@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
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@@ -69,6 +69,7 @@ function normalizeOverlapFeature(raw) {
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start: raw.start ?? 0,
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end: raw.end ?? 0,
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...(typeof raw.strand === 'number' && { strand: raw.strand }),
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...(raw.assembly_name && { assemblyName: raw.assembly_name }),
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...(raw.description && { description: raw.description }),
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...(raw.consequence_type && { consequenceType: raw.consequence_type }),
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...(raw.clinical_significance?.length && {
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@@ -161,6 +162,12 @@ function normalizeSpecies(raw) {
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// --- Service ---
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export class EnsemblService {
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baseUrl;
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/**
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* Default assembly per species for this process. The endpoint's assembly can
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* only change with a restart under a different ENSEMBL_BASE_URL, so a resolved
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* value is kept for the process lifetime; failed lookups are never stored.
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*/
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defaultAssemblies = new Map();
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constructor(_config, _storage) {
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this.baseUrl = getServerConfig().baseUrl;
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}
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@@ -320,6 +327,25 @@ export class EnsemblService {
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return [];
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return raw.map(normalizeOverlapFeature);
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}
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// --- Assembly ---
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/**
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* Plain default assembly name for a species (GRCh38, not the patch-level
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* GRCh38.p14), matching the per-feature `assembly_name` overlap rows carry.
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*/
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async getDefaultAssemblyName(species, ctx) {
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const cached = this.defaultAssemblies.get(species);
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if (cached)
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return cached;
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const raw = await this.fetchWithRetry(`/info/assembly/${encodeURIComponent(species)}`, ctx);
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const name = raw.default_coord_system_version;
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if (!name) {
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throw serviceUnavailable('Ensembl assembly info carried no default_coord_system_version.', {
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species,
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});
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}
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this.defaultAssemblies.set(species, name);
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return name;
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}
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// --- VEP ---
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async predictVariantHgvs(notation, species, ctx) {
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const path = `/vep/${encodeURIComponent(species)}/hgvs/${encodeURIComponent(notation)}`;
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@@ -1 +1 @@
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1
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-
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|
