@cyanheads/ensembl-mcp-server 0.4.4 → 0.5.0
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/AGENTS.md +1 -1
- package/CLAUDE.md +1 -1
- package/README.md +13 -10
- package/changelog/0.5.x/0.5.0.md +25 -0
- package/dist/mcp-server/prompts/definitions/gene-dossier.prompt.d.ts.map +1 -1
- package/dist/mcp-server/prompts/definitions/gene-dossier.prompt.js +12 -5
- package/dist/mcp-server/prompts/definitions/gene-dossier.prompt.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-homology.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-homology.tool.js +2 -0
- package/dist/mcp-server/tools/definitions/get-homology.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-sequence.tool.d.ts +14 -2
- package/dist/mcp-server/tools/definitions/get-sequence.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-sequence.tool.js +164 -49
- package/dist/mcp-server/tools/definitions/get-sequence.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-xrefs.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-xrefs.tool.js +2 -0
- package/dist/mcp-server/tools/definitions/get-xrefs.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-gene.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-gene.tool.js +10 -2
- package/dist/mcp-server/tools/definitions/lookup-gene.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/predict-variant.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/predict-variant.tool.js +4 -0
- package/dist/mcp-server/tools/definitions/predict-variant.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/query-region.tool.d.ts +6 -1
- package/dist/mcp-server/tools/definitions/query-region.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/query-region.tool.js +119 -24
- package/dist/mcp-server/tools/definitions/query-region.tool.js.map +1 -1
- package/dist/services/ensembl/ensembl-service.d.ts +11 -0
- package/dist/services/ensembl/ensembl-service.d.ts.map +1 -1
- package/dist/services/ensembl/ensembl-service.js +26 -0
- package/dist/services/ensembl/ensembl-service.js.map +1 -1
- package/dist/services/ensembl/types.d.ts +11 -0
- package/dist/services/ensembl/types.d.ts.map +1 -1
- package/package.json +2 -2
- package/server.json +3 -3
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-sequence.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-sequence.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,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;
|
|
1
|
+
{"version":3,"file":"get-sequence.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-sequence.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,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAG1E,MAAM,cAAc,GAAG,CAAC,SAAS,EAAE,MAAM,EAAE,KAAK,EAAE,SAAS,CAAU,CAAC;AAEtE;;;;GAIG;AACH,SAAS,eAAe,CAAC,GAAW,EAAE,KAAa,EAAE,MAAc;IACjE,OAAO,GAAG;SACP,WAAW,EAAE;SACb,KAAK,CAAC,oBAAoB,CAAC;SAC3B,IAAI,CAAC,CAAC,IAAI,EAAE,EAAE;QACb,MAAM,EAAE,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;QAC/B,OAAO,EAAE,KAAK,CAAC,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,EAAE,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC;IAC/D,CAAC,CAAC,CAAC;AACP,CAAC;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,sBAAsB,EAAE;IAC7D,KAAK,EAAE,cAAc;IACrB,WAAW,EACT,oGAAoG;QACpG,kGAAkG;QAClG,wGAAwG;QACxG,uGAAuG;QACvG,mGAAmG;QACnG,+FAA+F;QAC/F,qEAAqE;QACrE,oFAAoF;QACpF,2FAA2F;QAC3F,+FAA+F;QAC/F,qCAAqC;QACrC,4FAA4F;IAC9F,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,IAAI,EAAE;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,+EAA+E;YAC7E,0FAA0F;YAC1F,0FAA0F;YAC1F,wFAAwF,CAC3F;QACH,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,cAAc,CAAC;aACpB,OAAO,CAAC,SAAS,CAAC;aAClB,QAAQ,CACP,6BAA6B;YAC3B,yDAAyD;YACzD,yDAAyD;YACzD,iFAAiF;YACjF,6DAA6D;YAC7D,qGAAqG,CACxG;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,0DAA0D;YACxD,wFAAwF;YACxF,4DAA4D;YAC5D,6EAA6E,CAChF;QACH,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,mFAAmF;YACjF,kEAAkE,CACrE;QACH,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,qFAAqF;YACnF,kEAAkE,CACrE;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,8FAA8F;YAC5F,iGAAiG;YACjG,+FAA+F,CAClG;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,MAAM,CAAC;aACf,QAAQ,CACP,sEAAsE;YACpE,iEAAiE,CACpE;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;QACvE,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,0DAA0D,CAAC;QACrF,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,QAAQ,CACP,0FAA0F;YACxF,2FAA2F;YAC3F,0EAA0E,CAC7E;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,CACP,8FAA8F;YAC5F,kFAAkF,CACrF;QACH,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oDAAoD,CAAC;QACjF,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,wFAAwF;YACtF,sCAAsC,CACzC;QACH,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iDAAiD,CAAC;KAC/F,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,yFAAyF;YACvF,yBAAyB,CAC5B;KACJ;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,mDAAmD;YACzD,QAAQ,EACN,oEAAoE;gBACpE,wDAAwD;SAC3D;QACD;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,wFAAwF;YAC9F,QAAQ,EACN,+FAA+F;gBAC/F,8FAA8F;gBAC9F,4FAA4F;gBAC5F,oDAAoD;SACvD;QACD;YACE,MAAM,EAAE,iBAAiB;YACzB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,0DAA0D;YAChE,QAAQ,EACN,sEAAsE;gBACtE,oDAAoD;SACvD;QACD;YACE,MAAM,EAAE,gBAAgB;YACxB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EACF,uFAAuF;gBACvF,4FAA4F;YAC9F,QAAQ,EACN,yFAAyF;gBACzF,mFAAmF;gBACnF,kFAAkF;gBAClF,yEAAyE;SAC5E;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,mBAAmB,EAAE;YAChC,EAAE,EAAE,KAAK,CAAC,EAAE;YACZ,IAAI,EAAE,KAAK,CAAC,IAAI;YAChB,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,SAAS,EAAE,KAAK,CAAC,UAAU;SAC5B,CAAC,CAAC;QACH,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,qCAAqC;QACrC,sFAAsF;QACtF,iFAAiF;QACjF,+EAA+E;QAC/E,iFAAiF;QACjF,+EAA+E;QAC/E,2DAA2D;QAC3D,MAAM,gBAAgB,GAAG,2BAA2B,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QACpE,MAAM,YAAY,GAAG,kBAAkB,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAEvD,IAAI,QAAwB,CAAC;QAC7B,IAAI,gBAAgB,IAAI,YAAY,EAAE,CAAC;YACrC,kFAAkF;YAClF,iFAAiF;YACjF,IAAI,KAAK,CAAC,IAAI,KAAK,SAAS,EAAE,CAAC;gBAC7B,MAAM,GAAG,CAAC,IAAI,CACZ,eAAe,EACf,uCAAuC,KAAK,CAAC,IAAI,iCAAiC,KAAK,CAAC,EAAE,GAAG,EAC7F,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,eAAe,CAAC,EAAE,CACxC,CAAC;YACJ,CAAC;YACD,8EAA8E;YAC9E,8EAA8E;YAC9E,qDAAqD;YACrD,MAAM,UAAU,GAAG,KAAK,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;YACzC,MAAM,OAAO,GACX,KAAK,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAC,gBAAgB,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;YAC1F,MAAM,MAAM,GAAG,gBAAgB,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;YAC5E,IAAI,CAAC,OAAO,EAAE,CAAC;gBACb,MAAM,GAAG,CAAC,IAAI,CACZ,iBAAiB,EACjB,UAAU,KAAK,CAAC,EAAE,8FAA8F,EAChH,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,iBAAiB,CAAC,EAAE,CAC1C,CAAC;YACJ,CAAC;YACD,gFAAgF;YAChF,gFAAgF;YAChF,sDAAsD;YACtD,MAAM,CAAC,KAAK,GAAG,EAAE,EAAE,GAAG,GAAG,EAAE,CAAC,GAAG,MAAM;iBAClC,KAAK,CAAC,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC;iBAClC,KAAK,CAAC,GAAG,CAAC;iBACV,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,OAAO,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC,CAAC;YACpD,IAAI,KAAK,CAAC,MAAM,GAAG,GAAG,CAAC,MAAM,IAAI,CAAC,KAAK,CAAC,MAAM,KAAK,GAAG,CAAC,MAAM,IAAI,KAAK,GAAG,GAAG,CAAC,EAAE,CAAC;gBAC9E,MAAM,GAAG,CAAC,IAAI,CACZ,gBAAgB,EAChB,UAAU,KAAK,CAAC,EAAE,uBAAuB,KAAK,4BAA4B,GAAG,GAAG,EAChF,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,gBAAgB,CAAC,EAAE,CACzC,CAAC;YACJ,CAAC;YACD,QAAQ,GAAG,MAAM,OAAO;iBACrB,mBAAmB,CAAC,OAAO,EAAE,MAAM,EAAE,KAAK,CAAC,aAAa,EAAE,KAAK,CAAC,aAAa,EAAE,GAAG,CAAC;iBACnF,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,IAAI,+DAA+D,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBAC9E,MAAM,GAAG,CAAC,IAAI,CAAC,gBAAgB,EAAE,kBAAkB,KAAK,CAAC,EAAE,KAAK,GAAG,EAAE,EAAE;wBACrE,GAAG,GAAG,CAAC,WAAW,CAAC,gBAAgB,CAAC;qBACrC,CAAC,CAAC;gBACL,CAAC;gBACD,IAAI,iCAAiC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBAChD,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,UAAU,KAAK,CAAC,EAAE,eAAe,GAAG,EAAE,EAAE;wBAClE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;qBAChC,CAAC,CAAC;gBACL,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;QACP,CAAC;aAAM,CAAC;YACN,QAAQ,GAAG,MAAM,OAAO;iBACrB,eAAe,CAAC,KAAK,CAAC,EAAE,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,aAAa,EAAE,KAAK,CAAC,aAAa,EAAE,GAAG,CAAC;iBACpF,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,+EAA+E;gBAC/E,+EAA+E;gBAC/E,MAAM,QAAQ,GAAG,yBAAyB,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;gBACrD,IACE,mEAAmE,CAAC,IAAI,CAAC,GAAG,CAAC;oBAC7E,CAAC,CAAC,QAAQ;wBACR,CAAC,eAAe,CAAC,GAAG,EAAE,SAAS,EAAE,MAAM,CAAC;4BACtC,eAAe,CAAC,GAAG,EAAE,KAAK,EAAE,MAAM,CAAC;4BACnC,eAAe,CAAC,GAAG,EAAE,MAAM,EAAE,UAAU,CAAC;4BACxC,eAAe,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAC/B,CAAC;oBACD,MAAM,GAAG,CAAC,IAAI,CACZ,eAAe,EACf,wBAAwB,KAAK,CAAC,IAAI,oEAAoE;wBACpG,8EAA8E,EAChF,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,eAAe,CAAC,EAAE,CACxC,CAAC;gBACJ,CAAC;gBACD,IAAI,QAAQ,EAAE,CAAC;oBACb,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,MAAM,KAAK,CAAC,EAAE,wBAAwB,EAAE;wBAClE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;qBAChC,CAAC,CAAC;gBACL,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;QACP,CAAC;QAED,oFAAoF;QACpF,mFAAmF;QACnF,oEAAoE;QACpE,MAAM,EAAE,MAAM,EAAE,GAAG,QAAQ,CAAC;QAC5B,MAAM,GAAG,GAAG,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,MAAM,GAAG,KAAK,CAAC,UAAU,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC;QAC9F,MAAM,SAAS,GAAG,GAAG,GAAG,MAAM,CAAC;QAC/B,IAAI,KAAK,CAAC,MAAM,IAAI,MAAM,EAAE,CAAC;YAC3B,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,kCAAkC,KAAK,CAAC,MAAM,0CAA0C;gBACtF,YAAY,MAAM,CAAC,cAAc,EAAE,uDAAuD,CAC7F,CAAC;QACJ,CAAC;aAAM,IAAI,SAAS,EAAE,CAAC;YACrB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,WAAW,CAAC,GAAG,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,cAAc,EAAE,OAAO,MAAM,CAAC,cAAc,EAAE,cAAc;gBAC1F,eAAe,KAAK,CAAC,MAAM,4BAA4B,GAAG,+BAA+B;gBACzF,wDAAwD,CAC3D,CAAC;QACJ,CAAC;QAED,OAAO;YACL,GAAG,QAAQ;YACX,GAAG,EAAE,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,EAAE,GAAG,CAAC;YAC1C,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,SAAS;YACT,GAAG,CAAC,SAAS,IAAI,EAAE,UAAU,EAAE,GAAG,EAAE,CAAC;SACtC,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,KAAK,CAAC,IAAI,CAAC,gBAAgB,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;QACxC,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC;QAC3D,KAAK,CAAC,IAAI,CAAC,aAAa,MAAM,CAAC,IAAI,kBAAkB,MAAM,CAAC,MAAM,CAAC,cAAc,EAAE,IAAI,IAAI,EAAE,CAAC,CAAC;QAC/F,IAAI,MAAM,CAAC,WAAW;YAAE,KAAK,CAAC,IAAI,CAAC,oBAAoB,MAAM,CAAC,WAAW,EAAE,CAAC,CAAC;QAC7E,MAAM,MAAM,GAAG,MAAM,CAAC,SAAS;YAC7B,CAAC,CAAC,0BAA0B,MAAM,CAAC,UAAU,EAAE;YAC/C,CAAC,CAAC,6CAA6C,CAAC;QAClD,KAAK,CAAC,IAAI,CACR,eAAe,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,cAAc,EAAE,2BAA2B,MAAM,CAAC,MAAM,GAAG;YAC1F,MAAM,MAAM,CAAC,MAAM,CAAC,cAAc,EAAE,MAAM,MAAM,EAAE,CACrD,CAAC;QACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,IAAI,MAAM,CAAC,GAAG,EAAE,CAAC;YACf,KAAK,CAAC,IAAI,CAAC,KAAK,EAAE,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,CAAC;QACvC,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,0CAA0C,CAAC,CAAC;QACzD,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;
|
|
1
|
+
{"version":3,"file":"get-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;EAuH1B,CAAC"}
|
|
@@ -36,6 +36,8 @@ export const ensemblGetXrefs = tool('ensembl_get_xrefs', {
|
|
|
36
36
|
input: z.object({
|
|
37
37
|
id: z
|
|
38
38
|
.string()
|
|
39
|
+
.trim()
|
|
40
|
+
.min(1)
|
|
39
41
|
.describe('Ensembl stable gene ID (ENSG…) or transcript ID (ENST…). ' +
|
|
40
42
|
'Use ensembl_lookup_gene to get the stable ID from a gene symbol. ' +
|
|
41
43
|
