@cyanheads/ensembl-mcp-server 0.4.4 → 0.5.1

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Files changed (36) hide show
  1. package/AGENTS.md +15 -12
  2. package/CLAUDE.md +15 -12
  3. package/Dockerfile +110 -33
  4. package/README.md +25 -37
  5. package/changelog/0.5.x/0.5.0.md +25 -0
  6. package/changelog/0.5.x/0.5.1.md +28 -0
  7. package/dist/mcp-server/prompts/definitions/gene-dossier.prompt.d.ts.map +1 -1
  8. package/dist/mcp-server/prompts/definitions/gene-dossier.prompt.js +12 -5
  9. package/dist/mcp-server/prompts/definitions/gene-dossier.prompt.js.map +1 -1
  10. package/dist/mcp-server/tools/definitions/get-homology.tool.d.ts.map +1 -1
  11. package/dist/mcp-server/tools/definitions/get-homology.tool.js +6 -8
  12. package/dist/mcp-server/tools/definitions/get-homology.tool.js.map +1 -1
  13. package/dist/mcp-server/tools/definitions/get-sequence.tool.d.ts +14 -2
  14. package/dist/mcp-server/tools/definitions/get-sequence.tool.d.ts.map +1 -1
  15. package/dist/mcp-server/tools/definitions/get-sequence.tool.js +162 -53
  16. package/dist/mcp-server/tools/definitions/get-sequence.tool.js.map +1 -1
  17. package/dist/mcp-server/tools/definitions/get-xrefs.tool.js +3 -3
  18. package/dist/mcp-server/tools/definitions/get-xrefs.tool.js.map +1 -1
  19. package/dist/mcp-server/tools/definitions/lookup-gene.tool.d.ts.map +1 -1
  20. package/dist/mcp-server/tools/definitions/lookup-gene.tool.js +15 -15
  21. package/dist/mcp-server/tools/definitions/lookup-gene.tool.js.map +1 -1
  22. package/dist/mcp-server/tools/definitions/predict-variant.tool.d.ts.map +1 -1
  23. package/dist/mcp-server/tools/definitions/predict-variant.tool.js +10 -14
  24. package/dist/mcp-server/tools/definitions/predict-variant.tool.js.map +1 -1
  25. package/dist/mcp-server/tools/definitions/query-region.tool.d.ts +6 -1
  26. package/dist/mcp-server/tools/definitions/query-region.tool.d.ts.map +1 -1
  27. package/dist/mcp-server/tools/definitions/query-region.tool.js +121 -30
  28. package/dist/mcp-server/tools/definitions/query-region.tool.js.map +1 -1
  29. package/dist/services/ensembl/ensembl-service.d.ts +11 -0
  30. package/dist/services/ensembl/ensembl-service.d.ts.map +1 -1
  31. package/dist/services/ensembl/ensembl-service.js +26 -0
  32. package/dist/services/ensembl/ensembl-service.js.map +1 -1
  33. package/dist/services/ensembl/types.d.ts +11 -0
  34. package/dist/services/ensembl/types.d.ts.map +1 -1
  35. package/package.json +11 -10
  36. package/server.json +10 -24
@@ -90,13 +90,21 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
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  'Optional for symbol lookups — defaults to homo_sapiens; set it for other organisms. ' +
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  'Use ensembl_list_species to discover valid values.'),
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  ids: z
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- .array(z.string().describe('An Ensembl stable gene or transcript ID to resolve in this batch.'))
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+ .array(z
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+ .string()
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+ .trim()
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+ .min(1)
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+ .describe('An Ensembl stable gene or transcript ID to resolve in this batch.'))
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  .max(20)
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  .optional()
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  .describe('Batch lookup: up to 20 Ensembl stable IDs (ENSG…, ENST…). ' +
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  'Returns a succeeded/failed split. Provide exactly one of symbol, id, ids, or symbols.'),
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  symbols: z
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- .array(z.string().describe('A gene symbol to resolve in this batch (e.g. BRCA2, TP53).'))
