@cyanheads/ensembl-mcp-server 0.4.1 → 0.4.3

package/changelog/template.md

@@ -4,10 +4,11 @@
 # to author a new release. Set that file's H1 to `# <version> — YYYY-MM-DD`
 # with a concrete date.
 
-# Required. One-line GitHub Release-style headline. 350 character cap.
-# Default short and scannable. Don't pad, don't stitch unrelated changes with
-# semicolons — pick the headline. Quotes required: unquoted YAML treats `: `
-# inside the value as a key separator and fails GitHub's strict parser.
+# Required. One-line GitHub Release-style headline. 350 character cap — a
+# ceiling, not a target. Default short and scannable. Don't pad, don't stitch
+# unrelated changes with commas/semicolons into an inventory — pick the
+# headline, like a tag's theme line. Quotes required: unquoted YAML treats
+# `: ` inside the value as a key separator and fails GitHub's strict parser.
 summary: ""
 
 # Set `true` when consumers must change code to upgrade: API removals,
@@ -24,9 +25,10 @@ security: false
 
 # Optional free-form notes for maintenance agents processing this release.
 # Not rendered in CHANGELOG — consumed by agents running `maintenance` on
-# downstream servers. Use for adoption instructions that don't fit the
-# human-facing sections: new files to create, fields to populate, one-time
-# migration steps. Omit the field entirely when there's nothing to say.
+# downstream servers. ADOPTION STEPS ONLY — new files to create, fields to
+# populate, one-time migration steps. Never a second rendering of the body:
+# if a body bullet already says it, name the bullet's symbol instead of
+# re-explaining. Omit the field entirely when there's nothing to say.
 # agent-notes: |
 #   <instructions for downstream maintenance agents>
 ---
@@ -41,17 +43,54 @@ security: false
   each bullet with the symbol or concept name in **bold** so they can skip
   what's irrelevant and zoom in on what's not.
 
-  Tone: terse, fact-dense, not verbose. Default to one sentence per bullet —
-  name the symbol, state what changed, stop. Use a second sentence only when
-  it carries weight. If a bullet feels long, it is.
-
-  Cut: mechanism walkthroughs (those belong in JSDoc, CLAUDE.md/AGENTS.md, or the
-  relevant skill), ceremonial framings ("This release introduces…",
-  backwards-compat paragraphs), file-by-file test enumerations, internal
-  implementation notes. Prefer code/symbol names over English re-explanations.
+  Tone: terse, fact-dense, not verbose. Bullet shape: **symbol** + what
+  changed + at most one consumer-facing caveat. One sentence by default, two
+  when the second carries weight — a bullet past ~40 words or three sentences
+  is wrong. The depth lives one hop away: the linked issue carries the why,
+  the commit diff carries the how. The changelog names what changed and what
+  a consumer does about it; a reader who wants mechanism opens the link.
+
+  Model length on THIS guide, never on the previous entry — entries modeled
+  on entries compound.
+
+  Cut (each has shipped as a wall of text; these are the cruft):
+  - History/justification narration — how the bug worked, why the old
+    behavior was wrong. One short clause at most; the issue carries the story.
+  - Design-rationale defense — "chosen over Y because…", "guarding the
+    getter is not enough…". That is the author arguing with a reviewer;
+    reviewers read the PR, not the changelog.
+  - Defensive unchanged-clauses — "X is unchanged", "byte-identical to
+    <prev>". Keep one only where its absence would cause a real misread,
+    as a short parenthetical.
+  - Edge-case inventories — marker lists, not-flagged lists, escape tables.
+    Tests and the issue carry those.
+  - Mechanism walkthroughs (JSDoc, CLAUDE.md/AGENTS.md, or the relevant
+    skill own those), ceremonial framings ("This release introduces…"),
+    backwards-compat paragraphs, file-by-file test enumerations. Prefer
+    code/symbol names over English re-explanations.
+
+  Verified ≠ included: the every-claim-verified-from-the-diff rule bounds
+  the TRUTH of what you write, never the AMOUNT.
+
+  Example — same fact, right size:
+
+    TOO LONG: **`fetchWithTimeout`'s `timeoutMs` bounds the whole exchange**
+    (#341). `fetch` resolves once headers arrive and the deadline was
+    cleared as the helper returned, so a peer that answered promptly and
+    then stalled the stream held the request open indefinitely. A 2xx
+    carrying a body now comes back as a passthrough wrapper that disarms
+    the deadline when the body closes, errors, or is cancelled; …
+    [+90 more words of mechanism and edge cases]
+
+    RIGHT: **`fetchWithTimeout`'s `timeoutMs` now bounds the whole
+    exchange, not just the headers** (#341). A stalled body aborts with
+    the same `Timeout` error; the returned `Response` is a wrapper, so
+    identity assertions (`toBe(response)`) no longer hold.
 