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1
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|
|
@@ -85,6 +85,15 @@ export type RawOverlapFeature = {
|
|
|
85
85
|
/** 1-based position of an exon within its parent transcript. */
|
|
86
86
|
rank?: number;
|
|
87
87
|
};
|
|
88
|
+
/**
|
|
89
|
+
* `/info/assembly/:species` — only the fields read here. `assembly_name` is the
|
|
90
|
+
* patch-level identifier (GRCh38.p14); `default_coord_system_version` is the plain
|
|
91
|
+
* assembly name (GRCh38) that per-feature `assembly_name` values carry.
|
|
92
|
+
*/
|
|
93
|
+
export type RawAssemblyInfo = {
|
|
94
|
+
assembly_name?: string;
|
|
95
|
+
default_coord_system_version?: string;
|
|
96
|
+
};
|
|
88
97
|
export type RawVepTranscriptConsequence = {
|
|
89
98
|
transcript_id?: string;
|
|
90
99
|
gene_id?: string;
|
|
@@ -228,6 +237,8 @@ export type OverlapFeature = {
|
|
|
228
237
|
start: number;
|
|
229
238
|
end: number;
|
|
230
239
|
strand?: number;
|
|
240
|
+
/** Assembly the coordinates are on (e.g. GRCh38). Absent on regulatory features. */
|
|
241
|
+
assemblyName?: string;
|
|
231
242
|
description?: string;
|
|
232
243
|
consequenceType?: string;
|
|
233
244
|
clinicalSignificance?: string[];
|
|
@@ -1 +1 @@
|
|
|
1
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-
{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/services/ensembl/types.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAIH,MAAM,MAAM,aAAa,GAAG;IAC1B,EAAE,EAAE,MAAM,CAAC;IACX,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,UAAU,CAAC,EAAE,oBAAoB,EAAE,CAAC;IACpC,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB,CAAC;AAEF,MAAM,MAAM,oBAAoB,GAAG;IACjC,EAAE,EAAE,MAAM,CAAC;IACX,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB,CAAC;AAEF,MAAM,MAAM,mBAAmB,GAAG;IAChC,EAAE,EAAE,MAAM,CAAC;IACX,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,IAAI,CAAC,EAAE,KAAK,CAAC;QAAE,EAAE,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,GAAG,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IACzE,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB,CAAC;AAEF,MAAM,MAAM,iBAAiB,GAAG;IAC9B,EAAE,EAAE,MAAM,CAAC;IACX,GAAG,EAAE,MAAM,CAAC;IACZ,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB,CAAC;AAEF,MAAM,MAAM,iBAAiB,GAAG;IAC9B,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,qBAAqB,CAAC,EAAE,MAAM,EAAE,CAAC;IACjC,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,iEAAiE;IACjE,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,gEAAgE;IAChE,IAAI,CAAC,EAAE,MAAM,CAAC;CACf,CAAC;AAEF,MAAM,MAAM,2BAA2B,GAAG;IACxC,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,iBAAiB,CAAC,EAAE,MAAM,EAAE,CAAC;IAC7B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,IAAI,CAAC,EAAE;QAAE,UAAU,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;IAC7C,QAAQ,CAAC,EAAE;QAAE,UAAU,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;CAClD,CAAC;AAEF,MAAM,MAAM,mBAAmB,GAAG;IAChC,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,qBAAqB,CAAC,EAAE,MAAM,EAAE,CAAC;IACjC,WAAW,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACtC,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB,CAAC;AAEF,MAAM,MAAM,YAAY,GAAG;IACzB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,uBAAuB,CAAC,EAAE,MAAM,CAAC;IACjC,uBAAuB,CAAC,EAAE,2BAA2B,EAAE,CAAC;IACxD,kBAAkB,CAAC,EAAE,mBAAmB,EAAE,CAAC;CAC5C,CAAC;AAEF,MAAM,MAAM,gBAAgB,GAAG;IAC7B,EAAE,EAAE,MAAM,CAAC;IACX,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,MAAM,CAAC,EAAE;QACP,EAAE,CAAC,EAAE,MAAM,CAAC;QACZ,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;KACnB,CAAC;CACH,CAAC;AAEF,MAAM,MAAM,mBAAmB,GAAG;IAChC,IAAI,CAAC,EAAE,KAAK,CAAC;QACX,EAAE,EAAE,MAAM,CAAC;QACX,UAAU,CAAC,EAAE,gBAAgB,EAAE,CAAC;KACjC,CAAC,CAAC;CACJ,CAAC;AAEF,MAAM,MAAM,YAAY,GAAG;IACzB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;IACpB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB,CAAC;AAEF,MAAM,MAAM,cAAc,GAAG;IAC3B,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB,CAAC;AAEF,MAAM,MAAM,kBAAkB,GAAG;IAC/B,OAAO,CAAC,EAAE,cAAc,EAAE,CAAC;CAC5B,CAAC;AAIF,MAAM,MAAM,oBAAoB,GAAG;IACjC,KAAK,EAAE,MAAM,CAAC;CACf,CAAC;AAIF,MAAM,M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+