'xrefs/id returns the full cross-reference set (56+ entries for well-annotated genes like BRCA2).'),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-xrefs.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-xrefs.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,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,eAAe,GAAG,CAAC,CAAC,MAAM,CAAC;IAC/B,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sGAAsG,CACvG;IACH,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;IACtF,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,iFAAiF;QAC/E,+BAA+B,CAClC;IACH,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,oFAAoF,CAAC;IACjG,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;CACzF,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAC,mBAAmB,EAAE;IACvD,KAAK,EAAE,+BAA+B;IACtC,WAAW,EACT,8FAA8F;QAC9F,kGAAkG;QAClG,8FAA8F;QAC9F,gGAAgG;QAChG,iEAAiE;QACjE,qFAAqF;QACrF,6FAA6F;QAC7F,uCAAuC;IACzC,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,CACP,2DAA2D;YACzD,mEAAmE;YACnE,kGAAkG,CACrG;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,uEAAuE;YACrE,iEAAiE;YACjE,2DAA2D;YAC3D,gEAAgE;YAChE,+DAA+D,CAClE;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,eAAe,CAAC,QAAQ,CACtB,0FAA0F,CAC3F,CACF;aACA,QAAQ,CAAC,uDAAuD,CAAC;QACpE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4CAA4C,CAAC;QAC7E,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;KAC1E,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;KACvF;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iEAAiE;YACvE,QAAQ,EACN,wEAAwE;gBACxE,mFAAmF;SACtF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;QACtE,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,KAAK,GAAG,MAAM,OAAO;aACxB,YAAY,CAAC,KAAK,CAAC,EAAE,CAAC,IAAI,EAAE,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,SAAS,EAAE,GAAG,CAAC;aACrE,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YAC7D,IAAI,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC3B,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,OAAO,KAAK,CAAC,EAAE,yBAAyB,EAAE;oBACpE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;iBAChC,CAAC,CAAC;YACL,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC,CAAC,CAAC;QAEL,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACvB,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,wBAAwB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;YAC/E,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,iCAAiC,KAAK,CAAC,EAAE,GAAG,UAAU,IAAI;gBACxD,+DAA+D,CAClE,CAAC;QACJ,CAAC;QACD,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;QAE/B,OAAO,EAAE,KAAK,EAAE,UAAU,EAAE,KAAK,CAAC,MAAM,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC;IAClE,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,KAAK,CAAC,IAAI,CAAC,2BAA2B,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC;QAC1D,KAAK,CAAC,IAAI,CAAC,cAAc,MAAM,CAAC,UAAU,IAAI,CAAC,CAAC;QAEhD,IAAI,MAAM,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC9B,KAAK,CAAC,IAAI,CAAC,4BAA4B,CAAC,CAAC;YACzC,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACpD,CAAC;QAED,oCAAoC;QACpC,MAAM,IAAI,GAAG,IAAI,GAAG,EAA+B,CAAC;QACpD,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;YAC7B,MAAM,EAAE,GAAG,CAAC,CAAC,MAAM,IAAI,SAAS,CAAC;YACjC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC;YACpC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC;QACxB,CAAC;QAED,KAAK,MAAM,CAAC,EAAE,EAAE,OAAO,CAAC,IAAI,IAAI,EAAE,CAAC;YACjC,MAAM,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE,aAAa,CAAC;YAC9C,KAAK,CAAC,IAAI,CAAC,OAAO,WAAW,IAAI,EAAE,GAAG,WAAW,IAAI,WAAW,KAAK,EAAE,CAAC,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC7F,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;gBACxB,IAAI,IAAI,GAAG,OAAO,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,SAAS,IAAI,SAAS,IAAI,CAAC;gBAC9D,IAAI,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,SAAS,KAAK,CAAC,CAAC,SAAS;oBAAE,IAAI,IAAI,KAAK,CAAC,CAAC,SAAS,GAAG,CAAC;gBAC5E,IAAI,CAAC,CAAC,WAAW;oBAAE,IAAI,IAAI,KAAK,CAAC,CAAC,WAAW,EAAE,CAAC;gBAChD,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YACnB,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"}
|
|
1
|
+
{"version":3,"file":"get-xrefs.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-xrefs.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,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,eAAe,GAAG,CAAC,CAAC,MAAM,CAAC;IAC/B,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sGAAsG,CACvG;IACH,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;IACtF,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,iFAAiF;QAC/E,+BAA+B,CAClC;IACH,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,oFAAoF,CAAC;IACjG,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;CACzF,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAC,mBAAmB,EAAE;IACvD,KAAK,EAAE,+BAA+B;IACtC,WAAW,EACT,8FAA8F;QAC9F,kGAAkG;QAClG,8FAA8F;QAC9F,gGAAgG;QAChG,iEAAiE;QACjE,qFAAqF;QACrF,6FAA6F;QAC7F,uCAAuC;IACzC,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,IAAI,EAAE;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,2DAA2D;YACzD,mEAAmE;YACnE,kGAAkG,CACrG;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,uEAAuE;YACrE,iEAAiE;YACjE,2DAA2D;YAC3D,gEAAgE;YAChE,+DAA+D,CAClE;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC;aACL,KAAK,CACJ,eAAe,CAAC,QAAQ,CACtB,0FAA0F,CAC3F,CACF;aACA,QAAQ,CAAC,uDAAuD,CAAC;QACpE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4CAA4C,CAAC;QAC7E,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;KAC1E,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;KACvF;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iEAAiE;YACvE,QAAQ,EACN,wEAAwE;gBACxE,mFAAmF;SACtF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;QACtE,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,KAAK,GAAG,MAAM,OAAO;aACxB,YAAY,CAAC,KAAK,CAAC,EAAE,CAAC,IAAI,EAAE,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,SAAS,EAAE,GAAG,CAAC;aACrE,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YAC7D,IAAI,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC3B,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,OAAO,KAAK,CAAC,EAAE,yBAAyB,EAAE;oBACpE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;iBAChC,CAAC,CAAC;YACL,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC,CAAC,CAAC;QAEL,IAAI,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACvB,MAAM,UAAU,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,wBAAwB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;YAC/E,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,iCAAiC,KAAK,CAAC,EAAE,GAAG,UAAU,IAAI;gBACxD,+DAA+D,CAClE,CAAC;QACJ,CAAC;QACD,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;QAE/B,OAAO,EAAE,KAAK,EAAE,UAAU,EAAE,KAAK,CAAC,MAAM,EAAE,SAAS,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC;IAClE,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,KAAK,CAAC,IAAI,CAAC,2BAA2B,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC;QAC1D,KAAK,CAAC,IAAI,CAAC,cAAc,MAAM,CAAC,UAAU,IAAI,CAAC,CAAC;QAEhD,IAAI,MAAM,CAAC,KAAK,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC9B,KAAK,CAAC,IAAI,CAAC,4BAA4B,CAAC,CAAC;YACzC,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACpD,CAAC;QAED,oCAAoC;QACpC,MAAM,IAAI,GAAG,IAAI,GAAG,EAA+B,CAAC;QACpD,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;YAC7B,MAAM,EAAE,GAAG,CAAC,CAAC,MAAM,IAAI,SAAS,CAAC;YACjC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAAE,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC;YACpC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC;QACxB,CAAC;QAED,KAAK,MAAM,CAAC,EAAE,EAAE,OAAO,CAAC,IAAI,IAAI,EAAE,CAAC;YACjC,MAAM,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,EAAE,aAAa,CAAC;YAC9C,KAAK,CAAC,IAAI,CAAC,OAAO,WAAW,IAAI,EAAE,GAAG,WAAW,IAAI,WAAW,KAAK,EAAE,CAAC,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC7F,KAAK,MAAM,CAAC,IAAI,OAAO,EAAE,CAAC;gBACxB,IAAI,IAAI,GAAG,OAAO,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,SAAS,IAAI,SAAS,IAAI,CAAC;gBAC9D,IAAI,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,SAAS,KAAK,CAAC,CAAC,SAAS;oBAAE,IAAI,IAAI,KAAK,CAAC,CAAC,SAAS,GAAG,CAAC;gBAC5E,IAAI,CAAC,CAAC,WAAW;oBAAE,IAAI,IAAI,KAAK,CAAC,CAAC,WAAW,EAAE,CAAC;gBAChD,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;YACnB,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"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"lookup-gene.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-gene.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmEjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
|
1
|
+
{"version":3,"file":"lookup-gene.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-gene.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmEjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA6Q5B,CAAC"}
|
|
@@ -90,13 +90,21 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
|
|
|
90
90
|
'Optional for symbol lookups — defaults to homo_sapiens; set it for other organisms. ' +
|
|
91
91
|
'Use ensembl_list_species to discover valid values.'),
|
|
92
92
|
ids: z
|
|
93
|
-
.array(z
|
|
93
|
+
.array(z
|
|
94
|
+
.string()
|
|
95
|
+
.trim()
|
|
96
|
+
.min(1)
|
|
97
|
+
.describe('An Ensembl stable gene or transcript ID to resolve in this batch.'))
|
|
94
98
|
.max(20)
|
|
95
99
|
.optional()
|
|
96
100
|
.describe('Batch lookup: up to 20 Ensembl stable IDs (ENSG…, ENST…). ' +
|
|
97
101
|
'Returns a succeeded/failed split. Provide exactly one of symbol, id, ids, or symbols.'),
|
|
98
102
|
symbols: z
|
|
99
|
-
.array(z
|
|
103
|
+
.array(z
|
|
104
|
+
.string()
|
|
105
|
+
.trim()
|
|
106
|
+
.min(1)
|
|
107
|
+
.describe('A gene symbol to resolve in this batch (e.g. BRCA2, TP53).'))
|
|
100
108
|
.max(20)
|
|
101
109
|
.optional()
|
|
102
110
|
.describe('Batch lookup: up to 20 gene symbols. ' +
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"lookup-gene.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-gene.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,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,uBAAuB,GAAG,CAAC,CAAC,MAAM,CAAC;IACvC,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;IAChE,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;IACvE,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,oEAAoE,CAAC;IACjF,WAAW,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,0DAA0D,CAAC;IAC7F,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;IAC/F,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;IAC3F,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;IAChF,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;CAC/E,CAAC,CAAC;AAEH,MAAM,gBAAgB,GAAG,CAAC,CAAC,MAAM,CAAC;IAChC,EAAE,EAAE,CAAC;SACF,MAAM,EAAE;SACR,QAAQ,CAAC,2EAA2E,CAAC;IACxF,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,6EAA6E,CAAC;IAC1F,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iDAAiD,CAAC;IAC9F,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;IACnF,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,yDAAyD,CAAC;IACtE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;IACjF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kDAAkD,CAAC;IACzF,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;IACrF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;IAChF,YAAY,EAAE,CAAC;SACZ,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,oFAAoF,CAAC;IACjG,WAAW,EAAE,CAAC;SACX,KAAK,CAAC,uBAAuB,CAAC,QAAQ,CAAC,oCAAoC,CAAC,CAAC;SAC7E,QAAQ,EAAE;SACV,QAAQ,CAAC,gEAAgE,CAAC;CAC9E,CAAC,CAAC;AAEH,MAAM,iBAAiB,GAAG,CAAC,CAAC,MAAM,CAAC;IACjC,6FAA6F;IAC7F,SAAS,EAAE,CAAC;SACT,KAAK,CACJ,CAAC;SACE,MAAM,CAAC,EAAE,CAAC;SACV,WAAW,EAAE;SACb,QAAQ,CAAC,sEAAsE,CAAC,CACpF;SACA,QAAQ,CAAC,8EAA8E,CAAC;IAC3F,MAAM,EAAE,CAAC;SACN,KAAK,CACJ,CAAC;SACE,MAAM,CAAC,EAAE,CAAC;SACV,WAAW,EAAE;SACb,QAAQ,CACP,iGAAiG,CAClG,CACJ;SACA,QAAQ,CAAC,+EAA+E,CAAC;CAC7F,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,qBAAqB,EAAE;IAC3D,KAAK,EAAE,aAAa;IACpB,WAAW,EACT,2FAA2F;QAC3F,sGAAsG;QACtG,oGAAoG;QACpG,mGAAmG;QACnG,mGAAmG;QACnG,kGAAkG;QAClG,iGAAiG;IACnG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mDAAmD;YACjD,qEAAqE;YACrE,mCAAmC,CACtC;QACH,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mFAAmF;YACjF,wCAAwC,CAC3C;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,iFAAiF;YAC/E,kDAAkD;YAClD,sFAAsF;YACtF,oDAAoD,CACvD;QACH,GAAG,EAAE,CAAC;aACH,KAAK,CACJ,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mEAAmE,CAAC,CACzF;aACA,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,EAAE;aACV,QAAQ,CACP,4DAA4D;YAC1D,uFAAuF,CAC1F;QACH,OAAO,EAAE,CAAC;aACP,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4DAA4D,CAAC,CAAC;aACxF,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,EAAE;aACV,QAAQ,CACP,uCAAuC;YACrC,qEAAqE;YACrE,uFAAuF,CAC1F;QACH,kBAAkB,EAAE,CAAC;aAClB,OAAO,EAAE;aACT,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,+DAA+D;YAC7D,wEAAwE;YACxE,6CAA6C,CAChD;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,IAAI,EAAE,gBAAgB,CAAC,QAAQ,EAAE,CAAC,QAAQ,CACxC,uDAAuD,CACxD;QACD,KAAK,EAAE,iBAAiB,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAC1C,oDAAoD,CACrD;KACF,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,wDAAwD;YAC9D,QAAQ,EACN,iGAAiG;gBACjG,sGAAsG;SACzG;QACD;YACE,MAAM,EAAE,iBAAiB;YACzB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,mDAAmD;YACzD,QAAQ,EACN,6DAA6D;gBAC7D,2FAA2F;SAC9F;QACD;YACE,MAAM,EAAE,UAAU;YAClB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,oDAAoD;YAC1D,QAAQ,EACN,gGAAgG;SACnG;QACD;YACE,MAAM,EAAE,mBAAmB;YAC3B,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,4DAA4D;YAClE,QAAQ,EACN,qFAAqF;SACxF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,iBAAiB,EAAE;YAC9B,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,EAAE,EAAE,KAAK,CAAC,EAAE;YACZ,OAAO,EAAE,KAAK,CAAC,OAAO;YACtB,SAAS,EAAE,KAAK,CAAC,GAAG,EAAE,MAAM,IAAI,KAAK,CAAC,OAAO,EAAE,MAAM;SACtD,CAAC,CAAC;QACH,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,UAAU,GAAG;YACjB,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE;YACpB,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE;YAChB,KAAK,CAAC,GAAG,EAAE,MAAM;YACjB,KAAK,CAAC,OAAO,EAAE,MAAM;SACtB,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC;QACzB,IAAI,UAAU,GAAG,CAAC,EAAE,CAAC;YACnB,MAAM,GAAG,CAAC,IAAI,CAAC,mBAAmB,EAAE,sDAAsD,EAAE;gBAC1F,GAAG,GAAG,CAAC,WAAW,CAAC,mBAAmB,CAAC;aACxC,CAAC,CAAC;QACL,CAAC;QAED,uBAAuB;QACvB,IAAI,KAAK,CAAC,GAAG,EAAE,MAAM,EAAE,CAAC;YACtB,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,gBAAgB,CAAC,KAAK,CAAC,GAAG,EAAE,KAAK,CAAC,kBAAkB,EAAE,GAAG,CAAC,CAAC;YACrF,MAAM,SAAS,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;YAC3C,MAAM,WAAW,GAAG,IAAI,GAAG,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,CAAC;YACxC,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG;iBACrB,MAAM,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;iBACpC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE,wBAAwB,EAAE,CAAC,CAAC,CAAC;YACzE,OAAO,EAAE,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,EAAE,CAAC;QAC1C,CAAC;QAED,2BAA2B;QAC3B,IAAI,KAAK,CAAC,OAAO,EAAE,MAAM,EAAE,CAAC;YAC1B,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,cAAc,CAAC;YAC3D,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,kBAAkB,CAC1C,KAAK,CAAC,OAAO,EACb,UAAU,EACV,KAAK,CAAC,kBAAkB,EACxB,GAAG,CACJ,CAAC;YACF,MAAM,SAAS,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;YAC3C,MAAM,eAAe,GAAG,IAAI,GAAG,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,CAAC;YAC5C,MAAM,MAAM,GAAG,KAAK,CAAC,OAAO;iBACzB,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;iBACtC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBACX,KAAK,EAAE,CAAC;gBACR,KAAK,EAAE,UAAU,CAAC,qCAAqC,UAAU,GAAG;aACrE,CAAC,CAAC,CAAC;YACN,OAAO,EAAE,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,EAAE,CAAC;QAC1C,CAAC;QAED,wBAAwB;QACxB,IAAI,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,EAAE,CAAC;YACzB,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,cAAc,CAAC;YAC3D,MAAM,IAAI,GAAG,MAAM,OAAO;iBACvB,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,IAAI,EAAE,EAAE,UAAU,EAAE,KAAK,CAAC,kBAAkB,EAAE,GAAG,CAAC;iBAC1E,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,IAAI,oDAAoD,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBACnE,MAAM,GAAG,CAAC,IAAI,CACZ,WAAW,EACX,gBAAgB,KAAK,CAAC,MAAM,kBAAkB,UAAU,GAAG,EAC3D,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CACpC,CAAC;gBACJ,CAAC;gBACD,IAAI,+BAA+B,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBAC9C,MAAM,GAAG,CAAC,IAAI,CACZ,iBAAiB,EACjB,YAAY,UAAU,8BAA8B,EACpD;wBACE,GAAG,GAAG,CAAC,WAAW,CAAC,iBAAiB,CAAC;qBACtC,CACF,CAAC;gBACJ,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;YACL,OAAO,EAAE,IAAI,EAAE,CAAC;QAClB,CAAC;QAED,oBAAoB;QACpB,IAAI,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE,EAAE,CAAC;YACrB,MAAM,IAAI,GAAG,MAAM,OAAO;iBACvB,cAAc,CAAC,KAAK,CAAC,EAAE,CAAC,IAAI,EAAE,EAAE,KAAK,CAAC,kBAAkB,EAAE,GAAG,CAAC;iBAC9D,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,IAAI,yBAAyB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBACxC,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,YAAY,KAAK,CAAC,EAAE,yBAAyB,EAAE;wBACzE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;qBAChC,CAAC,CAAC;gBACL,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;YACL,OAAO,EAAE,IAAI,EAAE,CAAC;QAClB,CAAC;QAED,MAAM,GAAG,CAAC,IAAI,CAAC,UAAU,EAAE,qDAAqD,EAAE;YAChF,GAAG,GAAG,CAAC,WAAW,CAAC,UAAU,CAAC;SAC/B,CAAC,CAAC;IACL,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAG3B,MAAM,UAAU,GAAG,CAAC,CAAW,EAAE,EAAE;YACjC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,WAAW,IAAI,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC1C,KAAK,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC9B,IAAI,CAAC,CAAC,OAAO;gBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;YACvD,IAAI,CAAC,CAAC,OAAO;gBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;YACvD,IAAI,CAAC,CAAC,WAAW;gBAAE,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC;YACnE,IAAI,CAAC,CAAC,UAAU;gBAAE,KAAK,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC,UAAU,EAAE,CAAC,CAAC;YAChE,IAAI,CAAC,CAAC,KAAK,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;YACzD,IAAI,CAAC,CAAC,GAAG,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;YACnD,IAAI,CAAC,CAAC,MAAM,IAAI,IAAI;gBAClB,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC;YACrF,IAAI,CAAC,CAAC,YAAY;gBAAE,KAAK,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC,YAAY,EAAE,CAAC,CAAC;YAClE,IAAI,CAAC,CAAC,WAAW,EAAE,MAAM,EAAE,CAAC;gBAC1B,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,WAAW,CAAC,MAAM,MAAM,CAAC,CAAC;gBAC3D,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,CAAC;oBAC9B,MAAM,KAAK,GAAG,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC;oBAClD,MAAM,GAAG,GACP,CAAC,CAAC,KAAK,IAAI,IAAI,IAAI,CAAC,CAAC,GAAG,IAAI,IAAI;wBAC9B,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,MAAM,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,EAAE,EAAE;wBACjE,CAAC,CAAC,EAAE,CAAC;oBACT,MAAM,GAAG,GAAG,CAAC,CAAC,UAAU,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,UAAU,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;oBAC7D,KAAK,CAAC,IAAI,CACR,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,WAAW,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,GAAG,GAAG,GAAG,EAAE,CAClH,CAAC;gBACJ,CAAC;YACH,CAAC;QACH,CAAC,CAAC;QAEF,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;YAChB,UAAU,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;QAC1B,CAAC;aAAM,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;YACxB,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC;YAC3C,KAAK,CAAC,IAAI,CAAC,yBAAyB,CAAC,CAAC;YACtC,KAAK,CAAC,IAAI,CAAC,kBAAkB,SAAS,CAAC,MAAM,kBAAkB,MAAM,CAAC,MAAM,IAAI,CAAC,CAAC;YAClF,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;gBAC1B,UAAU,CAAC,CAAa,CAAC,CAAC;gBAC1B,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACjB,CAAC;YACD,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACtB,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC;gBACjC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;oBACvB,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;gBAC7C,CAAC;YACH,CAAC;QACH,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"}
|
|
1
|
+
{"version":3,"file":"lookup-gene.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-gene.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,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,uBAAuB,GAAG,CAAC,CAAC,MAAM,CAAC;IACvC,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;IAChE,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;IACvE,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,oEAAoE,CAAC;IACjF,WAAW,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,0DAA0D,CAAC;IAC7F,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;IAC/F,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;IAC3F,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;IAChF,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;CAC/E,CAAC,CAAC;AAEH,MAAM,gBAAgB,GAAG,CAAC,CAAC,MAAM,CAAC;IAChC,EAAE,EAAE,CAAC;SACF,MAAM,EAAE;SACR,QAAQ,CAAC,2EAA2E,CAAC;IACxF,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,6EAA6E,CAAC;IAC1F,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iDAAiD,CAAC;IAC9F,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;IACnF,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,yDAAyD,CAAC;IACtE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;IACjF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kDAAkD,CAAC;IACzF,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;IACrF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;IAChF,YAAY,EAAE,CAAC;SACZ,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,oFAAoF,CAAC;IACjG,WAAW,EAAE,CAAC;SACX,KAAK,CAAC,uBAAuB,CAAC,QAAQ,CAAC,oCAAoC,CAAC,CAAC;SAC7E,QAAQ,EAAE;SACV,QAAQ,CAAC,gEAAgE,CAAC;CAC9E,CAAC,CAAC;AAEH,MAAM,iBAAiB,GAAG,CAAC,CAAC,MAAM,CAAC;IACjC,6FAA6F;IAC7F,SAAS,EAAE,CAAC;SACT,KAAK,CACJ,CAAC;SACE,MAAM,CAAC,EAAE,CAAC;SACV,WAAW,EAAE;SACb,QAAQ,CAAC,sEAAsE,CAAC,CACpF;SACA,QAAQ,CAAC,8EAA8E,CAAC;IAC3F,MAAM,EAAE,CAAC;SACN,KAAK,CACJ,CAAC;SACE,MAAM,CAAC,EAAE,CAAC;SACV,WAAW,EAAE;SACb,QAAQ,CACP,iGAAiG,CAClG,CACJ;SACA,QAAQ,CAAC,+EAA+E,CAAC;CAC7F,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,qBAAqB,EAAE;IAC3D,KAAK,EAAE,aAAa;IACpB,WAAW,EACT,2FAA2F;QAC3F,sGAAsG;QACtG,oGAAoG;QACpG,mGAAmG;QACnG,mGAAmG;QACnG,kGAAkG;QAClG,iGAAiG;IACnG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mDAAmD;YACjD,qEAAqE;YACrE,mCAAmC,CACtC;QACH,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,mFAAmF;YACjF,wCAAwC,CAC3C;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,iFAAiF;YAC/E,kDAAkD;YAClD,sFAAsF;YACtF,oDAAoD,CACvD;QACH,GAAG,EAAE,CAAC;aACH,KAAK,CACJ,CAAC;aACE,MAAM,EAAE;aACR,IAAI,EAAE;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,mEAAmE,CAAC,CACjF;aACA,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,EAAE;aACV,QAAQ,CACP,4DAA4D;YAC1D,uFAAuF,CAC1F;QACH,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,EAAE;aACR,IAAI,EAAE;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,4DAA4D,CAAC,CAC1E;aACA,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,EAAE;aACV,QAAQ,CACP,uCAAuC;YACrC,qEAAqE;YACrE,uFAAuF,CAC1F;QACH,kBAAkB,EAAE,CAAC;aAClB,OAAO,EAAE;aACT,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,+DAA+D;YAC7D,wEAAwE;YACxE,6CAA6C,CAChD;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,IAAI,EAAE,gBAAgB,CAAC,QAAQ,EAAE,CAAC,QAAQ,CACxC,uDAAuD,CACxD;QACD,KAAK,EAAE,iBAAiB,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAC1C,oDAAoD,CACrD;KACF,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,wDAAwD;YAC9D,QAAQ,EACN,iGAAiG;gBACjG,sGAAsG;SACzG;QACD;YACE,MAAM,EAAE,iBAAiB;YACzB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,mDAAmD;YACzD,QAAQ,EACN,6DAA6D;gBAC7D,2FAA2F;SAC9F;QACD;YACE,MAAM,EAAE,UAAU;YAClB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,oDAAoD;YAC1D,QAAQ,EACN,gGAAgG;SACnG;QACD;YACE,MAAM,EAAE,mBAAmB;YAC3B,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,4DAA4D;YAClE,QAAQ,EACN,qFAAqF;SACxF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,iBAAiB,EAAE;YAC9B,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,EAAE,EAAE,KAAK,CAAC,EAAE;YACZ,OAAO,EAAE,KAAK,CAAC,OAAO;YACtB,SAAS,EAAE,KAAK,CAAC,GAAG,EAAE,MAAM,IAAI,KAAK,CAAC,OAAO,EAAE,MAAM;SACtD,CAAC,CAAC;QACH,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,UAAU,GAAG;YACjB,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE;YACpB,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE;YAChB,KAAK,CAAC,GAAG,EAAE,MAAM;YACjB,KAAK,CAAC,OAAO,EAAE,MAAM;SACtB,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC;QACzB,IAAI,UAAU,GAAG,CAAC,EAAE,CAAC;YACnB,MAAM,GAAG,CAAC,IAAI,CAAC,mBAAmB,EAAE,sDAAsD,EAAE;gBAC1F,GAAG,GAAG,CAAC,WAAW,CAAC,mBAAmB,CAAC;aACxC,CAAC,CAAC;QACL,CAAC;QAED,uBAAuB;QACvB,IAAI,KAAK,CAAC,GAAG,EAAE,MAAM,EAAE,CAAC;YACtB,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,gBAAgB,CAAC,KAAK,CAAC,GAAG,EAAE,KAAK,CAAC,kBAAkB,EAAE,GAAG,CAAC,CAAC;YACrF,MAAM,SAAS,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;YAC3C,MAAM,WAAW,GAAG,IAAI,GAAG,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,CAAC;YACxC,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG;iBACrB,MAAM,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;iBACpC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE,KAAK,EAAE,MAAM,EAAE,wBAAwB,EAAE,CAAC,CAAC,CAAC;YACzE,OAAO,EAAE,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,EAAE,CAAC;QAC1C,CAAC;QAED,2BAA2B;QAC3B,IAAI,KAAK,CAAC,OAAO,EAAE,MAAM,EAAE,CAAC;YAC1B,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,cAAc,CAAC;YAC3D,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,kBAAkB,CAC1C,KAAK,CAAC,OAAO,EACb,UAAU,EACV,KAAK,CAAC,kBAAkB,EACxB,GAAG,CACJ,CAAC;YACF,MAAM,SAAS,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;YAC3C,MAAM,eAAe,GAAG,IAAI,GAAG,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,CAAC;YAC5C,MAAM,MAAM,GAAG,KAAK,CAAC,OAAO;iBACzB,