   Narrative intro: skip by default. Add one short sentence only when the
-  release theme genuinely needs framing the bullets can't carry.
+  release theme genuinely needs framing the bullets can't carry. When many
+  bullets share one upgrade consequence, state it ONCE — intro line or
+  agent-notes — never per bullet.
 
   Sections: Keep a Changelog order — Added, Changed, Deprecated, Removed,
   Fixed, Security. Include only sections with entries; delete the rest

package/dist/config/server-config.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,QAAA,MAAM,kBAAkB;;iBAQtB,CAAC;AAIH,wBAAgB,eAAe;;EAK9B;AAED,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC"}
+{"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,QAAA,MAAM,kBAAkB;;iBAOtB,CAAC;AAIH,wBAAgB,eAAe;;EAK9B;AAED,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC"}

package/dist/config/server-config.js

@@ -8,8 +8,7 @@ const ServerConfigSchema = z.object({
     baseUrl: z
         .string()
         .default('https://rest.ensembl.org')
-        .describe('Ensembl REST API base URL. Override to point at GRCh37 legacy endpoint ' +
-        '(https://grch37.rest.ensembl.org) or a local mirror.'),
+        .describe('Ensembl REST API base URL. Override to point at the GRCh37 legacy endpoint (https://grch37.rest.ensembl.org) or a local mirror.'),
 });
 let _config;
 export function getServerConfig() {

package/dist/config/server-config.js.map

@@ -1 +1 @@
-{"version":3,"file":"server-config.js","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,+BAA+B,CAAC;AAE/D,MAAM,kBAAkB,GAAG,CAAC,CAAC,MAAM,CAAC;IAClC,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,OAAO,CAAC,0BAA0B,CAAC;SACnC,QAAQ,CACP,yEAAyE;QACvE,sDAAsD,CACzD;CACJ,CAAC,CAAC;AAEH,IAAI,OAAuD,CAAC;AAE5D,MAAM,UAAU,eAAe;IAC7B,OAAO,KAAK,cAAc,CAAC,kBAAkB,EAAE;QAC7C,OAAO,EAAE,kBAAkB;KAC5B,CAAC,CAAC;IACH,OAAO,OAAO,CAAC;AACjB,CAAC"}
+{"version":3,"file":"server-config.js","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,+BAA+B,CAAC;AAE/D,MAAM,kBAAkB,GAAG,CAAC,CAAC,MAAM,CAAC;IAClC,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,OAAO,CAAC,0BAA0B,CAAC;SACnC,QAAQ,CACP,iIAAiI,CAClI;CACJ,CAAC,CAAC;AAEH,IAAI,OAAuD,CAAC;AAE5D,MAAM,UAAU,eAAe;IAC7B,OAAO,KAAK,cAAc,CAAC,kBAAkB,EAAE;QAC7C,OAAO,EAAE,kBAAkB;KAC5B,CAAC,CAAC;IACH,OAAO,OAAO,CAAC;AACjB,CAAC"}

package/dist/index.js

@@ -19,6 +19,14 @@ import { initEnsemblService } from './services/ensembl/ensembl-service.js';
 await createApp({
     name: 'ensembl-mcp-server',
     title: 'ensembl-mcp-server',
+    cacheHints: {
+        'prompts/list': { ttlMs: 3_600_000, cacheScope: 'public' },
+        'resources/list': { ttlMs: 3_600_000, cacheScope: 'public' },
+        'resources/read': { ttlMs: 300_000, cacheScope: 'public' },
+        'resources/templates/list': { ttlMs: 3_600_000, cacheScope: 'public' },
+        'server/discover': { ttlMs: 3_600_000, cacheScope: 'public' },
+        'tools/list': { ttlMs: 3_600_000, cacheScope: 'public' },
+    },
     tools: [
         ensemblListSpecies,
         ensemblLookupGene,

