@cyanheads/ensembl-mcp-server 0.4.3 → 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 +45 -19
- package/CLAUDE.md +45 -19
- package/README.md +95 -68
- package/changelog/0.4.x/0.4.4.md +27 -0
- package/changelog/0.5.x/0.5.0.md +25 -0
- package/changelog/template.md +9 -26
- package/dist/index.js +7 -0
- package/dist/index.js.map +1 -1
- 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 +10 -9
- package/server.json +3 -3
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{"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;;;;;;;;;;;;;;;;;;;;
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{"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"}
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@@ -36,6 +36,8 @@ export const ensemblGetXrefs = tool('ensembl_get_xrefs', {
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input: z.object({
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.string()
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|
+
.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
|
-
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+
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@@ -1 +1 @@
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1
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-
{"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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1
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+
{"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"}
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@@ -117,6 +117,8 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
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117
117
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input: z.object({
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118
118
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variant: z
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119
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.string()
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120
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+
.trim()
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121
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+
.min(1)
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120
122
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.describe('Variant in one of three formats: ' +
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'(1) HGVS notation — transcript-relative: ENST00000380152.8:c.2T>A; ' +
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122
124
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'genomic: 13:g.32316462T>A; ' +
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@@ -127,6 +129,8 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
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127
129
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'though a chr-prefixed name is also accepted.'),
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128
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species: z
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129
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.string()
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132
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+
.trim()
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133
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+
.min(1)
|
|
130
134
|
.default('homo_sapiens')
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131
135
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.describe('Species in Ensembl internal format. Default is homo_sapiens. ' +
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132
136
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'For non-human variants, set the appropriate species ' +
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@@ -1 +1 @@
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1
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-
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1
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@@ -15,6 +15,7 @@ export declare const ensemblQueryRegion: import("@cyanheads/mcp-ts-core").ToolDe
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15
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variation: "variation";
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16
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}>>>;
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17
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biotype: z.ZodOptional<z.ZodString>;
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18
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+
max_results: z.ZodDefault<z.ZodNumber>;
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18
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}, z.core.$strip>, z.ZodObject<{
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19
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features: z.ZodArray<z.ZodObject<{
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20
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id: z.ZodOptional<z.ZodString>;
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@@ -34,10 +35,11 @@ export declare const ensemblQueryRegion: import("@cyanheads/mcp-ts-core").ToolDe
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34
35
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totalCount: z.ZodNumber;
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35
36
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region: z.ZodString;
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36
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species: z.ZodString;
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38
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+
assemblyName: z.ZodOptional<z.ZodString>;
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37
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}, z.core.$strip>, readonly [{
|
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38
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readonly reason: "invalid_region";
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39
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readonly code: JsonRpcErrorCode.ValidationError;
|
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40
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-
readonly when:
|
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42
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+
readonly when: string;
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41
43
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readonly recovery: string;
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42
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}, {
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45
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readonly reason: "invalid_species";
|
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@@ -46,5 +48,8 @@ export declare const ensemblQueryRegion: import("@cyanheads/mcp-ts-core").ToolDe
|
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46
48
|
readonly recovery: "Call ensembl_list_species to discover valid species names in lowercase_underscore format.";
|
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47
49
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}], {
|
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48
50
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readonly notice: z.ZodOptional<z.ZodString>;
|
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51
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+
readonly truncated: z.ZodOptional<z.ZodBoolean>;
|
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52
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+
readonly shown: z.ZodOptional<z.ZodNumber>;
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53
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+
readonly cap: z.ZodOptional<z.ZodNumber>;
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49
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}>;
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50
55
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//# sourceMappingURL=query-region.tool.d.ts.map
|
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@@ -1 +1 @@
|
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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;
|
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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"}
|
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@@ -40,26 +40,48 @@ const FeatureSchema = z.object({
|
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|
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
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+
'variation in an 85 kb region matches 44,000+ entries. Explicitly include variation, regulatory, ' +
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67
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'transcript, or exon only when needed. The response returns up to max_results features (default 100) ' +
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'while totalCount always reports the full count; set max_results to 0 for every feature, or query a ' +
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'smaller region to see a different slice. Exon rows carry the parent transcript ID, so the same exon ' +
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53
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'appears once per transcript it belongs to.',
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annotations: { readOnlyHint: true, openWorldHint: true, idempotentHint: true },
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input: z.object({
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species: z
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.string()
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+
.trim()
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76
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.min(1)
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.describe('Species in Ensembl internal format (e.g. homo_sapiens, mus_musculus). ' +
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'Use ensembl_list_species to discover valid values.'),
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region: z
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.string()
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-
.