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+ .array(z
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+ .string()
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+ .trim()
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+ .min(1)
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+ .describe('A gene symbol to resolve in this batch (e.g. BRCA2, TP53).'))
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  .max(20)
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  .optional()
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  .describe('Batch lookup: up to 20 gene symbols. ' +
@@ -156,9 +164,7 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
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  input.symbols?.length,
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  ].filter(Boolean).length;
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  if (inputCount > 1) {
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- throw ctx.fail('conflicting_input', 'Provide exactly one of: symbol, id, ids, or symbols.', {
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- ...ctx.recoveryFor('conflicting_input'),
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- });
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+ throw ctx.fail('conflicting_input', 'Provide exactly one of: symbol, id, ids, or symbols.');
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  }
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  // --- Batch by IDs ---
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  if (input.ids?.length) {
@@ -192,12 +198,10 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
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  .catch((err) => {
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  const msg = err instanceof Error ? err.message : String(err);
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  if (/not found|no stable id|no results|no valid lookup/i.test(msg)) {
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- throw ctx.fail('not_found', `Gene symbol "${input.symbol}" not found in ${speciesStr}.`, { ...ctx.recoveryFor('not_found') });
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+ throw ctx.fail('not_found', `Gene symbol "${input.symbol}" not found in ${speciesStr}.`);
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  }
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  if (/species|invalid|unrecognized/i.test(msg)) {
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- throw ctx.fail('invalid_species', `Species "${speciesStr}" not recognized by Ensembl.`, {
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- ...ctx.recoveryFor('invalid_species'),
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- });
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+ throw ctx.fail('invalid_species', `Species "${speciesStr}" not recognized by Ensembl.`);
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  }
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  throw err;
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  });
@@ -210,17 +214,13 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
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  .catch((err) => {
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  const msg = err instanceof Error ? err.message : String(err);
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  if (/not found|no stable id/i.test(msg)) {
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- throw ctx.fail('not_found', `Gene ID "${input.id}" not found in Ensembl.`, {
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- ...ctx.recoveryFor('not_found'),
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- });
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+ throw ctx.fail('not_found', `Gene ID "${input.id}" not found in Ensembl.`);
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  }
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  throw err;
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  });
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  return { gene };
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  }
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- throw ctx.fail('no_input', 'Provide symbol (with species), id, ids, or symbols.', {
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- ...ctx.recoveryFor('no_input'),
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- });
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+ throw ctx.fail('no_input', 'Provide symbol (with species), id, ids, or symbols.');
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  },
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  format: (result) => {
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  const lines = [];
@@ -1 +1 @@
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@@ -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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAyVhC,CAAC"}
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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmVhC,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 ' +
@@ -210,12 +214,10 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
210
214
  .catch((err) => {
211
215
  const msg = err instanceof Error ? err.message : String(err);
212
216
  if (/invalid|unrecognized|parse|malformed/i.test(msg)) {
213
- throw ctx.fail('invalid_notation', `Invalid region+allele notation "${input.variant}": ${msg}`, { ...ctx.recoveryFor('invalid_notation') });
217
+ throw ctx.fail('invalid_notation', `Invalid region+allele notation "${input.variant}": ${msg}`);
214
218
  }
215
219
  if (/not found|outside/i.test(msg)) {
216
- throw ctx.fail('not_found', `Variant location not found: ${msg}`, {
217
- ...ctx.recoveryFor('not_found'),
218
- });
220
+ throw ctx.fail('not_found', `Variant location not found: ${msg}`);
219
221
  }
220
222
  throw err;
221
223
  });
@@ -227,12 +229,10 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
227
229
  const msg = err instanceof Error ? err.message : String(err);
228
230
  // A well-formed rsID that dbSNP does not know reports "No variant found with ID …".