{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/services/ensembl/types.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAIH,MAAM,MAAM,aAAa,GAAG;IAC1B,EAAE,EAAE,MAAM,CAAC;IACX,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,UAAU,CAAC,EAAE,oBAAoB,EAAE,CAAC;IACpC,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB,CAAC;AAEF,MAAM,MAAM,oBAAoB,GAAG;IACjC,EAAE,EAAE,MAAM,CAAC;IACX,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,WAAW,CAAC,EAAE,MAAM,CAAC;CACtB,CAAC;AAEF,MAAM,MAAM,mBAAmB,GAAG;IAChC,EAAE,EAAE,MAAM,CAAC;IACX,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,IAAI,CAAC,EAAE,KAAK,CAAC;QAAE,EAAE,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAC;QAAC,GAAG,EAAE,MAAM,CAAC;QAAC,MAAM,EAAE,MAAM,CAAA;KAAE,CAAC,CAAC;IACzE,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB,CAAC;AAEF,MAAM,MAAM,iBAAiB,GAAG;IAC9B,EAAE,EAAE,MAAM,CAAC;IACX,GAAG,EAAE,MAAM,CAAC;IACZ,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB,CAAC;AAEF,MAAM,MAAM,iBAAiB,GAAG;IAC9B,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,qBAAqB,CAAC,EAAE,MAAM,EAAE,CAAC;IACjC,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,iEAAiE;IACjE,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,gEAAgE;IAChE,IAAI,CAAC,EAAE,MAAM,CAAC;CACf,CAAC;AAEF;;;;GAIG;AACH,MAAM,MAAM,eAAe,GAAG;IAC5B,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,4BAA4B,CAAC,EAAE,MAAM,CAAC;CACvC,CAAC;AAEF,MAAM,MAAM,2BAA2B,GAAG;IACxC,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,iBAAiB,CAAC,EAAE,MAAM,EAAE,CAAC;IAC7B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,IAAI,CAAC,EAAE;QAAE,UAAU,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;IAC7C,QAAQ,CAAC,EAAE;QAAE,UAAU,EAAE,MAAM,CAAC;QAAC,KAAK,EAAE,MAAM,CAAA;KAAE,CAAC;CAClD,CAAC;AAEF,MAAM,MAAM,mBAAmB,GAAG;IAChC,EAAE,CAAC,EAAE,MAAM,CAAC;IACZ,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,qBAAqB,CAAC,EAAE,MAAM,EAAE,CAAC;IACjC,WAAW,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IACtC,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB,CAAC;AAEF,MAAM,MAAM,YAAY,GAAG;IACzB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,uBAAuB,CAAC,EAAE,MAAM,CAAC;IACjC,uBAAuB,CAAC,EAAE,2BAA2B,EAAE,CAAC;IACxD,kBAAkB,CAAC,EAAE,mBAAmB,EAAE,CAAC;CAC5C,CAAC;AAEF,MAAM,MAAM,gBAAgB,GAAG;IAC7B,EAAE,EAAE,MAAM,CAAC;IACX,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,MAAM,CAAC,EAAE;QACP,EAAE,CAAC,EAAE,MAAM,CAAC;QACZ,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,OAAO,CAAC,EAAE,MAAM,CAAC;QACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;KACnB,CAAC;CACH,CAAC;AAEF,MAAM,MAAM,mBAAmB,GAAG;IAChC,IAAI,CAAC,EAAE,KAAK,CAAC;QACX,EAAE,EAAE,MAAM,CAAC;QACX,UAAU,CAAC,EAAE,gBAAgB,EAAE,CAAC;KACjC,CAAC,CAAC;CACJ,CAAC;AAEF,MAAM,MAAM,YAAY,GAAG;IACzB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;IACpB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB,CAAC;AAEF,MAAM,MAAM,cAAc,GAAG;IAC3B,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC;IAClB,OAAO,CAAC,EAAE,MAAM,EAAE,CAAC;IACnB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB,CAAC;AAEF,MAAM,MAAM,kBAAkB,GAAG;IAC/B,OA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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/ensembl-mcp-server",
|
|
3
|
-
"version": "0.
|
|
3
|
+
"version": "0.5.0",
|
|
4
4
|
"mcpName": "io.github.cyanheads/ensembl-mcp-server",
|
|
5
5
|
"description": "Look up genes, fetch sequences, predict variant consequences, find orthologs, and retrieve cross-database xrefs from Ensembl REST via MCP. STDIO or Streamable HTTP.",
|
|
6
6
|
"type": "module",
|
|
@@ -98,7 +98,7 @@
|
|
|
98
98
|
"devDependencies": {
|
|
99
99
|
"@biomejs/biome": "^2.5.14",
|
|
100
100
|
"@socketsecurity/bun-security-scanner": "^1.1.2",
|
|
101
|
-
"@types/node": "^26.6.
|
|
101
|
+
"@types/node": "^26.6.2",
|
|
102
102
|
"depcheck": "^1.4.7",
|
|
103
103
|
"ignore": "^7.0.9",
|
|
104
104
|
"tsc-alias": "^1.9.5",
|
package/server.json
CHANGED
|
@@ -6,7 +6,7 @@
|
|
|
6
6
|
"url": "https://github.com/cyanheads/ensembl-mcp-server",
|
|
7
7
|
"source": "github"
|
|
8
8
|
},
|
|
9
|
-
"version": "0.
|
|
9
|
+
"version": "0.5.0",
|
|
10
10
|
"remotes": [
|
|
11
11
|
{
|
|
12
12
|
"type": "streamable-http",
|
|
@@ -19,7 +19,7 @@
|
|
|
19
19
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
20
20
|
"identifier": "@cyanheads/ensembl-mcp-server",
|
|
21
21
|
"runtimeHint": "bun",
|
|
22
|
-
"version": "0.
|
|
22
|
+
"version": "0.5.0",
|
|
23
23
|
"packageArguments": [
|
|
24
24
|
{
|
|
25
25
|
"type": "positional",
|
|
@@ -55,7 +55,7 @@
|
|
|
55
55
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
56
56
|
"identifier": "@cyanheads/ensembl-mcp-server",
|
|
57
57
|
"runtimeHint": "bun",
|
|
58
|
-
"version": "0.
|
|
58
|
+
"version": "0.5.0",
|
|
59
59
|
"packageArguments": [
|
|
60
60
|
{
|
|
61
61
|
"type": "positional",
|