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,wBAAwB,EAAE,MAAM,yDAAyD,CAAC;AACnG,OAAO,EAAE,mBAAmB,EAAE,MAAM,qDAAqD,CAAC;AAC1F,OAAO,EACL,gCAAgC,EAChC,sBAAsB,GACvB,MAAM,wDAAwD,CAAC;AAChE,OAAO,EAAE,yBAAyB,EAAE,MAAM,2DAA2D,CAAC;AACtG,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,eAAe,EAAE,MAAM,kDAAkD,CAAC;AACnF,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,iBAAiB,EAAE,MAAM,oDAAoD,CAAC;AACvF,OAAO,EAAE,qBAAqB,EAAE,MAAM,wDAAwD,CAAC;AAC/F,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAE3E,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,oBAAoB;IAC1B,KAAK,EAAE,oBAAoB;IAC3B,KAAK,EAAE;QACL,kBAAkB;QAClB,iBAAiB;QACjB,kBAAkB;QAClB,kBAAkB;QAClB,qBAAqB;QACrB,kBAAkB;QAClB,eAAe;KAChB;IACD,SAAS,EAAE;QACT,mBAAmB;QACnB,yBAAyB;QACzB,sBAAsB;QACtB,gCAAgC;KACjC;IACD,OAAO,EAAE,CAAC,wBAAwB,CAAC;IACnC,YAAY,EAAE;;;;oHAIoG;IAClH,KAAK,CAAC,IAAI;QACR,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;IAChD,CAAC;CACF,CAAC,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,wBAAwB,EAAE,MAAM,yDAAyD,CAAC;AACnG,OAAO,EAAE,mBAAmB,EAAE,MAAM,qDAAqD,CAAC;AAC1F,OAAO,EACL,gCAAgC,EAChC,sBAAsB,GACvB,MAAM,wDAAwD,CAAC;AAChE,OAAO,EAAE,yBAAyB,EAAE,MAAM,2DAA2D,CAAC;AACtG,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,eAAe,EAAE,MAAM,kDAAkD,CAAC;AACnF,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,iBAAiB,EAAE,MAAM,oDAAoD,CAAC;AACvF,OAAO,EAAE,qBAAqB,EAAE,MAAM,wDAAwD,CAAC;AAC/F,OAAO,EAAE,kBAAkB,EAAE,MAAM,qDAAqD,CAAC;AACzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAE3E,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,oBAAoB;IAC1B,KAAK,EAAE,oBAAoB;IAC3B,UAAU,EAAE;QACV,cAAc,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC1D,gBAAgB,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC5D,gBAAgB,EAAE,EAAE,KAAK,EAAE,OAAO,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC1D,0BAA0B,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QACtE,iBAAiB,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC7D,YAAY,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;KACzD;IACD,KAAK,EAAE;QACL,kBAAkB;QAClB,iBAAiB;QACjB,kBAAkB;QAClB,kBAAkB;QAClB,qBAAqB;QACrB,kBAAkB;QAClB,eAAe;KAChB;IACD,SAAS,EAAE;QACT,mBAAmB;QACnB,yBAAyB;QACzB,sBAAsB;QACtB,gCAAgC;KACjC;IACD,OAAO,EAAE,CAAC,wBAAwB,CAAC;IACnC,YAAY,EAAE;;;;oHAIoG;IAClH,KAAK,CAAC,IAAI;QACR,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;IAChD,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/gene.resource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"gene.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gene.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,mBAAmB;;;;;;;GA2D9B,CAAC"}
+{"version":3,"file":"gene.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gene.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,mBAAmB;;;;;;;GA6D9B,CAAC"}

package/dist/mcp-server/resources/definitions/gene.resource.js

@@ -33,7 +33,9 @@ export const ensemblGeneResource = resource('ensembl://gene/{id}', {
         const gene = await service.lookupGeneById(params.id, true, ctx).catch((err) => {
             const msg = err instanceof Error ? err.message : String(err);
             if (/not found/i.test(msg)) {
-                throw ctx.fail('not_found', `Gene ${params.id} not found in Ensembl.`);
+                throw ctx.fail('not_found', `Gene ${params.id} not found in Ensembl.`, {
+                    ...ctx.recoveryFor('not_found'),
+                });
             }
             throw err;
         });