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,eAAe,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;iBACtC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBACX,KAAK,EAAE,CAAC;gBACR,KAAK,EAAE,UAAU,CAAC,qCAAqC,UAAU,GAAG;aACrE,CAAC,CAAC,CAAC;YACN,OAAO,EAAE,KAAK,EAAE,EAAE,SAAS,EAAE,MAAM,EAAE,EAAE,CAAC;QAC1C,CAAC;QAED,wBAAwB;QACxB,IAAI,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,EAAE,CAAC;YACzB,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,cAAc,CAAC;YAC3D,MAAM,IAAI,GAAG,MAAM,OAAO;iBACvB,UAAU,CAAC,KAAK,CAAC,MAAM,CAAC,IAAI,EAAE,EAAE,UAAU,EAAE,KAAK,CAAC,kBAAkB,EAAE,GAAG,CAAC;iBAC1E,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,IAAI,oDAAoD,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBACnE,MAAM,GAAG,CAAC,IAAI,CACZ,WAAW,EACX,gBAAgB,KAAK,CAAC,MAAM,kBAAkB,UAAU,GAAG,EAC3D,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CACpC,CAAC;gBACJ,CAAC;gBACD,IAAI,+BAA+B,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBAC9C,MAAM,GAAG,CAAC,IAAI,CACZ,iBAAiB,EACjB,YAAY,UAAU,8BAA8B,EACpD;wBACE,GAAG,GAAG,CAAC,WAAW,CAAC,iBAAiB,CAAC;qBACtC,CACF,CAAC;gBACJ,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;YACL,OAAO,EAAE,IAAI,EAAE,CAAC;QAClB,CAAC;QAED,oBAAoB;QACpB,IAAI,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE,EAAE,CAAC;YACrB,MAAM,IAAI,GAAG,MAAM,OAAO;iBACvB,cAAc,CAAC,KAAK,CAAC,EAAE,CAAC,IAAI,EAAE,EAAE,KAAK,CAAC,kBAAkB,EAAE,GAAG,CAAC;iBAC9D,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,IAAI,yBAAyB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBACxC,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,YAAY,KAAK,CAAC,EAAE,yBAAyB,EAAE;wBACzE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;qBAChC,CAAC,CAAC;gBACL,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;YACL,OAAO,EAAE,IAAI,EAAE,CAAC;QAClB,CAAC;QAED,MAAM,GAAG,CAAC,IAAI,CAAC,UAAU,EAAE,qDAAqD,EAAE;YAChF,GAAG,GAAG,CAAC,WAAW,CAAC,UAAU,CAAC;SAC/B,CAAC,CAAC;IACL,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAG3B,MAAM,UAAU,GAAG,CAAC,CAAW,EAAE,EAAE;YACjC,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,WAAW,IAAI,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC1C,KAAK,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC9B,IAAI,CAAC,CAAC,OAAO;gBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;YACvD,IAAI,CAAC,CAAC,OAAO;gBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;YACvD,IAAI,CAAC,CAAC,WAAW;gBAAE,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC;YACnE,IAAI,CAAC,CAAC,UAAU;gBAAE,KAAK,CAAC,IAAI,CAAC,mBAAmB,CAAC,CAAC,UAAU,EAAE,CAAC,CAAC;YAChE,IAAI,CAAC,CAAC,KAAK,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;YACzD,IAAI,CAAC,CAAC,GAAG,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;YACnD,IAAI,CAAC,CAAC,MAAM,IAAI,IAAI;gBAClB,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC;YACrF,IAAI,CAAC,CAAC,YAAY;gBAAE,KAAK,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC,YAAY,EAAE,CAAC,CAAC;YAClE,IAAI,CAAC,CAAC,WAAW,EAAE,MAAM,EAAE,CAAC;gBAC1B,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,WAAW,CAAC,MAAM,MAAM,CAAC,CAAC;gBAC3D,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,CAAC;oBAC9B,MAAM,KAAK,GAAG,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,CAAC;oBAClD,MAAM,GAAG,GACP,CAAC,CAAC,KAAK,IAAI,IAAI,IAAI,CAAC,CAAC,GAAG,IAAI,IAAI;wBAC9B,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,MAAM,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,EAAE,EAAE;wBACjE,CAAC,CAAC,EAAE,CAAC;oBACT,MAAM,GAAG,GAAG,CAAC,CAAC,UAAU,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,UAAU,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;oBAC7D,KAAK,CAAC,IAAI,CACR,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,WAAW,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,GAAG,GAAG,GAAG,EAAE,CAClH,CAAC;gBACJ,CAAC;YACH,CAAC;QACH,CAAC,CAAC;QAEF,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;YAChB,UAAU,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;QAC1B,CAAC;aAAM,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;YACxB,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC;YAC3C,KAAK,CAAC,IAAI,CAAC,yBAAyB,CAAC,CAAC;YACtC,KAAK,CAAC,IAAI,CAAC,kBAAkB,SAAS,CAAC,MAAM,kBAAkB,MAAM,CAAC,MAAM,IAAI,CAAC,CAAC;YAClF,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;gBAC1B,UAAU,CAAC,CAAa,CAAC,CAAC;gBAC1B,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACjB,CAAC;YACD,IAAI,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACtB,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC;gBACjC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;oBACvB,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,KAAK,OAAO,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;gBAC7C,CAAC;YACH,CAAC;QACH,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"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predict-variant.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/predict-variant.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA+HjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
|
1
|
+
{"version":3,"file":"predict-variant.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/predict-variant.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA+HjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6VhC,CAAC"}
|
|
@@ -117,6 +117,8 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
|
|
|
117
117
|
input: z.object({
|
|
118
118
|
variant: z
|
|
119
119
|
.string()
|
|
120
|
+
.trim()
|
|
121
|
+
.min(1)
|
|
120
122
|
.describe('Variant in one of three formats: ' +
|
|
121
123
|
'(1) HGVS notation — transcript-relative: ENST00000380152.8:c.2T>A; ' +
|
|
122
124
|
'genomic: 13:g.32316462T>A; ' +
|
|
@@ -127,6 +129,8 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
|
|
|
127
129
|
'though a chr-prefixed name is also accepted.'),
|
|
128
130
|
species: z
|
|
129
131
|
.string()
|
|
132
|
+
.trim()
|
|
133
|
+
.min(1)
|
|
130
134
|
.default('homo_sapiens')
|
|
131
135
|
.describe('Species in Ensembl internal format. Default is homo_sapiens. ' +
|
|
132
136
|
'For non-human variants, set the appropriate species ' +
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"predict-variant.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/predict-variant.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,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAG1E,MAAM,2BAA2B,GAAG,CAAC,CAAC,MAAM,CAAC;IAC3C,YAAY,EAAE,CAAC;SACZ,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,yDAAyD,CAAC;IACtE,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,4DAA4D,CAAC;IACzE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;IAC7E,gBAAgB,EAAE,CAAC;SAChB,KAAK,CACJ,CAAC;SACE,MAAM,EAAE;SACR,QAAQ,CAAC,4EAA4E,CAAC,CAC1F;SACA,QAAQ,CAAC,0DAA0D,CAAC;IACvE,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,mGAAmG,CACpG;IACH,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;IACpF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;IACvF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;IAC7F,UAAU,EAAE,CAAC;SACV,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,8DAA8D,CAAC;IAC3E,IAAI,EAAE,CAAC;SACJ,MAAM,CAAC;QACN,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4CAA4C,CAAC;QAC7E,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,CAAC,oEAAoE,CAAC;KAClF,CAAC;SACD,QAAQ,EAAE;SACV,QAAQ,CAAC,mFAAmF,CAAC;IAChG,QAAQ,EAAE,CAAC;SACR,MAAM,CAAC;QACN,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,CAAC,uEAAuE,CAAC;QACpF,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,CAAC,sEAAsE,CAAC;KACpF,CAAC;SACD,QAAQ,EAAE;SACV,QAAQ,CACP,uFAAuF,CACxF;CACJ,CAAC,CAAC;AAEH,MAAM,sBAAsB,GAAG,CAAC,CAAC,MAAM,CAAC;IACtC,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;IAC1F,YAAY,EAAE,CAAC;SACZ,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,uDAAuD,CAAC;IACpE,oBAAoB,EAAE,CAAC;SACpB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gEAAgE,CAAC,CAAC;SAC5F,QAAQ,EAAE;SACV,QAAQ,CAAC,qEAAqE,CAAC;IAClF,MAAM,EAAE,CAAC;SACN,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iDAAiD,CAAC,CAAC;SAC7E,QAAQ,EAAE;SACV,QAAQ,CACP,oEAAoE;QAClE,0FAA0F,CAC7F;IACH,WAAW,EAAE,CAAC;SACX,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,yFAAyF;QACvF,iEAAiE,CACpE;CACJ,CAAC,CAAC;AAEH,MAAM,eAAe,GAAG,CAAC,CAAC,MAAM,CAAC;IAC/B,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iDAAiD,CAAC;IACxF,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;IAC3E,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;IAC1E,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;IACtE,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;IACnF,qBAAqB,EAAE,CAAC;SACrB,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,wEAAwE;QACtE,2DAA2D,CAC9D;IACH,sBAAsB,EAAE,CAAC;SACtB,KAAK,CACJ,2BAA2B,CAAC,QAAQ,CAClC,6GAA6G,CAC9G,CACF;SACA,QAAQ,CACP,yFAAyF;QACvF,yFAAyF;QACzF,8FAA8F,CACjG;IACH,2BAA2B,EAAE,CAAC;SAC3B,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sFAAsF;QACpF,oEAAoE,CACvE;IACH,iBAAiB,EAAE,CAAC;SACjB,KAAK,CACJ,sBAAsB,CAAC,QAAQ,CAC7B,sFAAsF,CACvF,CACF;SACA,QAAQ,CACP,8EAA8E;QAC5E,kCAAkC,CACrC;CACJ,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,qBAAqB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACnE,KAAK,EAAE,wBAAwB;IAC/B,WAAW,EACT,8GAA8G;QAC9G,kGAAkG;QAClG,2GAA2G;QAC3G,2GAA2G;QAC3G,0GAA0G;QAC1G,uFAAuF;QACvF,yGAAyG;QACzG,iDAAiD;QACjD,qGAAqG;QACrG,oGAAoG;QACpG,uGAAuG;QACvG,iFAAiF;IACnF,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,CACP,mCAAmC;YACjC,qEAAqE;YACrE,6BAA6B;YAC7B,0EAA0E;YAC1E,+CAA+C;YAC/C,+BAA+B;YAC/B,2FAA2F;YAC3F,8CAA8C,CACjD;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,OAAO,CAAC,cAAc,CAAC;aACvB,QAAQ,CACP,+DAA+D;YAC7D,sDAAsD;YACtD,mFAAmF,CACtF;QACH,2BAA2B,EAAE,CAAC;aAC3B,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,4FAA4F;YAC1F,mFAAmF;YACnF,4DAA4D;YAC5D,mFAAmF,CACtF;QACH,0BAA0B,EAAE,CAAC;aAC1B,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,+FAA+F;YAC7F,8FAA8F;YAC9F,wEAAwE;YACxE,oDAAoD,CACvD;QACH,4BAA4B,EAAE,CAAC;aAC5B,OAAO,EAAE;aACT,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,2EAA2E;YACzE,sEAAsE,CACzE;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,eAAe,CAAC,QAAQ,CACtB,6GAA6G,CAC9G,CACF;aACA,QAAQ,CACP,6DAA6D;YAC3D,oFAAoF,CACvF;QACH,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;KAC/E,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,oEAAoE,CAAC;QACjF,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,EAAE;aACV,QAAQ,CAAC,+EAA+E,CAAC;QAC5F,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,0EAA0E,CAAC;QACvF,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;KACtF;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,kBAAkB;YAC1B,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,+DAA+D;YACrE,QAAQ,EACN,qFAAqF;gBACrF,6EAA6E;gBAC7E,oEAAoE;SACvE;QACD;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,6EAA6E;YACnF,QAAQ,EACN,4EAA4E;gBAC5E,8EAA8E;SACjF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,2BAA2B,EAAE,EAAE,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC;QAC9F,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,gFAAgF;QAChF,+EAA+E;QAC/E,MAAM,mBAAmB,GAAG,mCAAmC,CAAC;QAChE,MAAM,WAAW,GAAG,UAAU,CAAC;QAC/B,MAAM,WAAW,GAAG,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,mBAAmB,CAAC,CAAC;QAE7D,IAAI,OAAoB,CAAC;QACzB,IAAI,WAAW,EAAE,CAAC;YAChB,MAAM,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,MAAM,EAAE,MAAM,CAAC,GAAG,WAO3C,CAAC;YACF,OAAO,GAAG,MAAM,OAAO;iBACpB,oBAAoB,CACnB,GAAG,EACH,MAAM,CAAC,KAAK,CAAC,EACb,MAAM,CAAC,GAAG,CAAC,EACX,MAAM,CAAC,MAAM,CAAC,EACd,MAAM,EACN,KAAK,CAAC,OAAO,EACb,GAAG,CACJ;iBACA,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,IAAI,uCAAuC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBACtD,MAAM,GAAG,CAAC,IAAI,CACZ,kBAAkB,EAClB,mCAAmC,KAAK,CAAC,OAAO,MAAM,GAAG,EAAE,EAC3D,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,kBAAkB,CAAC,EAAE,CAC3C,CAAC;gBACJ,CAAC;gBACD,IAAI,oBAAoB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBACnC,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,+BAA+B,GAAG,EAAE,EAAE;wBAChE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;qBAChC,CAAC,CAAC;gBACL,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;QACP,CAAC;aAAM,IAAI,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,EAAE,CAAC;YAC3C,OAAO,GAAG,MAAM,OAAO;iBACpB,gBAAgB,CAAC,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC;iBACnD,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,oFAAoF;gBACpF,IAAI,uCAAuC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBACtD,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,sBAAsB,KAAK,CAAC,OAAO,sBAAsB,EAAE;wBACrF,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;qBAChC,CAAC,CAAC;gBACL,CAAC;gBACD,IAAI,uCAAuC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBACtD,MAAM,GAAG,CAAC,IAAI,CACZ,kBAAkB,EAClB,+BAA+B,KAAK,CAAC,OAAO,MAAM,GAAG,EAAE,EACvD,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,kBAAkB,CAAC,EAAE,CAC3C,CAAC;gBACJ,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;QACP,CAAC;aAAM,CAAC;YACN,OAAO,GAAG,MAAM,OAAO;iBACpB,kBAAkB,CAAC,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC;iBACrD,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,IAAI,4CAA4C,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBAC3D,MAAM,GAAG,CAAC,IAAI,CAAC,kBAAkB,EAAE,0BAA0B,KAAK,CAAC,OAAO,MAAM,GAAG,EAAE,EAAE;wBACrF,GAAG,GAAG,CAAC,WAAW,CAAC,kBAAkB,CAAC;qBACvC,CAAC,CAAC;gBACL,CAAC;gBACD,IAAI,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBAC3B,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,WAAW,KAAK,CAAC,OAAO,aAAa,EAAE;wBACjE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;qBAChC,CAAC,CAAC;gBACL,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;QACP,CAAC;QAED,qFAAqF;QACrF,+EAA+E;QAC/E,yEAAyE;QACzE,MAAM,eAAe,GAAG,KAAK,CAAC,2BAA2B,GAAG,CAAC,CAAC;QAC9D,MAAM,SAAS,GAAG,KAAK,CAAC,0BAA0B,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,4BAA4B,CAAC;QAC9F,IAAI,iBAAiB,GAAG,CAAC,CAAC;QAC1B,IAAI,iBAAiB,GAAG,CAAC,CAAC;QAC1B,IAAI,YAAY,GAAG,KAAK,CAAC;QAEzB,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;YAC/B,iBAAiB,IAAI,CAAC,CAAC,sBAAsB,CAAC,MAAM,CAAC;YACrD,MAAM,sBAAsB,GAAG,eAAe;gBAC5C,CAAC,CAAC,CAAC,CAAC,sBAAsB,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,2BAA2B,CAAC;gBACtE,CAAC,CAAC,CAAC,CAAC,sBAAsB,CAAC;YAC7B,iBAAiB,IAAI,sBAAsB,CAAC,MAAM,CAAC;YAEnD,MAAM,iBAAiB,GAAG,CAAC,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE;gBACvD,IAAI,CAAC,EAAE,CAAC,MAAM;oBAAE,OAAO,EAAE,CAAC;gBAC1B,MAAM,WAAW,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC;gBACrC,MAAM,MAAM,GAAG,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,0BAA0B,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,MAAM,CAAC;gBAC5F,IAAI,MAAM,CAAC,MAAM,GAAG,WAAW;oBAAE,YAAY,GAAG,IAAI,CAAC;gBACrD,OAAO,EAAE,GAAG,EAAE,EAAE,MAAM,EAAE,WAAW,EAAE,CAAC;YACxC,CAAC,CAAC,CAAC;YAEH,OAAO;gBACL,GAAG,CAAC;gBACJ,sBAAsB;gBACtB,2BAA2B,EAAE,CAAC,CAAC,sBAAsB,CAAC,MAAM;gBAC5D,iBAAiB;aAClB,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACxB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,uBAAuB,KAAK,CAAC,OAAO,KAAK;gBACvC,oFAAoF,CACvF,CAAC;QACJ,CAAC;aAAM,CAAC;YACN,+EAA+E;YAC/E,qFAAqF;YACrF,MAAM,SAAS,GAAa,EAAE,CAAC;YAC/B,MAAM,mBAAmB,GAAG,iBAAiB,GAAG,iBAAiB,CAAC;YAClE,IAAI,mBAAmB,GAAG,CAAC,EAAE,CAAC;gBAC5B,SAAS,CAAC,IAAI,CACZ,WAAW,iBAAiB,OAAO,iBAAiB,0BAA0B,CAC/E,CAAC;YACJ,CAAC;YACD,IAAI,YAAY,EAAE,CAAC;gBACjB,SAAS,CAAC,IAAI,CACZ,wBAAwB,KAAK,CAAC,0BAA0B,wBAAwB,CACjF,CAAC;YACJ,CAAC;YACD,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACzB,MAAM,QAAQ,GACZ,GAAG,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,sDAAsD;oBAC7E,+DAA+D,CAAC;gBAClE,IAAI,mBAAmB,GAAG,CAAC,EAAE,CAAC;oBAC5B,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC;wBACnB,KAAK,EAAE,iBAAiB;wBACxB,GAAG,EAAE,KAAK,CAAC,2BAA2B;wBACtC,QAAQ;qBACT,CAAC,CAAC;gBACL,CAAC;qBAAM,CAAC;oBACN,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC;gBAC9B,CAAC;YACH,CAAC;QACH,CAAC;QACD,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;QAEhC,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC;IACxD,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAE3B,KAAK,CAAC,IAAI,CAAC,mBAAmB,MAAM,CAAC,UAAU,UAAU,MAAM,CAAC,UAAU,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC;QAEhG,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,2CAA2C,CAAC,CAAC;YACxD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACpD,CAAC;QAED,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC,KAAK,IAAI,SAAS,EAAE,CAAC,CAAC;YACrD,IAAI,CAAC,CAAC,UAAU,IAAI,CAAC,CAAC,KAAK,IAAI,IAAI,EAAE,CAAC;gBACpC,KAAK,CAAC,IAAI,CACR,iBAAiB,CAAC,CAAC,UAAU,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CACjI,CAAC;YACJ,CAAC;YACD,IAAI,CAAC,CAAC,qBAAqB,EAAE,CAAC;gBAC5B,KAAK,CAAC,IAAI,CAAC,gCAAgC,CAAC,CAAC,qBAAqB,EAAE,CAAC,CAAC;YACxE,CAAC;YAED,IAAI,CAAC,CAAC,iBAAiB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACnC,KAAK,CAAC,IAAI,CAAC,iCAAiC,CAAC,CAAC;gBAC9C,KAAK,MAAM,EAAE,IAAI,CAAC,CAAC,iBAAiB,EAAE,CAAC;oBACrC,IAAI,MAAM,GAAG,KAAK,EAAE,CAAC,EAAE,IAAI,OAAO,EAAE,CAAC;oBACrC,IAAI,EAAE,CAAC,YAAY;wBAAE,MAAM,IAAI,KAAK,EAAE,CAAC,YAAY,GAAG,CAAC;oBACvD,IAAI,EAAE,CAAC,oBAAoB,EAAE,MAAM,EAAE,CAAC;wBACpC,MAAM,IAAI,MAAM,EAAE,CAAC,oBAAoB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;oBACvD,CAAC;oBACD,IAAI,EAAE,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC;wBACtB,MAAM,WAAW,GAAG,EAAE,CAAC,WAAW,IAAI,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC;wBACvD,MAAM,YAAY,GAChB,WAAW,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM;4BAC5B,CAAC,CAAC,aAAa,EAAE,CAAC,MAAM,CAAC,MAAM,OAAO,WAAW,GAAG;4BACpD,CAAC,CAAC,EAAE,CAAC;wBACT,MAAM,IAAI,cAAc,EAAE,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,YAAY,EAAE,CAAC;oBAChE,CAAC;oBACD,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;gBACrB,CAAC;YACH,CAAC;YAED,IAAI,CAAC,CAAC,sBAAsB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,OAAO,GAAG,CAAC,CAAC,sBAAsB,CAAC,MAAM,CAAC;gBAChD,MAAM,OAAO,GAAG,CAAC,CAAC,2BAA2B,IAAI,OAAO,CAAC;gBACzD,MAAM,OAAO,GAAG,OAAO,GAAG,OAAO,CAAC,CAAC,CAAC,GAAG,OAAO,OAAO,OAAO,EAAE,CAAC,CAAC,CAAC,GAAG,OAAO,EAAE,CAAC;gBAC9E,KAAK,CAAC,IAAI,CAAC,gCAAgC,OAAO,MAAM,CAAC,CAAC;gBAC1D,KAAK,MAAM,EAAE,IAAI,CAAC,CAAC,sBAAsB,EAAE,CAAC;oBAC1C,MAAM,SAAS,GAAG,EAAE,CAAC,UAAU,IAAI,EAAE,CAAC,MAAM,IAAI,SAAS,CAAC;oBAC1D,KAAK,CAAC,IAAI,CAAC,UAAU,SAAS,MAAM,EAAE,CAAC,YAAY,IAAI,SAAS,EAAE,CAAC,CAAC;oBACpE,IAAI,EAAE,CAAC,MAAM,IAAI,EAAE,CAAC,UAAU;wBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,EAAE,CAAC,MAAM,EAAE,CAAC,CAAC;oBACxE,KAAK,CAAC,IAAI,CACR,eAAe,EAAE,CAAC,MAAM,IAAI,SAAS,uBAAuB,EAAE,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAC7F,CAAC;oBACF,IAAI,EAAE,CAAC,OAAO;wBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,EAAE,CAAC,OAAO,EAAE,CAAC,CAAC;oBACzD,IAAI,EAAE,CAAC,KAAK;wBAAE,KAAK,CAAC,IAAI,CAAC,cAAc,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC;oBACnD,IAAI,EAAE,CAAC,KAAK;wBAAE,KAAK,CAAC,IAAI,CAAC,cAAc,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC;oBACnD,IAAI,EAAE,CAAC,UAAU;wBAAE,KAAK,CAAC,IAAI,CAAC,oBAAoB,EAAE,CAAC,UAAU,EAAE,CAAC,CAAC;oBACnE,IAAI,EAAE,CAAC,IAAI,EAAE,CAAC;wBACZ,KAAK,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC,IAAI,CAAC,UAAU,YAAY,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;oBACrF,CAAC;oBACD,IAAI,EAAE,CAAC,QAAQ,EAAE,CAAC;wBAChB,KAAK,CAAC,IAAI,CACR,iBAAiB,EAAE,CAAC,QAAQ,CAAC,UAAU,YAAY,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CACnF,CAAC;oBACJ,CAAC;gBACH,CAAC;YACH,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"}
|
|
1
|
+
{"version":3,"file":"predict-variant.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/predict-variant.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,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAG1E,MAAM,2BAA2B,GAAG,CAAC,CAAC,MAAM,CAAC;IAC3C,YAAY,EAAE,CAAC;SACZ,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,yDAAyD,CAAC;IACtE,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,4DAA4D,CAAC;IACzE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;IAC7E,gBAAgB,EAAE,CAAC;SAChB,KAAK,CACJ,CAAC;SACE,MAAM,EAAE;SACR,QAAQ,CAAC,4EAA4E,CAAC,CAC1F;SACA,QAAQ,CAAC,0DAA0D,CAAC;IACvE,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,mGAAmG,CACpG;IACH,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;IACpF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;IACvF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;IAC7F,UAAU,EAAE,CAAC;SACV,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,8DAA8D,CAAC;IAC3E,IAAI,EAAE,CAAC;SACJ,MAAM,CAAC;QACN,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4CAA4C,CAAC;QAC7E,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,CAAC,oEAAoE,CAAC;KAClF,CAAC;SACD,QAAQ,EAAE;SACV,QAAQ,CAAC,mFAAmF,CAAC;IAChG,QAAQ,EAAE,CAAC;SACR,MAAM,CAAC;QACN,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,CAAC,uEAAuE,CAAC;QACpF,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,CAAC,sEAAsE,CAAC;KACpF,CAAC;SACD,QAAQ,EAAE;SACV,QAAQ,CACP,uFAAuF,CACxF;CACJ,CAAC,CAAC;AAEH,MAAM,sBAAsB,GAAG,CAAC,CAAC,MAAM,CAAC;IACtC,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;IAC1F,YAAY,EAAE,CAAC;SACZ,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,uDAAuD,CAAC;IACpE,oBAAoB,EAAE,CAAC;SACpB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gEAAgE,CAAC,CAAC;SAC5F,QAAQ,EAAE;SACV,QAAQ,CAAC,qEAAqE,CAAC;IAClF,MAAM,EAAE,CAAC;SACN,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iDAAiD,CAAC,CAAC;SAC7E,QAAQ,EAAE;SACV,QAAQ,CACP,oEAAoE;QAClE,0FAA0F,CAC7F;IACH,WAAW,EAAE,CAAC;SACX,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,yFAAyF;QACvF,iEAAiE,CACpE;CACJ,CAAC,CAAC;AAEH,MAAM,eAAe,GAAG,CAAC,CAAC,MAAM,CAAC;IAC/B,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iDAAiD,CAAC;IACxF,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;IAC3E,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;IAC1E,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;IACtE,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;IACnF,qBAAqB,EAAE,CAAC;SACrB,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,wEAAwE;QACtE,2DAA2D,CAC9D;IACH,sBAAsB,EAAE,CAAC;SACtB,KAAK,CACJ,2BAA2B,CAAC,QAAQ,CAClC,6GAA6G,CAC9G,CACF;SACA,QAAQ,CACP,yFAAyF;QACvF,yFAAyF;QACzF,8FAA8F,CACjG;IACH,2BAA2B,EAAE,CAAC;SAC3B,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sFAAsF;QACpF,oEAAoE,CACvE;IACH,iBAAiB,EAAE,CAAC;SACjB,KAAK,CACJ,sBAAsB,CAAC,QAAQ,CAC7B,sFAAsF,CACvF,CACF;SACA,QAAQ,CACP,8EAA8E;QAC5E,kCAAkC,CACrC;CACJ,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,qBAAqB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACnE,KAAK,EAAE,wBAAwB;IAC/B,WAAW,EACT,8GAA8G;QAC9G,kGAAkG;QAClG,2GAA2G;QAC3G,2GAA2G;QAC3G,0GAA0G;QAC1G,uFAAuF;QACvF,yGAAyG;QACzG,iDAAiD;QACjD,qGAAqG;QACrG,oGAAoG;QACpG,uGAAuG;QACvG,iFAAiF;IACnF,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,IAAI,EAAE;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,mCAAmC;YACjC,qEAAqE;YACrE,6BAA6B;YAC7B,0EAA0E;YAC1E,+CAA+C;YAC/C,+BAA+B;YAC/B,2FAA2F;YAC3F,8CAA8C,CACjD;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,IAAI,EAAE;aACN,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,cAAc,CAAC;aACvB,QAAQ,CACP,+DAA+D;YAC7D,sDAAsD;YACtD,mFAAmF,CACtF;QACH,2BAA2B,EAAE,CAAC;aAC3B,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,4FAA4F;YAC1F,mFAAmF;YACnF,4DAA4D;YAC5D,mFAAmF,CACtF;QACH,0BAA0B,EAAE,CAAC;aAC1B,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,+FAA+F;YAC7F,8FAA8F;YAC9F,wEAAwE;YACxE,oDAAoD,CACvD;QACH,4BAA4B,EAAE,CAAC;aAC5B,OAAO,EAAE;aACT,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,2EAA2E;YACzE,sEAAsE,CACzE;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,eAAe,CAAC,QAAQ,CACtB,6GAA6G,CAC9G,CACF;aACA,QAAQ,CACP,6DAA6D;YAC3D,oFAAoF,CACvF;QACH,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;KAC/E,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,oEAAoE,CAAC;QACjF,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,EAAE;aACV,QAAQ,CAAC,+EAA+E,CAAC;QAC5F,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,0EAA0E,CAAC;QACvF,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;KACtF;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,kBAAkB;YAC1B,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,+DAA+D;YACrE,QAAQ,EACN,qFAAqF;gBACrF,6EAA6E;gBAC7E,oEAAoE;SACvE;QACD;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,6EAA6E;YACnF,QAAQ,EACN,4EAA4E;gBAC5E,8EAA8E;SACjF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,2BAA2B,EAAE,EAAE,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC;QAC9F,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,gFAAgF;QAChF,+EAA+E;QAC/E,MAAM,mBAAmB,GAAG,mCAAmC,CAAC;QAChE,MAAM,WAAW,GAAG,UAAU,CAAC;QAC/B,MAAM,WAAW,GAAG,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,mBAAmB,CAAC,CAAC;QAE7D,IAAI,OAAoB,CAAC;QACzB,IAAI,WAAW,EAAE,CAAC;YAChB,MAAM,CAAC,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,MAAM,EAAE,MAAM,CAAC,GAAG,WAO3C,CAAC;YACF,OAAO,GAAG,MAAM,OAAO;iBACpB,oBAAoB,CACnB,GAAG,EACH,MAAM,CAAC,KAAK,CAAC,EACb,MAAM,CAAC,GAAG,CAAC,EACX,MAAM,CAAC,MAAM,CAAC,EACd,MAAM,EACN,KAAK,CAAC,OAAO,EACb,GAAG,CACJ;iBACA,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,IAAI,uCAAuC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBACtD,MAAM,GAAG,CAAC,IAAI,CACZ,kBAAkB,EAClB,mCAAmC,KAAK,CAAC,OAAO,MAAM,GAAG,EAAE,EAC3D,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