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.trim()
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.min(1)
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.describe('Genomic region in chr:start-end format (e.g. 13:32315086-32400268). Ensembl serves at most ' +
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84
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+
'5,000,000 bases per region; split a larger area into smaller windows. ' +
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'Ensembl normalizes chromosome names and canonical vertebrate output omits the chr prefix ' +
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64
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'(13, not chr13); a chr-prefixed name like chr13 is also accepted. ' +
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65
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'For large regions (>100 kb), limit to gene feature type to avoid overwhelming results.'),
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@@ -67,35 +89,62 @@ export const ensemblQueryRegion = tool('ensembl_query_region', {
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.array(z
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68
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.enum(FEATURE_TYPES)
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69
91
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.describe('A feature type to retrieve: gene, transcript, variation, regulatory, or exon.'))
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+
.min(1, `Provide at least one feature type: ${FEATURE_TYPES.join(', ')}.`)
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70
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.default(['gene'])
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.describe('Feature types to retrieve. Default is gene only. ' +
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-
'Requesting variation in a large region can
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.describe('Feature types to retrieve — at least one. Default is gene only. ' +
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'Requesting variation in a large region can match tens of thousands of features. ' +
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'Include variation only for targeted small regions (single gene loci or smaller).'),
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biotype: z
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.string()
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.optional()
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.describe('Optional biotype filter (e.g. protein_coding, lncRNA, SNV). ' +
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'Applied server-side by Ensembl. Not all feature types support biotype filtering.'),
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max_results: z
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.number()
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.int()
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.min(0)
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.default(100)
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.describe('Maximum number of features to return. A gene-length region can hold tens of thousands of ' +
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'variation features; the default keeps the response compact. Set to 0 to return every ' +
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'feature uncapped. totalCount always reports the true number found before this cap.'),
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}),
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output: z.object({
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features: z
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.array(FeatureSchema.describe('A single genomic feature overlapping the queried region.'))
|
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-
.describe('Genomic features found in the requested region.'
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.describe('Genomic features found in the requested region, capped to max_results. ' +
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'totalCount reports the full count found before the cap.'),
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totalCount: z
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.number()
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.describe('
|
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.describe('Total number of features found in the region before the max_results cap. ' +
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'Exceeds the returned features count when the list was capped.'),
|
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87
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region: z.string().describe('The region queried, as provided.'),
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species: z.string().describe('The species queried.'),
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assemblyName: z
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.string()
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.optional()
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.describe('Genome assembly the coordinates are on (e.g. GRCh38). Omitted only when it could not be ' +
|
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+
'resolved, in which case the notice says so.'),
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89
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}),
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enrichment: {
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-
notice: z
|
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+
notice: z
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.string()
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.optional()
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.describe('Guidance about the result set: empty, large, capped, or missing assembly.'),
|
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truncated: z
|
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.boolean()
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.optional()
|
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.describe('True when the feature list was capped at max_results.'),
|
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shown: z.number().optional().describe('Number of features returned after the max_results cap.'),
|
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138
|
+
cap: z.number().optional().describe('The max_results limit applied to the feature list.'),
|
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|
},
|
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errors: [
|
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141
|
{
|
|
95
142
|
reason: 'invalid_region',
|
|
96
143
|
code: JsonRpcErrorCode.ValidationError,
|
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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 ' +
|
|
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+
'the 5,000,000-base maximum.',
|
|
146
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+
recovery: 'Use the format chr:start-end (e.g. 13:32315086-32400268) spanning at most 5,000,000 bases; ' +
|
|
147
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+
'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
|
+
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@@ -9,6 +9,12 @@ import type { StorageService } from '@cyanheads/mcp-ts-core/storage';
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|
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;
|
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@@ -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
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+
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