package/dist/mcp-server/resources/definitions/gene.resource.js.map

@@ -1 +1 @@
-{"version":3,"file":"gene.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gene.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,CAAC,MAAM,mBAAmB,GAAG,QAAQ,CAAC,qBAAqB,EAAE;IACjE,IAAI,EAAE,cAAc;IACpB,WAAW,EACT,yGAAyG;QACzG,uDAAuD;QACvD,0EAA0E;IAC5E,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,CACP,kCAAkC;YAChC,4EAA4E;YAC5E,+CAA+C,CAClD;KACJ,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,8CAA8C;YACpD,QAAQ,EACN,+EAA+E;gBAC/E,qEAAqE;SACxE;KACF;IAED,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,wBAAwB,EAAE,EAAE,EAAE,EAAE,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;QAC3D,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,IAAI,GAAG,MAAM,OAAO,CAAC,cAAc,CAAC,MAAM,CAAC,EAAE,EAAE,IAAI,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACrF,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,QAAQ,MAAM,CAAC,EAAE,wBAAwB,CAAC,CAAC;YACzE,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC,CAAC,CAAC;QAEH,OAAO,IAAI,CAAC;IACd,CAAC;IAED,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE;YACT;gBACE,GAAG,EAAE,gCAAgC;gBACrC,IAAI,EAAE,sBAAsB;gBAC5B,WAAW,EAAE,kDAAkD;gBAC/D,QAAQ,EAAE,kBAAkB;aAC7B;YACD;gBACE,GAAG,EAAE,gCAAgC;gBACrC,IAAI,EAAE,qBAAqB;gBAC3B,WAAW,EAAE,4BAA4B;gBACzC,QAAQ,EAAE,kBAAkB;aAC7B;SACF;KACF,CAAC;CACH,CAAC,CAAC"}
+{"version":3,"file":"gene.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/gene.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,CAAC,MAAM,mBAAmB,GAAG,QAAQ,CAAC,qBAAqB,EAAE;IACjE,IAAI,EAAE,cAAc;IACpB,WAAW,EACT,yGAAyG;QACzG,uDAAuD;QACvD,0EAA0E;IAC5E,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,CACP,kCAAkC;YAChC,4EAA4E;YAC5E,+CAA+C,CAClD;KACJ,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,8CAA8C;YACpD,QAAQ,EACN,+EAA+E;gBAC/E,qEAAqE;SACxE;KACF;IAED,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,wBAAwB,EAAE,EAAE,EAAE,EAAE,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;QAC3D,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,IAAI,GAAG,MAAM,OAAO,CAAC,cAAc,CAAC,MAAM,CAAC,EAAE,EAAE,IAAI,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACrF,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,QAAQ,MAAM,CAAC,EAAE,wBAAwB,EAAE;oBACrE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;iBAChC,CAAC,CAAC;YACL,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC,CAAC,CAAC;QAEH,OAAO,IAAI,CAAC;IACd,CAAC;IAED,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE;YACT;gBACE,GAAG,EAAE,gCAAgC;gBACrC,IAAI,EAAE,sBAAsB;gBAC5B,WAAW,EAAE,kDAAkD;gBAC/D,QAAQ,EAAE,kBAAkB;aAC7B;YACD;gBACE,GAAG,EAAE,gCAAgC;gBACrC,IAAI,EAAE,qBAAqB;gBAC3B,WAAW,EAAE,4BAA4B;gBACzC,QAAQ,EAAE,kBAAkB;aAC7B;SACF;KACF,CAAC;CACH,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/species.resource.d.ts

@@ -8,11 +8,11 @@ import { z } from '@cyanheads/mcp-ts-core';
 export declare const ensemblSpeciesResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{}, z.core.$strip>, undefined, undefined>;
 export declare const ensemblSpeciesByDivisionResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
     division: z.ZodEnum<{
-        EnsemblVertebrates: "EnsemblVertebrates";
-        EnsemblPlants: "EnsemblPlants";
         EnsemblFungi: "EnsemblFungi";
         EnsemblMetazoa: "EnsemblMetazoa";
+        EnsemblPlants: "EnsemblPlants";
         EnsemblProtists: "EnsemblProtists";
+        EnsemblVertebrates: "EnsemblVertebrates";
     }>;
 }, z.core.$strip>, undefined, undefined>;
 //# sourceMappingURL=species.resource.d.ts.map

package/dist/mcp-server/resources/definitions/transcript.resource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"transcript.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/transcript.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,yBAAyB;;;;;;;GAqDpC,CAAC"}
+{"version":3,"file":"transcript.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/transcript.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,yBAAyB;;;;;;;GAuDpC,CAAC"}

