0 +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"}
|