,kBAAkB,CAAC,EAAE,CAC3C,CAAC;gBACJ,CAAC;gBACD,IAAI,oBAAoB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBACnC,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,+BAA+B,GAAG,EAAE,EAAE;wBAChE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;qBAChC,CAAC,CAAC;gBACL,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;QACP,CAAC;aAAM,IAAI,WAAW,CAAC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,EAAE,CAAC;YAC3C,OAAO,GAAG,MAAM,OAAO;iBACpB,gBAAgB,CAAC,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC;iBACnD,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,oFAAoF;gBACpF,IAAI,uCAAuC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBACtD,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,sBAAsB,KAAK,CAAC,OAAO,sBAAsB,EAAE;wBACrF,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;qBAChC,CAAC,CAAC;gBACL,CAAC;gBACD,IAAI,uCAAuC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBACtD,MAAM,GAAG,CAAC,IAAI,CACZ,kBAAkB,EAClB,+BAA+B,KAAK,CAAC,OAAO,MAAM,GAAG,EAAE,EACvD,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,kBAAkB,CAAC,EAAE,CAC3C,CAAC;gBACJ,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;QACP,CAAC;aAAM,CAAC;YACN,OAAO,GAAG,MAAM,OAAO;iBACpB,kBAAkB,CAAC,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC;iBACrD,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,IAAI,4CAA4C,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBAC3D,MAAM,GAAG,CAAC,IAAI,CAAC,kBAAkB,EAAE,0BAA0B,KAAK,CAAC,OAAO,MAAM,GAAG,EAAE,EAAE;wBACrF,GAAG,GAAG,CAAC,WAAW,CAAC,kBAAkB,CAAC;qBACvC,CAAC,CAAC;gBACL,CAAC;gBACD,IAAI,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBAC3B,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,WAAW,KAAK,CAAC,OAAO,aAAa,EAAE;wBACjE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;qBAChC,CAAC,CAAC;gBACL,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;QACP,CAAC;QAED,qFAAqF;QACrF,+EAA+E;QAC/E,yEAAyE;QACzE,MAAM,eAAe,GAAG,KAAK,CAAC,2BAA2B,GAAG,CAAC,CAAC;QAC9D,MAAM,SAAS,GAAG,KAAK,CAAC,0BAA0B,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,4BAA4B,CAAC;QAC9F,IAAI,iBAAiB,GAAG,CAAC,CAAC;QAC1B,IAAI,iBAAiB,GAAG,CAAC,CAAC;QAC1B,IAAI,YAAY,GAAG,KAAK,CAAC;QAEzB,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;YAC/B,iBAAiB,IAAI,CAAC,CAAC,sBAAsB,CAAC,MAAM,CAAC;YACrD,MAAM,sBAAsB,GAAG,eAAe;gBAC5C,CAAC,CAAC,CAAC,CAAC,sBAAsB,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,2BAA2B,CAAC;gBACtE,CAAC,CAAC,CAAC,CAAC,sBAAsB,CAAC;YAC7B,iBAAiB,IAAI,sBAAsB,CAAC,MAAM,CAAC;YAEnD,MAAM,iBAAiB,GAAG,CAAC,CAAC,iBAAiB,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE;gBACvD,IAAI,CAAC,EAAE,CAAC,MAAM;oBAAE,OAAO,EAAE,CAAC;gBAC1B,MAAM,WAAW,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC;gBACrC,MAAM,MAAM,GAAG,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,0BAA0B,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,MAAM,CAAC;gBAC5F,IAAI,MAAM,CAAC,MAAM,GAAG,WAAW;oBAAE,YAAY,GAAG,IAAI,CAAC;gBACrD,OAAO,EAAE,GAAG,EAAE,EAAE,MAAM,EAAE,WAAW,EAAE,CAAC;YACxC,CAAC,CAAC,CAAC;YAEH,OAAO;gBACL,GAAG,CAAC;gBACJ,sBAAsB;gBACtB,2BAA2B,EAAE,CAAC,CAAC,sBAAsB,CAAC,MAAM;gBAC5D,iBAAiB;aAClB,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACxB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,uBAAuB,KAAK,CAAC,OAAO,KAAK;gBACvC,oFAAoF,CACvF,CAAC;QACJ,CAAC;aAAM,CAAC;YACN,+EAA+E;YAC/E,qFAAqF;YACrF,MAAM,SAAS,GAAa,EAAE,CAAC;YAC/B,MAAM,mBAAmB,GAAG,iBAAiB,GAAG,iBAAiB,CAAC;YAClE,IAAI,mBAAmB,GAAG,CAAC,EAAE,CAAC;gBAC5B,SAAS,CAAC,IAAI,CACZ,WAAW,iBAAiB,OAAO,iBAAiB,0BAA0B,CAC/E,CAAC;YACJ,CAAC;YACD,IAAI,YAAY,EAAE,CAAC;gBACjB,SAAS,CAAC,IAAI,CACZ,wBAAwB,KAAK,CAAC,0BAA0B,wBAAwB,CACjF,CAAC;YACJ,CAAC;YACD,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACzB,MAAM,QAAQ,GACZ,GAAG,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,sDAAsD;oBAC7E,+DAA+D,CAAC;gBAClE,IAAI,mBAAmB,GAAG,CAAC,EAAE,CAAC;oBAC5B,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC;wBACnB,KAAK,EAAE,iBAAiB;wBACxB,GAAG,EAAE,KAAK,CAAC,2BAA2B;wBACtC,QAAQ;qBACT,CAAC,CAAC;gBACL,CAAC;qBAAM,CAAC;oBACN,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC;gBAC9B,CAAC;YACH,CAAC;QACH,CAAC;QACD,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;QAEhC,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC;IACxD,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAE3B,KAAK,CAAC,IAAI,CAAC,mBAAmB,MAAM,CAAC,UAAU,UAAU,MAAM,CAAC,UAAU,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC;QAEhG,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,2CAA2C,CAAC,CAAC;YACxD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACpD,CAAC;QAED,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC,KAAK,IAAI,SAAS,EAAE,CAAC,CAAC;YACrD,IAAI,CAAC,CAAC,UAAU,IAAI,CAAC,CAAC,KAAK,IAAI,IAAI,EAAE,CAAC;gBACpC,KAAK,CAAC,IAAI,CACR,iBAAiB,CAAC,CAAC,UAAU,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CACjI,CAAC;YACJ,CAAC;YACD,IAAI,CAAC,CAAC,qBAAqB,EAAE,CAAC;gBAC5B,KAAK,CAAC,IAAI,CAAC,gCAAgC,CAAC,CAAC,qBAAqB,EAAE,CAAC,CAAC;YACxE,CAAC;YAED,IAAI,CAAC,CAAC,iBAAiB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACnC,KAAK,CAAC,IAAI,CAAC,iCAAiC,CAAC,CAAC;gBAC9C,KAAK,MAAM,EAAE,IAAI,CAAC,CAAC,iBAAiB,EAAE,CAAC;oBACrC,IAAI,MAAM,GAAG,KAAK,EAAE,CAAC,EAAE,IAAI,OAAO,EAAE,CAAC;oBACrC,IAAI,EAAE,CAAC,YAAY;wBAAE,MAAM,IAAI,KAAK,EAAE,CAAC,YAAY,GAAG,CAAC;oBACvD,IAAI,EAAE,CAAC,oBAAoB,EAAE,MAAM,EAAE,CAAC;wBACpC,MAAM,IAAI,MAAM,EAAE,CAAC,oBAAoB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;oBACvD,CAAC;oBACD,IAAI,EAAE,CAAC,MAAM,EAAE,MAAM,EAAE,CAAC;wBACtB,MAAM,WAAW,GAAG,EAAE,CAAC,WAAW,IAAI,EAAE,CAAC,MAAM,CAAC,MAAM,CAAC;wBACvD,MAAM,YAAY,GAChB,WAAW,GAAG,EAAE,CAAC,MAAM,CAAC,MAAM;4BAC5B,CAAC,CAAC,aAAa,EAAE,CAAC,MAAM,CAAC,MAAM,OAAO,WAAW,GAAG;4BACpD,CAAC,CAAC,EAAE,CAAC;wBACT,MAAM,IAAI,cAAc,EAAE,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,YAAY,EAAE,CAAC;oBAChE,CAAC;oBACD,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;gBACrB,CAAC;YACH,CAAC;YAED,IAAI,CAAC,CAAC,sBAAsB,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,OAAO,GAAG,CAAC,CAAC,sBAAsB,CAAC,MAAM,CAAC;gBAChD,MAAM,OAAO,GAAG,CAAC,CAAC,2BAA2B,IAAI,OAAO,CAAC;gBACzD,MAAM,OAAO,GAAG,OAAO,GAAG,OAAO,CAAC,CAAC,CAAC,GAAG,OAAO,OAAO,OAAO,EAAE,CAAC,CAAC,CAAC,GAAG,OAAO,EAAE,CAAC;gBAC9E,KAAK,CAAC,IAAI,CAAC,gCAAgC,OAAO,MAAM,CAAC,CAAC;gBAC1D,KAAK,MAAM,EAAE,IAAI,CAAC,CAAC,sBAAsB,EAAE,CAAC;oBAC1C,MAAM,SAAS,GAAG,EAAE,CAAC,UAAU,IAAI,EAAE,CAAC,MAAM,IAAI,SAAS,CAAC;oBAC1D,KAAK,CAAC,IAAI,CAAC,UAAU,SAAS,MAAM,EAAE,CAAC,YAAY,IAAI,SAAS,EAAE,CAAC,CAAC;oBACpE,IAAI,EAAE,CAAC,MAAM,IAAI,EAAE,CAAC,UAAU;wBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,EAAE,CAAC,MAAM,EAAE,CAAC,CAAC;oBACxE,KAAK,CAAC,IAAI,CACR,eAAe,EAAE,CAAC,MAAM,IAAI,SAAS,uBAAuB,EAAE,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAC7F,CAAC;oBACF,IAAI,EAAE,CAAC,OAAO;wBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,EAAE,CAAC,OAAO,EAAE,CAAC,CAAC;oBACzD,IAAI,EAAE,CAAC,KAAK;wBAAE,KAAK,CAAC,IAAI,CAAC,cAAc,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC;oBACnD,IAAI,EAAE,CAAC,KAAK;wBAAE,KAAK,CAAC,IAAI,CAAC,cAAc,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC;oBACnD,IAAI,EAAE,CAAC,UAAU;wBAAE,KAAK,CAAC,IAAI,CAAC,oBAAoB,EAAE,CAAC,UAAU,EAAE,CAAC,CAAC;oBACnE,IAAI,EAAE,CAAC,IAAI,EAAE,CAAC;wBACZ,KAAK,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC,IAAI,CAAC,UAAU,YAAY,EAAE,CAAC,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;oBACrF,CAAC;oBACD,IAAI,EAAE,CAAC,QAAQ,EAAE,CAAC;wBAChB,KAAK,CAAC,IAAI,CACR,iBAAiB,EAAE,CAAC,QAAQ,CAAC,UAAU,YAAY,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CACnF,CAAC;oBACJ,CAAC;gBACH,CAAC;YACH,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"}
|
|
@@ -15,6 +15,7 @@ export declare const ensemblQueryRegion: import("@cyanheads/mcp-ts-core").ToolDe
|
|
|
15
15
|
variation: "variation";
|
|
16
16
|
}>>>;
|
|
17
17
|
biotype: z.ZodOptional<z.ZodString>;
|
|
18
|
+
max_results: z.ZodDefault<z.ZodNumber>;
|
|
18
19
|
}, z.core.$strip>, z.ZodObject<{
|
|
19
20
|
features: z.ZodArray<z.ZodObject<{
|
|
20
21
|
id: z.ZodOptional<z.ZodString>;
|
|
@@ -34,10 +35,11 @@ export declare const ensemblQueryRegion: import("@cyanheads/mcp-ts-core").ToolDe
|
|
|
34
35
|
totalCount: z.ZodNumber;
|
|
35
36
|
region: z.ZodString;
|
|
36
37
|
species: z.ZodString;
|
|
38
|
+
assemblyName: z.ZodOptional<z.ZodString>;
|
|
37
39
|
}, z.core.$strip>, readonly [{
|
|
38
40
|
readonly reason: "invalid_region";
|
|
39
41
|
readonly code: JsonRpcErrorCode.ValidationError;
|
|
40
|
-
readonly when:
|
|
42
|
+
readonly when: string;
|
|
41
43
|
readonly recovery: string;
|
|
42
44
|
}, {
|
|
43
45
|
readonly reason: "invalid_species";
|
|
@@ -46,5 +48,8 @@ export declare const ensemblQueryRegion: import("@cyanheads/mcp-ts-core").ToolDe
|
|
|
46
48
|
readonly recovery: "Call ensembl_list_species to discover valid species names in lowercase_underscore format.";
|
|
47
49
|
}], {
|
|
48
50
|
readonly notice: z.ZodOptional<z.ZodString>;
|
|
51
|
+
readonly truncated: z.ZodOptional<z.ZodBoolean>;
|
|
52
|
+
readonly shown: z.ZodOptional<z.ZodNumber>;
|
|
53
|
+
readonly cap: z.ZodOptional<z.ZodNumber>;
|
|
49
54
|
}>;
|
|
50
55
|
//# sourceMappingURL=query-region.tool.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"query-region.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/query-region.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;
|
|
1
|
+
{"version":3,"file":"query-region.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/query-region.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyDjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA0Q7B,CAAC"}
|
|
@@ -40,26 +40,48 @@ const FeatureSchema = z.object({
|
|
|
40
40
|
.optional()
|
|
41
41
|
.describe('Position (1-based) of an exon within its parent transcript.'),
|
|
42
42
|
});
|
|
43
|
+
/**
|
|
44
|
+
* Linear-time `/invalid.*region/i`: "invalid" followed later on the same line by
|
|
45
|
+
* "region". Ensembl echoes the caller's region into its error text, and the
|
|
46
|
+
* backtracking regex is quadratic in that echo.
|
|
47
|
+
*/
|
|
48
|
+
function mentionsInvalidRegion(msg) {
|
|
49
|
+
return msg
|
|
50
|
+
.toLowerCase()
|
|
51
|
+
.split(/[\n\r\u2028\u2029]/)
|
|
52
|
+
.some((line) => {
|
|
53
|
+
const at = line.indexOf('invalid');
|
|
54
|
+
return at !== -1 && line.includes('region', at + 'invalid'.length);
|
|
55
|
+
});
|
|
56
|
+
}
|
|
43
57
|
export const ensemblQueryRegion = tool('ensembl_query_region', {
|
|
44
58
|
title: 'Query Genomic Region',
|
|
45
59
|
description: 'Find genomic features overlapping a chromosomal region: genes, transcripts, variants, regulatory ' +
|
|
46
|
-
'elements, or exons. Returns each feature with its stable ID, type, location, biotype, and name
|
|
60
|
+
'elements, or exons. Returns each feature with its stable ID, type, location, biotype, and name, ' +
|
|
61
|
+
'plus the genome assembly the coordinates are on. ' +
|
|
47
62
|
'Useful for "what\'s in this locus?" and for seeding follow-up lookups. Region format is chr:start-end ' +
|
|
48
|
-
'(e.g. 13:32315086-32400268 for the BRCA2 locus)
|
|
49
|
-
'vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed
|
|
50
|
-
'accepted. The feature parameter defaults to gene only
|
|
51
|
-
'variation in an 85 kb region
|
|
52
|
-
'transcript, or exon only when needed.
|
|
63
|
+
'(e.g. 13:32315086-32400268 for the BRCA2 locus), spanning at most 5,000,000 bases. Ensembl normalizes ' +
|
|
64
|
+
'chromosome names and canonical vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed ' +
|
|
65
|
+
'name like chr13 is also accepted. The feature parameter defaults to gene only — requesting ' +
|
|
66
|
+
'variation in an 85 kb region matches 44,000+ entries. Explicitly include variation, regulatory, ' +
|
|
67
|
+
'transcript, or exon only when needed. The response returns up to max_results features (default 100) ' +
|
|
68
|
+
'while totalCount always reports the full count; set max_results to 0 for every feature, or query a ' +
|
|
69
|
+
'smaller region to see a different slice. Exon rows carry the parent transcript ID, so the same exon ' +
|
|
53
70
|
'appears once per transcript it belongs to.',
|
|
54
71
|
annotations: { readOnlyHint: true, openWorldHint: true, idempotentHint: true },
|
|
55
72
|
input: z.object({
|
|
56
73
|
species: z
|
|
57
74
|
.string()
|
|
75
|
+
.trim()
|
|
76
|
+
.min(1)
|
|
58
77
|
.describe('Species in Ensembl internal format (e.g. homo_sapiens, mus_musculus). ' +
|
|
59
78
|
'Use ensembl_list_species to discover valid values.'),
|
|
60
79
|
region: z
|
|
61
80
|
.string()
|
|
62
|
-
.