package/dist/mcp-server/resources/definitions/transcript.resource.js

@@ -33,7 +33,9 @@ export const ensemblTranscriptResource = resource('ensembl://transcript/{id}', {
         const transcript = await service.lookupTranscript(params.id, ctx).catch((err) => {
             const msg = err instanceof Error ? err.message : String(err);
             if (/not found/i.test(msg)) {
-                throw ctx.fail('not_found', `Transcript ${params.id} not found in Ensembl.`);
+                throw ctx.fail('not_found', `Transcript ${params.id} not found in Ensembl.`, {
+                    ...ctx.recoveryFor('not_found'),
+                });
             }
             throw err;
         });

package/dist/mcp-server/resources/definitions/transcript.resource.js.map

@@ -1 +1 @@
-{"version":3,"file":"transcript.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/transcript.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,CAAC,MAAM,yBAAyB,GAAG,QAAQ,CAAC,2BAA2B,EAAE;IAC7E,IAAI,EAAE,oBAAoB;IAC1B,WAAW,EACT,0FAA0F;QAC1F,+FAA+F;QAC/F,2FAA2F;IAC7F,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,CACP,wCAAwC;YACtC,4EAA4E;YAC5E,+CAA+C,CAClD;KACJ,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,oDAAoD;YAC1D,QAAQ,EACN,+EAA+E;gBAC/E,6EAA6E;SAChF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,8BAA8B,EAAE,EAAE,EAAE,EAAE,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;QACjE,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,UAAU,GAAG,MAAM,OAAO,CAAC,gBAAgB,CAAC,MAAM,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACvF,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,cAAc,MAAM,CAAC,EAAE,wBAAwB,CAAC,CAAC;YAC/E,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC,CAAC,CAAC;QAEH,OAAO,UAAU,CAAC;IACpB,CAAC;IAED,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE;YACT;gBACE,GAAG,EAAE,sCAAsC;gBAC3C,IAAI,EAAE,+CAA+C;gBACrD,WAAW,EAAE,qCAAqC;gBAClD,QAAQ,EAAE,kBAAkB;aAC7B;SACF;KACF,CAAC;CACH,CAAC,CAAC"}
+{"version":3,"file":"transcript.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/transcript.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,CAAC,MAAM,yBAAyB,GAAG,QAAQ,CAAC,2BAA2B,EAAE;IAC7E,IAAI,EAAE,oBAAoB;IAC1B,WAAW,EACT,0FAA0F;QAC1F,+FAA+F;QAC/F,2FAA2F;IAC7F,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,CACP,wCAAwC;YACtC,4EAA4E;YAC5E,+CAA+C,CAClD;KACJ,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,oDAAoD;YAC1D,QAAQ,EACN,+EAA+E;gBAC/E,6EAA6E;SAChF;KACF;IAED,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,8BAA8B,EAAE,EAAE,EAAE,EAAE,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;QACjE,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,MAAM,UAAU,GAAG,MAAM,OAAO,CAAC,gBAAgB,CAAC,MAAM,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACvF,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,cAAc,MAAM,CAAC,EAAE,wBAAwB,EAAE;oBAC3E,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;iBAChC,CAAC,CAAC;YACL,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC,CAAC,CAAC;QAEH,OAAO,UAAU,CAAC;IACpB,CAAC;IAED,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE;YACT;gBACE,GAAG,EAAE,sCAAsC;gBAC3C,IAAI,EAAE,+CAA+C;gBACrD,WAAW,EAAE,qCAAqC;gBAClD,QAAQ,EAAE,kBAAkB;aAC7B;SACF;KACF,CAAC;CACH,CAAC,CAAC"}

package/dist/mcp-server/tools/definitions/get-homology.tool.d.ts

@@ -10,10 +10,11 @@ export declare const ensemblGetHomology: import("@cyanheads/mcp-ts-core").ToolDe
     species: z.ZodDefault<z.ZodString>;
     target_species: z.ZodOptional<z.ZodString>;
     type: z.ZodDefault<z.ZodEnum<{
+        all: "all";
         orthologues: "orthologues";
         paralogues: "paralogues";
-        all: "all";
     }>>;
+    max_results: z.ZodDefault<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     homologs: z.ZodArray<z.ZodObject<{
         targetId: z.ZodString;
@@ -44,5 +45,8 @@ export declare const ensemblGetHomology: import("@cyanheads/mcp-ts-core").ToolDe
     readonly recovery: "Provide exactly one: a gene symbol (with optional species) or a stable Ensembl gene ID.";
 }], {
     readonly notice: z.ZodOptional<z.ZodString>;
+    readonly truncated: z.ZodOptional<z.ZodBoolean>;
+    readonly shown: z.ZodOptional<z.ZodNumber>;
+    readonly cap: z.ZodOptional<z.ZodNumber>;
 }>;
 //# sourceMappingURL=get-homology.tool.d.ts.map