229
231
  if (/not found|no variant|unknown variant/i.test(msg)) {
230
- throw ctx.fail('not_found', `Variant identifier ${input.variant} not found in dbSNP.`, {
231
- ...ctx.recoveryFor('not_found'),
232
- });
232
+ throw ctx.fail('not_found', `Variant identifier ${input.variant} not found in dbSNP.`);
233
233
  }
234
234
  if (/invalid|unrecognized|parse|malformed/i.test(msg)) {
235
- throw ctx.fail('invalid_notation', `Invalid variant identifier "${input.variant}": ${msg}`, { ...ctx.recoveryFor('invalid_notation') });
235
+ throw ctx.fail('invalid_notation', `Invalid variant identifier "${input.variant}": ${msg}`);
236
236
  }
237
237
  throw err;
238
238
  });
@@ -243,14 +243,10 @@ export const ensemblPredictVariant = tool('ensembl_predict_variant', {
243
243
  .catch((err) => {
244
244
  const msg = err instanceof Error ? err.message : String(err);
245
245
  if (/invalid|unrecognized|parse|malformed|hgvs/i.test(msg)) {
246
- throw ctx.fail('invalid_notation', `Invalid HGVS notation "${input.variant}": ${msg}`, {
247
- ...ctx.recoveryFor('invalid_notation'),
248
- });
246
+ throw ctx.fail('invalid_notation', `Invalid HGVS notation "${input.variant}": ${msg}`);
249
247
  }
250
248
  if (/not found/i.test(msg)) {
251
- throw ctx.fail('not_found', `Variant ${input.variant} not found.`, {
252
- ...ctx.recoveryFor('not_found'),
253
- });
249
+ throw ctx.fail('not_found', `Variant ${input.variant} not found.`);
254
250
  }
255
251
  throw err;
256
252
  });
@@ -1 +1 @@
1
- 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@@ -15,6 +15,7 @@ export declare const ensemblQueryRegion: import("@cyanheads/mcp-ts-core").ToolDe
15
15
  variation: "variation";
16
16
  }>>>;
17
17
  biotype: z.ZodOptional<z.ZodString>;
18
+ max_results: z.ZodDefault<z.ZodNumber>;
18
19
  }, z.core.$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: "The region string could not be parsed or contains invalid coordinates.";
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;AA0CjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4K7B,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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsQ7B,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). Ensembl normalizes chromosome names and canonical ' +
49
- 'vertebrate output omits the chr prefix (13, not chr13); a chr-prefixed name like chr13 is also ' +
50
- 'accepted. The feature parameter defaults to gene only to prevent overwhelming returns — requesting ' +
51
- 'variation in an 85 kb region returns 44,000+ entries. Explicitly include variation, regulatory, ' +
52
- 'transcript, or exon only when needed. Exon rows carry the parent transcript ID, so the same exon ' +
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
- .describe('Genomic region in chr:start-end format (e.g. 13:32315086-32400268). ' +
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 return tens of thousands of features. ' +
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('Number of features returned. Note: very large regions may return truncated results.'),
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.string().optional().describe('Warning or guidance about the result set.'),
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 or contains invalid coordinates.',
98
- recovery: 'Use the format chr:start-end (e.g. 13:32315086-32400268). ' +
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.',
@@ -113,47 +162,89 @@ 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 (/invalid.*region|coordinate|parse/i.test(msg) ||
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)) {
125
- throw ctx.fail('invalid_region', `Invalid region "${input.region}": ${msg}`, {
126
- ...ctx.recoveryFor('invalid_region'),
127
- });
175
+ /no slice found|cannot request a slice|could not decode region/i.test(msg) ||
176
+ /maximum allowed length/i.test(msg)) {
177
+ throw ctx.fail('invalid_region', `Invalid region "${input.region}": ${msg}`);
128
178
  }
129
179
  if (/species|invalid|unrecognized/i.test(msg)) {
130
- throw ctx.fail('invalid_species', `Species "${input.species}" not recognized.`, {
131
- ...ctx.recoveryFor('invalid_species'),
132
- });
180
+ throw ctx.fail('invalid_species', `Species "${input.species}" not recognized.`);
133
181
  }
134
182
  throw err;
135
183
  });
136
- if (features.length === 0) {
137
- ctx.enrich.notice(`No ${input.feature.join(', ')} features found in ${input.region} for ${input.species}. ` +
184
+ // Ensembl returns the full overlap set with no paging; cap post-fetch so wide
185
+ // regions stay compact by default. totalCount stays the true pre-cap count
186
+ // (max_results = 0 disables the cap).