|
|
81
|
+
.trim()
|
|
82
|
+
.min(1)
|
|
83
|
+
.describe('Genomic region in chr:start-end format (e.g. 13:32315086-32400268). Ensembl serves at most ' +
|
|
84
|
+
'5,000,000 bases per region; split a larger area into smaller windows. ' +
|
|
63
85
|
'Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix ' +
|
|
64
86
|
'(13, not chr13); a chr-prefixed name like chr13 is also accepted. ' +
|
|
65
87
|
'For large regions (>100 kb), limit to gene feature type to avoid overwhelming results.'),
|
|
@@ -67,35 +89,62 @@ export const ensemblQueryRegion = tool('ensembl_query_region', {
|
|
|
67
89
|
.array(z
|
|
68
90
|
.enum(FEATURE_TYPES)
|
|
69
91
|
.describe('A feature type to retrieve: gene, transcript, variation, regulatory, or exon.'))
|
|
92
|
+
.min(1, `Provide at least one feature type: ${FEATURE_TYPES.join(', ')}.`)
|
|
70
93
|
.default(['gene'])
|
|
71
|
-
.describe('Feature types to retrieve. Default is gene only. ' +
|
|
72
|
-
'Requesting variation in a large region can
|
|
94
|
+
.describe('Feature types to retrieve — at least one. Default is gene only. ' +
|
|
95
|
+
'Requesting variation in a large region can match tens of thousands of features. ' +
|
|
73
96
|
'Include variation only for targeted small regions (single gene loci or smaller).'),
|
|
74
97
|
biotype: z
|
|
75
98
|
.string()
|
|
76
99
|
.optional()
|
|
77
100
|
.describe('Optional biotype filter (e.g. protein_coding, lncRNA, SNV). ' +
|
|
78
101
|
'Applied server-side by Ensembl. Not all feature types support biotype filtering.'),
|
|
102
|
+
max_results: z
|
|
103
|
+
.number()
|
|
104
|
+
.int()
|
|
105
|
+
.min(0)
|
|
106
|
+
.default(100)
|
|
107
|
+
.describe('Maximum number of features to return. A gene-length region can hold tens of thousands of ' +
|
|
108
|
+
'variation features; the default keeps the response compact. Set to 0 to return every ' +
|
|
109
|
+
'feature uncapped. totalCount always reports the true number found before this cap.'),
|
|
79
110
|
}),
|
|
80
111
|
output: z.object({
|
|
81
112
|
features: z
|
|
82
113
|
.array(FeatureSchema.describe('A single genomic feature overlapping the queried region.'))
|
|
83
|
-
.describe('Genomic features found in the requested region.'
|
|
114
|
+
.describe('Genomic features found in the requested region, capped to max_results. ' +
|
|
115
|
+
'totalCount reports the full count found before the cap.'),
|
|
84
116
|
totalCount: z
|
|
85
117
|
.number()
|
|
86
|
-
.describe('
|
|
118
|
+
.describe('Total number of features found in the region before the max_results cap. ' +
|
|
119
|
+
'Exceeds the returned features count when the list was capped.'),
|
|
87
120
|
region: z.string().describe('The region queried, as provided.'),
|
|
88
121
|
species: z.string().describe('The species queried.'),
|
|
122
|
+
assemblyName: z
|
|
123
|
+
.string()
|
|
124
|
+
.optional()
|
|
125
|
+
.describe('Genome assembly the coordinates are on (e.g. GRCh38). Omitted only when it could not be ' +
|
|
126
|
+
'resolved, in which case the notice says so.'),
|
|
89
127
|
}),
|
|
90
128
|
enrichment: {
|
|
91
|
-
notice: z
|
|
129
|
+
notice: z
|
|
130
|
+
.string()
|
|
131
|
+
.optional()
|
|
132
|
+
.describe('Guidance about the result set: empty, large, capped, or missing assembly.'),
|
|
133
|
+
truncated: z
|
|
134
|
+
.boolean()
|
|
135
|
+
.optional()
|
|
136
|
+
.describe('True when the feature list was capped at max_results.'),
|
|
137
|
+
shown: z.number().optional().describe('Number of features returned after the max_results cap.'),
|
|
138
|
+
cap: z.number().optional().describe('The max_results limit applied to the feature list.'),
|
|
92
139
|
},
|
|
93
140
|
errors: [
|
|
94
141
|
{
|
|
95
142
|
reason: 'invalid_region',
|
|
96
143
|
code: JsonRpcErrorCode.ValidationError,
|
|
97
|
-
when: 'The region string could not be parsed
|
|
98
|
-
|
|
144
|
+
when: 'The region string could not be parsed, contains invalid coordinates, or spans more than ' +
|
|
145
|
+
'the 5,000,000-base maximum.',
|
|
146
|
+
recovery: 'Use the format chr:start-end (e.g. 13:32315086-32400268) spanning at most 5,000,000 bases; ' +
|
|
147
|
+
'split a larger area into smaller windows. ' +
|
|
99
148
|
'Chromosome names normalize either way — canonical vertebrate names omit the chr prefix ' +
|
|
100
149
|
'(13, not chr13), but a chr-prefixed name is also accepted. ' +
|
|
101
150
|
'Verify coordinates are within the chromosome bounds for the target assembly.',
|
|
@@ -113,15 +162,18 @@ export const ensemblQueryRegion = tool('ensembl_query_region', {
|
|
|
113
162
|
region: input.region,
|
|
114
163
|
features: input.feature,
|
|
115
164
|
biotype: input.biotype,
|
|
165
|
+
maxResults: input.max_results,
|
|
116
166
|
});
|
|
117
167
|
const service = getEnsemblService();
|
|
118
168
|
const features = await service
|
|
119
169
|
.queryRegion(input.species, input.region, input.feature, input.biotype, ctx)
|
|
120
170
|
.catch((err) => {
|
|
121
171
|
const msg = err instanceof Error ? err.message : String(err);
|
|
122
|
-
if (
|
|
172
|
+
if (mentionsInvalidRegion(msg) ||
|
|
173
|
+
/coordinate|parse/i.test(msg) ||
|
|
123
174
|
/is not a valid start|is not a valid end|is not a valid chr/i.test(msg) ||
|
|
124
|
-
/no slice found/i.test(msg)
|
|
175
|
+
/no slice found|cannot request a slice|could not decode region/i.test(msg) ||
|
|
176
|
+
/maximum allowed length/i.test(msg)) {
|
|
125
177
|
throw ctx.fail('invalid_region', `Invalid region "${input.region}": ${msg}`, {
|
|
126
178
|
...ctx.recoveryFor('invalid_region'),
|
|
127
179
|
});
|
|
@@ -133,27 +185,70 @@ export const ensemblQueryRegion = tool('ensembl_query_region', {
|
|
|
133
185
|
}
|
|
134
186
|
throw err;
|
|
135
187
|
});
|
|
136
|
-
|
|
137
|
-
|
|
188
|
+
// Ensembl returns the full overlap set with no paging; cap post-fetch so wide
|
|
189
|
+
// regions stay compact by default. totalCount stays the true pre-cap count
|
|
190
|
+
// (max_results = 0 disables the cap).
|
|
191
|
+
const totalCount = features.length;
|
|
192
|
+
const returned = input.max_results > 0 ? features.slice(0, input.max_results) : features;
|
|
193
|
+
// Every overlap row type except regulatory carries its assembly, so read it from
|
|
194
|
+
// the full set at no request cost; only an empty or regulatory-only result needs
|
|
195
|
+
// the species-default lookup. A failed lookup degrades to a notice, but a
|
|
196
|
+
// cancelled request still fails.
|
|
197
|
+
const assemblyName = features.find((f) => f.assemblyName)?.assemblyName ??
|
|
198
|
+
(await service.getDefaultAssemblyName(input.species, ctx).catch((err) => {
|
|
199
|
+
if (ctx.signal.aborted)
|
|
200
|
+
throw err;
|
|
201
|
+
ctx.log.warning('Assembly lookup failed', {
|
|
202
|
+
species: input.species,
|
|
203
|
+
error: err instanceof Error ? err.message : String(err),
|
|
204
|
+
});
|
|
205
|
+
return;
|
|
206
|
+
}));
|
|
207
|
+
// ctx.enrich.notice is last-wins, so every applicable fragment composes into ONE string.
|
|
208
|
+
const fragments = [];
|
|
209
|
+
if (totalCount === 0) {
|
|
210
|
+
fragments.push(`No ${input.feature.join(', ')} features found in ${input.region} for ${input.species}. ` +
|
|
138
211
|
'The region may be intergenic, or the coordinates may not cover the intended locus. ' +
|
|
139
212
|
'Use ensembl_lookup_gene to confirm the locus coordinates.');
|
|
140
213
|
}
|
|
141
|
-
|
|
142
|
-
|
|
214
|
+
const capped = returned.length < totalCount;
|
|
215
|
+
if (capped) {
|
|
216
|
+
fragments.push(`Showing ${returned.length} of ${totalCount} features. ` +
|
|
217
|
+
'Raise max_results (0 returns all) or query a smaller region for the rest.');
|
|
218
|
+
}
|
|
219
|
+
if (totalCount > 1000) {
|
|
220
|
+
fragments.push(`Large result set (${totalCount} features). ` +
|
|
143
221
|
'Consider narrowing the region or filtering by biotype to reduce context usage.');
|
|
144
222
|
}
|
|
145
|
-
|
|
223
|
+
if (!assemblyName) {
|
|
224
|
+
fragments.push(`The assembly for ${input.species} could not be resolved, so assemblyName is omitted; ` +
|
|
225
|
+
'ensembl_lookup_gene reports the assembly for any gene in this region.');
|
|
226
|
+
}
|
|
227
|
+
if (fragments.length > 0) {
|
|
228
|
+
const guidance = fragments.join(' ');
|
|
229
|
+
if (capped) {
|
|
230
|
+
ctx.enrich.truncated({ shown: returned.length, cap: input.max_results, guidance });
|
|
231
|
+
}
|
|
232
|
+
else {
|
|
233
|
+
ctx.enrich.notice(guidance);
|
|
234
|
+
}
|
|
235
|
+
}
|
|
146
236
|
return {
|
|
147
|
-
features,
|
|
148
|
-
totalCount
|
|
237
|
+
features: returned,
|
|
238
|
+
totalCount,
|
|
149
239
|
region: input.region,
|
|
150
240
|
species: input.species,
|
|
241
|
+
...(assemblyName && { assemblyName }),
|
|
151
242
|
};
|
|
152
243
|
},
|
|
153
244
|
format: (result) => {
|
|
154
245
|
const lines = [];
|
|
155
246
|
lines.push(`## Genomic Region: ${result.species} ${result.region}`);
|
|
156
|
-
|
|
247
|
+
if (result.assemblyName)
|
|
248
|
+
lines.push(`**Assembly:** ${result.assemblyName}`);
|
|
249
|
+
const shown = result.features.length;
|
|
250
|
+
const found = result.totalCount > shown ? `${shown} of ${result.totalCount}` : `${result.totalCount}`;
|
|
251
|
+
lines.push(`**Features found:** ${found}\n`);
|
|
157
252
|
if (result.features.length === 0) {
|
|
158
253
|
lines.push('No features found in this region.');
|
|
159
254
|
return [{ type: 'text', text: lines.join('\n') }];
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"query-region.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/query-region.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,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,aAAa,GAAG,CAAC,MAAM,EAAE,YAAY,EAAE,WAAW,EAAE,YAAY,EAAE,MAAM,CAAU,CAAC;AAEzF,MAAM,aAAa,GAAG,CAAC,CAAC,MAAM,CAAC;IAC7B,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uDAAuD,CAAC;IAC3F,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;IACjF,WAAW,EAAE,CAAC;SACX,MAAM,EAAE;SACR,QAAQ,CAAC,iEAAiE,CAAC;IAC9E,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,4DAA4D,CAAC;IACzE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;IACtE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;IACzE,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;IACrE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;IAChF,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oCAAoC,CAAC;IACjF,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,sDAAsD,CAAC;IACnE,oBAAoB,EAAE,CAAC;SACpB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC,CAAC;SAC5E,QAAQ,EAAE;SACV,QAAQ,CAAC,+EAA+E,CAAC;IAC5F,QAAQ,EAAE,CAAC;SACR,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sFAAsF;QACpF,wFAAwF;QACxF,sCAAsC,CACzC;IACH,IAAI,EAAE,CAAC;SACJ,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,6DAA6D,CAAC;CAC3E,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,sBAAsB,EAAE;IAC7D,KAAK,EAAE,sBAAsB;IAC7B,WAAW,EACT,mGAAmG;QACnG,kGAAkG;QAClG,wGAAwG;QACxG,
|
|
1
|
+