package/dist/mcp-server/tools/definitions/get-homology.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get-homology.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-homology.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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgM7B,CAAC"}
+{"version":3,"file":"get-homology.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-homology.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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkP7B,CAAC"}

package/dist/mcp-server/tools/definitions/get-homology.tool.js

@@ -73,18 +73,40 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
             'orthologues: genes related by speciation (cross-species equivalents). ' +
             'paralogues: genes related by duplication (within or across species). ' +
             'all: both orthologs and paralogs.'),
+        max_results: z
+            .number()
+            .int()
+            .min(0)
+            .default(25)
+            .describe('Maximum number of homologs to return. Broad orthology queries ' +
+            '(e.g. BRCA2 across all species) can return 150+ homologs; the default keeps ' +
+            'responses focused. Set to 0 to return every homolog uncapped. ' +
+            'totalCount always reports the true number available before this cap.'),
     }),
     output: z.object({
         homologs: z
             .array(HomologyEntrySchema.describe('A single homologous gene with its stable ID, species, homology type, and sequence identity metrics.'))
-            .describe('Homologous genes found for the query gene.'),
-        totalCount: z.number().describe('Total number of homologs returned.'),
+            .describe('Homologous genes found for the query gene, capped to max_results. ' +
+            'totalCount reports the full count available before the cap.'),
+        totalCount: z
+            .number()
+            .describe('Total number of homologs available before the max_results cap. ' +
+            'Exceeds the returned homologs count when the list was capped.'),
         queryId: z.string().describe('The resolved Ensembl gene ID used for the homology query.'),
         querySpecies: z.string().describe('The source species used for the query.'),
         queryType: z.string().describe('The homology type queried (orthologues, paralogues, or all).'),
     }),
     enrichment: {
-        notice: z.string().optional().describe('Guidance when no homologs are found.'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Guidance when no homologs are found or the list was capped.'),
+        truncated: z
+            .boolean()
+            .optional()
+            .describe('True when the homolog list was capped at max_results.'),
+        shown: z.number().optional().describe('Number of homologs returned after the max_results cap.'),
+        cap: z.number().optional().describe('The max_results limit applied to the homolog list.'),
     },
     errors: [
         {
@@ -117,10 +139,12 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
         });
         const service = getEnsemblService();
         if (!input.symbol?.trim() && !input.id?.trim()) {
-            throw ctx.fail('no_input', 'Provide either symbol (with species) or a stable gene ID.');
+            throw ctx.fail('no_input', 'Provide either symbol (with species) or a stable gene ID.', {
+                ...ctx.recoveryFor('no_input'),
+            });
         }
         if (input.id?.trim() && input.symbol?.trim()) {
-            throw ctx.fail('conflicting_input', 'Provide either symbol or id, not both — they may resolve to different genes.');
+            throw ctx.fail('conflicting_input', 'Provide either symbol or id, not both — they may resolve to different genes.', { ...ctx.recoveryFor('conflicting_input') });
         }
         const idTrimmed = input.id?.trim();
         const symbolTrimmed = input.symbol?.trim();
@@ -132,7 +156,9 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
                 .catch((err) => {
                 const msg = err instanceof Error ? err.message : String(err);
                 if (/not found|no valid lookup|page not found/i.test(msg)) {
-                    throw ctx.fail('not_found', `Gene ID "${idTrimmed}" not found in Ensembl.`);
+                    throw ctx.fail('not_found', `Gene ID "${idTrimmed}" not found in Ensembl.`, {
+                        ...ctx.recoveryFor('not_found'),
+                    });
                 }
                 throw err;
             });
@@ -148,7 +174,7 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
                 const msg = err instanceof Error ? err.message : String(err);
                 // Ensembl returns {"error":"<species_name>"} for invalid gene symbols in homology endpoint
                 if (/not found|no valid lookup/i.test(msg) || msg === input.species) {
-                    throw ctx.fail('not_found', `Gene symbol "${submittedSymbol}" not found in ${input.species}.`);
+                    throw ctx.fail('not_found', `Gene symbol "${submittedSymbol}" not found in ${input.species}.`, { ...ctx.recoveryFor('not_found') });
                 }
                 throw err;
             });
@@ -157,15 +183,27 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
             // fall back to the submitted symbol only when the response carried no data entry.
             queryId = result.resolvedQueryId ?? submittedSymbol;
         }
-        if (homologs.length === 0) {
+        // Ensembl returns the full homolog set; cap post-fetch so broad orthology
+        // queries stay compact by default. totalCount stays the true available count
+        // so a caller is never misled about completeness (max_results = 0 disables).
+        const availableCount = homologs.length;
+        const returned = input.max_results > 0 ? homologs.slice(0, input.max_results) : homologs;
+        if (returned.length === 0) {
             ctx.enrich.notice(`No ${input.type} found for "${queryId}" in ${input.species}` +
                 (input.target_species ? ` targeting ${input.target_species}` : '') +
                 '. Try type=all or remove the target_species filter.');
         }
-        ctx.enrich.total(homologs.length);
+        else if (returned.length < availableCount) {
+            ctx.enrich.truncated({
+                shown: returned.length,
+                cap: input.max_results,
+                guidance: `Showing ${returned.length} of ${availableCount} homologs. ` +
+                    'Raise max_results (0 returns all) or set target_species to narrow to one species.',
+            });
+        }
         return {
-            homologs,
-            totalCount: homologs.length,
+            homologs: returned,
+            totalCount: availableCount,
             queryId,
             querySpecies: input.species,
             queryType: input.type,
@@ -174,7 +212,9 @@ export const ensemblGetHomology = tool('ensembl_get_homology', {
     format: (result) => {
         const lines = [];
         lines.push(`## Homologs of ${result.queryId} (${result.querySpecies})`);
-        lines.push(`**Type:** ${result.queryType} | **Found:** ${result.totalCount}\n`);
+        const shown = result.homologs.length;
+        const foundLabel = result.totalCount > shown ? `${shown} of ${result.totalCount}` : `${result.totalCount}`;
+        lines.push(`**Type:** ${result.queryType} | **Found:** ${foundLabel}\n`);
         if (result.homologs.length === 0) {
             lines.push('No homologs found. Try type=all or remove the target_species filter.');
             return [{ type: 'text', text: lines.join('\n') }];