187
+ const totalCount = features.length;
188
+ const returned = input.max_results > 0 ? features.slice(0, input.max_results) : features;
189
+ // Every overlap row type except regulatory carries its assembly, so read it from
190
+ // the full set at no request cost; only an empty or regulatory-only result needs
191
+ // the species-default lookup. A failed lookup degrades to a notice, but a
192
+ // cancelled request still fails.
193
+ const assemblyName = features.find((f) => f.assemblyName)?.assemblyName ??
194
+ (await service.getDefaultAssemblyName(input.species, ctx).catch((err) => {
195
+ if (ctx.signal.aborted)
196
+ throw err;
197
+ ctx.log.warning('Assembly lookup failed', {
198
+ species: input.species,
199
+ error: err instanceof Error ? err.message : String(err),
200
+ });
201
+ return;
202
+ }));
203
+ // ctx.enrich.notice is last-wins, so every applicable fragment composes into ONE string.
204
+ const fragments = [];
205
+ if (totalCount === 0) {
206
+ fragments.push(`No ${input.feature.join(', ')} features found in ${input.region} for ${input.species}. ` +
138
207
  'The region may be intergenic, or the coordinates may not cover the intended locus. ' +
139
208
  'Use ensembl_lookup_gene to confirm the locus coordinates.');
140
209
  }
141
- else if (features.length > 1000) {
142
- ctx.enrich.notice(`Large result set (${features.length} features). ` +
210
+ const capped = returned.length < totalCount;
211
+ if (capped) {
212
+ fragments.push(`Showing ${returned.length} of ${totalCount} features. ` +
213
+ 'Raise max_results (0 returns all) or query a smaller region for the rest.');
214
+ }
215
+ if (totalCount > 1000) {
216
+ fragments.push(`Large result set (${totalCount} features). ` +
143
217
  'Consider narrowing the region or filtering by biotype to reduce context usage.');
144
218
  }
145
- ctx.enrich.total(features.length);
219
+ if (!assemblyName) {
220
+ fragments.push(`The assembly for ${input.species} could not be resolved, so assemblyName is omitted; ` +
221
+ 'ensembl_lookup_gene reports the assembly for any gene in this region.');
222
+ }
223
+ if (fragments.length > 0) {
224
+ const guidance = fragments.join(' ');
225
+ if (capped) {
226
+ ctx.enrich.truncated({ shown: returned.length, cap: input.max_results, guidance });
227
+ }
228
+ else {
229
+ ctx.enrich.notice(guidance);
230
+ }
231
+ }
146
232
  return {
147
- features,
148
- totalCount: features.length,
233
+ features: returned,
234
+ totalCount,
149
235
  region: input.region,
150
236
  species: input.species,
237
+ ...(assemblyName && { assemblyName }),
151
238
  };
152
239
  },
153
240
  format: (result) => {
154
241
  const lines = [];
155
242
  lines.push(`## Genomic Region: ${result.species} ${result.region}`);
156
- lines.push(`**Features found:** ${result.totalCount}\n`);
243
+ if (result.assemblyName)
244
+ lines.push(`**Assembly:** ${result.assemblyName}`);
245
+ const shown = result.features.length;
246
+ const found = result.totalCount > shown ? `${shown} of ${result.totalCount}` : `${result.totalCount}`;
247
+ lines.push(`**Features found:** ${found}\n`);
157
248
  if (result.features.length === 0) {
158
249
  lines.push('No features found in this region.');
159
250
  return [{ type: 'text', text: lines.join('\n') }];
@@ -1 +1 @@
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1
+ 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@@ -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
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