{"version":3,"file":"query-region.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/query-region.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,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,aAAa,GAAG,CAAC,MAAM,EAAE,YAAY,EAAE,WAAW,EAAE,YAAY,EAAE,MAAM,CAAU,CAAC;AAEzF,MAAM,aAAa,GAAG,CAAC,CAAC,MAAM,CAAC;IAC7B,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uDAAuD,CAAC;IAC3F,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;IACjF,WAAW,EAAE,CAAC;SACX,MAAM,EAAE;SACR,QAAQ,CAAC,iEAAiE,CAAC;IAC9E,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,4DAA4D,CAAC;IACzE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;IACtE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;IACzE,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;IACrE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;IAChF,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oCAAoC,CAAC;IACjF,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,sDAAsD,CAAC;IACnE,oBAAoB,EAAE,CAAC;SACpB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC,CAAC;SAC5E,QAAQ,EAAE;SACV,QAAQ,CAAC,+EAA+E,CAAC;IAC5F,QAAQ,EAAE,CAAC;SACR,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sFAAsF;QACpF,wFAAwF;QACxF,sCAAsC,CACzC;IACH,IAAI,EAAE,CAAC;SACJ,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,6DAA6D,CAAC;CAC3E,CAAC,CAAC;AAEH;;;;GAIG;AACH,SAAS,qBAAqB,CAAC,GAAW;IACxC,OAAO,GAAG;SACP,WAAW,EAAE;SACb,KAAK,CAAC,oBAAoB,CAAC;SAC3B,IAAI,CAAC,CAAC,IAAI,EAAE,EAAE;QACb,MAAM,EAAE,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;QACnC,OAAO,EAAE,KAAK,CAAC,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,QAAQ,EAAE,EAAE,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC;IACrE,CAAC,CAAC,CAAC;AACP,CAAC;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,sBAAsB,EAAE;IAC7D,KAAK,EAAE,sBAAsB;IAC7B,WAAW,EACT,mGAAmG;QACnG,kGAAkG;QAClG,mDAAmD;QACnD,wGAAwG;QACxG,wGAAwG;QACxG,wGAAwG;QACxG,6FAA6F;QAC7F,kGAAkG;QAClG,sGAAsG;QACtG,qGAAqG;QACrG,sGAAsG;QACtG,4CAA4C;IAC9C,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,IAAI,EAAE;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,wEAAwE;YACtE,oDAAoD,CACvD;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,IAAI,EAAE;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,6FAA6F;YAC3F,wEAAwE;YACxE,2FAA2F;YAC3F,oEAAoE;YACpE,wFAAwF,CAC3F;QACH,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,IAAI,CAAC,aAAa,CAAC;aACnB,QAAQ,CACP,+EAA+E,CAChF,CACJ;aACA,GAAG,CAAC,CAAC,EAAE,sCAAsC,aAAa,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC;aACzE,OAAO,CAAC,CAAC,MAAM,CAAC,CAAC;aACjB,QAAQ,CACP,kEAAkE;YAChE,kFAAkF;YAClF,kFAAkF,CACrF;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,8DAA8D;YAC5D,kFAAkF,CACrF;QACH,WAAW,EAAE,CAAC;aACX,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,GAAG,CAAC;aACZ,QAAQ,CACP,2FAA2F;YACzF,uFAAuF;YACvF,oFAAoF,CACvF;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC,aAAa,CAAC,QAAQ,CAAC,0DAA0D,CAAC,CAAC;aACzF,QAAQ,CACP,yEAAyE;YACvE,yDAAyD,CAC5D;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,CACP,2EAA2E;YACzE,+DAA+D,CAClE;QACH,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;QAC/D,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QACpD,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,0FAA0F;YACxF,6CAA6C,CAChD;KACJ,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,2EAA2E,CAAC;QACxF,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,EAAE;aACV,QAAQ,CAAC,uDAAuD,CAAC;QACpE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;QAC/F,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oDAAoD,CAAC;KAC1F;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,gBAAgB;YACxB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EACF,0FAA0F;gBAC1F,6BAA6B;YAC/B,QAAQ,EACN,6FAA6F;gBAC7F,4CAA4C;gBAC5C,yFAAyF;gBACzF,6DAA6D;gBAC7D,8EAA8E;SACjF;QACD;YACE,MAAM,EAAE,iBAAiB;YACzB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,mDAAmD;YACzD,QAAQ,EACN,2FAA2F;SAC9F;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,iBAAiB,EAAE;YAC9B,OAAO,EAAE,KAAK,CAAC,OAAO;YACtB,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,QAAQ,EAAE,KAAK,CAAC,OAAO;YACvB,OAAO,EAAE,KAAK,CAAC,OAAO;YACtB,UAAU,EAAE,KAAK,CAAC,WAAW;SAC9B,CAAC,CAAC;QACH,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,QAAQ,GAAG,MAAM,OAAO;aAC3B,WAAW,CAAC,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC;aAC3E,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YAC7D,IACE,qBAAqB,CAAC,GAAG,CAAC;gBAC1B,mBAAmB,CAAC,IAAI,CAAC,GAAG,CAAC;gBAC7B,6DAA6D,CAAC,IAAI,CAAC,GAAG,CAAC;gBACvE,gEAAgE,CAAC,IAAI,CAAC,GAAG,CAAC;gBAC1E,yBAAyB,CAAC,IAAI,CAAC,GAAG,CAAC,EACnC,CAAC;gBACD,MAAM,GAAG,CAAC,IAAI,CAAC,gBAAgB,EAAE,mBAAmB,KAAK,CAAC,MAAM,MAAM,GAAG,EAAE,EAAE;oBAC3E,GAAG,GAAG,CAAC,WAAW,CAAC,gBAAgB,CAAC;iBACrC,CAAC,CAAC;YACL,CAAC;YACD,IAAI,+BAA+B,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC9C,MAAM,GAAG,CAAC,IAAI,CAAC,iBAAiB,EAAE,YAAY,KAAK,CAAC,OAAO,mBAAmB,EAAE;oBAC9E,GAAG,GAAG,CAAC,WAAW,CAAC,iBAAiB,CAAC;iBACtC,CAAC,CAAC;YACL,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC,CAAC,CAAC;QAEL,8EAA8E;QAC9E,2EAA2E;QAC3E,sCAAsC;QACtC,MAAM,UAAU,GAAG,QAAQ,CAAC,MAAM,CAAC;QACnC,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC;QAEzF,iFAAiF;QACjF,iFAAiF;QACjF,0EAA0E;QAC1E,iCAAiC;QACjC,MAAM,YAAY,GAChB,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,YAAY,CAAC,EAAE,YAAY;YAClD,CAAC,MAAM,OAAO,CAAC,sBAAsB,CAAC,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBAC/E,IAAI,GAAG,CAAC,MAAM,CAAC,OAAO;oBAAE,MAAM,GAAG,CAAC;gBAClC,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,wBAAwB,EAAE;oBACxC,OAAO,EAAE,KAAK,CAAC,OAAO;oBACtB,KAAK,EAAE,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC;iBACxD,CAAC,CAAC;gBACH,OAAO;YACT,CAAC,CAAC,CAAC,CAAC;QAEN,yFAAyF;QACzF,MAAM,SAAS,GAAa,EAAE,CAAC;QAC/B,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;YACrB,SAAS,CAAC,IAAI,CACZ,MAAM,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,sBAAsB,KAAK,CAAC,MAAM,QAAQ,KAAK,CAAC,OAAO,IAAI;gBACvF,qFAAqF;gBACrF,2DAA2D,CAC9D,CAAC;QACJ,CAAC;QACD,MAAM,MAAM,GAAG,QAAQ,CAAC,MAAM,GAAG,UAAU,CAAC;QAC5C,IAAI,MAAM,EAAE,CAAC;YACX,SAAS,CAAC,IAAI,CACZ,WAAW,QAAQ,CAAC,MAAM,OAAO,UAAU,aAAa;gBACtD,2EAA2E,CAC9E,CAAC;QACJ,CAAC;QACD,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;YACtB,SAAS,CAAC,IAAI,CACZ,qBAAqB,UAAU,cAAc;gBAC3C,gFAAgF,CACnF,CAAC;QACJ,CAAC;QACD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,SAAS,CAAC,IAAI,CACZ,oBAAoB,KAAK,CAAC,OAAO,sDAAsD;gBACrF,uEAAuE,CAC1E,CAAC;QACJ,CAAC;QACD,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACzB,MAAM,QAAQ,GAAG,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YACrC,IAAI,MAAM,EAAE,CAAC;gBACX,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,QAAQ,CAAC,MAAM,EAAE,GAAG,EAAE,KAAK,CAAC,WAAW,EAAE,QAAQ,EAAE,CAAC,CAAC;YACrF,CAAC;iBAAM,CAAC;gBACN,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC;YAC9B,CAAC;QACH,CAAC;QAED,OAAO;YACL,QAAQ,EAAE,QAAQ;YAClB,UAAU;YACV,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,OAAO,EAAE,KAAK,CAAC,OAAO;YACtB,GAAG,CAAC,YAAY,IAAI,EAAE,YAAY,EAAE,CAAC;SACtC,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,KAAK,CAAC,IAAI,CAAC,sBAAsB,MAAM,CAAC,OAAO,IAAI,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC;QACpE,IAAI,MAAM,CAAC,YAAY;YAAE,KAAK,CAAC,IAAI,CAAC,iBAAiB,MAAM,CAAC,YAAY,EAAE,CAAC,CAAC;QAC5E,MAAM,KAAK,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC;QACrC,MAAM,KAAK,GACT,MAAM,CAAC,UAAU,GAAG,KAAK,CAAC,CAAC,CAAC,GAAG,KAAK,OAAO,MAAM,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC,UAAU,EAAE,CAAC;QAC1F,KAAK,CAAC,IAAI,CAAC,uBAAuB,KAAK,IAAI,CAAC,CAAC;QAE7C,IAAI,MAAM,CAAC,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,KAAK,CAAC,IAAI,CAAC,mCAAmC,CAAC,CAAC;YAChD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACpD,CAAC;QAED,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,QAAQ,EAAE,CAAC;YAChC,MAAM,KAAK,GAAG,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,WAAW,CAAC;YAC9C,KAAK,CAAC,IAAI,CAAC,OAAO,KAAK,EAAE,CAAC,CAAC;YAC3B,IAAI,CAAC,CAAC,EAAE;gBAAE,KAAK,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACxC,KAAK,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC;YACzC,IAAI,CAAC,CAAC,OAAO;gBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;YACvD,KAAK,CAAC,IAAI,CACR,iBAAiB,CAAC,CAAC,UAAU,IAAI,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,MAAM,IAAI,IAAI,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CACrI,CAAC;YACF,IAAI,CAAC,CAAC,QAAQ,EAAE,CAAC;gBACf,KAAK,CAAC,IAAI,CACR,0BAA0B,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,IAAI,IAAI,IAAI,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CACxF,CAAC;YACJ,CAAC;YACD,IAAI,CAAC,CAAC,WAAW;gBAAE,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,WAAW,EAAE,CAAC,CAAC;YACnE,IAAI,CAAC,CAAC,eAAe;gBAAE,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,eAAe,EAAE,CAAC,CAAC;YAC3E,IAAI,CAAC,CAAC,oBAAoB,EAAE,MAAM,EAAE,CAAC;gBACnC,KAAK,CAAC,IAAI,CAAC,8BAA8B,CAAC,CAAC,oBAAoB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YAChF,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"}
|
|
@@ -9,6 +9,12 @@ import type { StorageService } from '@cyanheads/mcp-ts-core/storage';
|
|
|
9
9
|
import type { GeneRecord, HomologyResult, OverlapFeature, SequenceRecord, SpeciesInfo, TranscriptRecord, VepRecord, XrefEntry } from './types.js';
|
|
10
10
|
export declare class EnsemblService {
|
|
11
11
|
private readonly baseUrl;
|
|
12
|
+
/**
|
|
13
|
+
* Default assembly per species for this process. The endpoint's assembly can
|
|
14
|
+
* only change with a restart under a different ENSEMBL_BASE_URL, so a resolved
|
|
15
|
+
* value is kept for the process lifetime; failed lookups are never stored.
|
|
16
|
+
*/
|
|
17
|
+
private readonly defaultAssemblies;
|
|
12
18
|
constructor(_config: AppConfig, _storage: StorageService);
|
|
13
19
|
private fetchJson;
|
|
14
20
|
private fetchWithRetry;
|
|
@@ -20,6 +26,11 @@ export declare class EnsemblService {
|
|
|
20
26
|
getSequenceById(id: string, type: string, expand5prime: number, expand3prime: number, ctx: Context): Promise<SequenceRecord>;
|
|
21
27
|
getSequenceByRegion(species: string, region: string, expand5prime: number, expand3prime: number, ctx: Context): Promise<SequenceRecord>;
|
|
22
28
|
queryRegion(species: string, region: string, features: string[], biotype: string | undefined, ctx: Context): Promise<OverlapFeature[]>;
|
|
29
|
+
/**
|
|
30
|
+
* Plain default assembly name for a species (GRCh38, not the patch-level
|
|
31
|
+
* GRCh38.p14), matching the per-feature `assembly_name` overlap rows carry.
|
|
32
|
+
*/
|
|
33
|
+
getDefaultAssemblyName(species: string, ctx: Context): Promise<string>;
|
|
23
34
|
predictVariantHgvs(notation: string, species: string, ctx: Context): Promise<VepRecord[]>;
|
|
24
35
|
predictVariantRegion(chr: string, start: number, end: number, strand: number, allele: string, species: string, ctx: Context): Promise<VepRecord[]>;
|
|
25
36
|
predictVariantId(id: string, species: string, ctx: Context): Promise<VepRecord[]>;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ensembl-service.d.ts","sourceRoot":"","sources":["../../../src/services/ensembl/ensembl-service.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,+BAA+B,CAAC;AAE/D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AAGrE,OAAO,KAAK,EAEV,UAAU,EAEV,cAAc,EACd,cAAc,
|
|
1
|
+
{"version":3,"file":"ensembl-service.d.ts","sourceRoot":"","sources":["../../../src/services/ensembl/ensembl-service.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,+BAA+B,CAAC;AAE/D,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,gCAAgC,CAAC;AAGrE,OAAO,KAAK,EAEV,UAAU,EAEV,cAAc,EACd,cAAc,EAUd,cAAc,EACd,WAAW,EACX,gBAAgB,EAChB,SAAS,EACT,SAAS,EACV,MAAM,YAAY,CAAC;AAsKpB,qBAAa,cAAc;IACzB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;IACjC;;;;OAIG;IACH,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAA6B;IAE/D,YAAY,OAAO,EAAE,SAAS,EAAE,QAAQ,EAAE,cAAc,EAEvD;YAIa,SAAS;IAmFvB,OAAO,CAAC,cAAc;IAuBhB,UAAU,CACd,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,MAAM,EACf,iBAAiB,EAAE,OAAO,EAC1B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,UAAU,CAAC,CAKrB;IAEK,cAAc,CAAC,EAAE,EAAE,MAAM,EAAE,iBAAiB,EAAE,OAAO,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,UAAU,CAAC,CAK9F;IAEK,gBAAgB,CACpB,GAAG,EAAE,MAAM,EAAE,EACb,iBAAiB,EAAE,OAAO,EAC1B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC,CAYlC;IAEK,kBAAkB,CACtB,OAAO,EAAE,MAAM,EAAE,EACjB,OAAO,EAAE,MAAM,EACf,iBAAiB,EAAE,OAAO,EAC1B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC,CAalC;IAIK,gBAAgB,CAAC,EAAE,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,gBAAgB,CAAC,CAI1E;IAIK,eAAe,CACnB,EAAE,EAAE,MAAM,EACV,IAAI,EAAE,MAAM,EACZ,YAAY,EAAE,MAAM,EACpB,YAAY,EAAE,MAAM,EACpB,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,cAAc,CAAC,CAWzB;IAEK,mBAAmB,CACvB,OAAO,EAAE,MAAM,EACf,MAAM,EAAE,MAAM,EACd,YAAY,EAAE,MAAM,EACpB,YAAY,EAAE,MAAM,EACpB,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,cAAc,CAAC,CAQzB;IAIK,WAAW,CACf,OAAO,EAAE,MAAM,EACf,MAAM,EAAE,MAAM,EACd,QAAQ,EAAE,MAAM,EAAE,EAClB,OAAO,EAAE,MAAM,GAAG,SAAS,EAC3B,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,cAAc,EAAE,CAAC,CAO3B;IAID;;;OAGG;IACG,sBAAsB,CAAC,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAe3E;IAIK,kBAAkB,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,SAAS,EAAE,CAAC,CAK9F;IAEK,oBAAoB,CACxB,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,MAAM,EACb,GAAG,EAAE,MAAM,EACX,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,MAAM,EACf,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,SAAS,EAAE,CAAC,CAMtB;IAEK,gBAAgB,CAAC,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,SAAS,EAAE,CAAC,CAKtF;IAIK,mBAAmB,CACvB,MAAM,EAAE,MAAM,EACd,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,aAAa,EAAE,MAAM,GAAG,SAAS,EACjC,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,cAAc,CAAC,CAKzB;IAEK,eAAe,CACnB,EAAE,EAAE,MAAM,EACV,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,aAAa,EAAE,MAAM,GAAG,SAAS,EACjC,GAAG,EAAE,OAAO,GACX,OAAO,CAAC,cAAc,CAAC,CAKzB;IAIK,YAAY,CAAC,EAAE,EAAE,MAAM,EAAE,MAAM,EAAE,MAAM,GAAG,SAAS,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,SAAS,EAAE,CAAC,CAM7F;IAIK,WAAW,CAAC,QAAQ,EAAE,MAAM,GAAG,SAAS,EAAE,GAAG,EAAE,OAAO,GAAG,OAAO,CAAC,WAAW,EAAE,CAAC,CAKpF;CACF;AAMD,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,cAAc,GAAG,IAAI,CAEnF;AAED,wBAAgB,iBAAiB,IAAI,cAAc,CAKlD"}
|