package/dist/mcp-server/tools/definitions/get-homology.tool.js.map

@@ -1 +1 @@
-{"version":3,"file":"get-homology.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-homology.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAG1E,MAAM,cAAc,GAAG,CAAC,aAAa,EAAE,YAAY,EAAE,KAAK,CAAU,CAAC;AAErE,MAAM,mBAAmB,GAAG,CAAC,CAAC,MAAM,CAAC;IACnC,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iEAAiE,CAAC;IAChG,aAAa,EAAE,CAAC;SACb,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,gEAAgE,CAAC;IAC7E,IAAI,EAAE,CAAC;SACJ,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,0EAA0E;QACxE,wDAAwD,CAC3D;IACH,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,wEAAwE;QACtE,kDAAkD,CACrD;IACH,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,iEAAiE;QAC/D,oEAAoE,CACvE;IACH,aAAa,EAAE,CAAC;SACb,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sEAAsE;QACpE,wCAAwC,CAC3C;CACJ,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,sBAAsB,EAAE;IAC7D,KAAK,EAAE,mBAAmB;IAC1B,WAAW,EACT,sGAAsG;QACtG,4GAA4G;QAC5G,wGAAwG;QACxG,6FAA6F;QAC7F,0GAA0G;QAC1G,gDAAgD;IAClD,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,wDAAwD;YACtD,qEAAqE;YACrE,6BAA6B,CAChC;QACH,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,iDAAiD;YAC/C,8DAA8D;YAC9D,iCAAiC,CACpC;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,OAAO,CAAC,cAAc,CAAC;aACvB,QAAQ,CACP,qFAAqF;YACnF,6EAA6E,CAChF;QACH,cAAc,EAAE,CAAC;aACd,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,+EAA+E;YAC7E,wDAAwD;YACxD,oDAAoD,CACvD;QACH,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,cAAc,CAAC;aACpB,OAAO,CAAC,aAAa,CAAC;aACtB,QAAQ,CACP,8BAA8B;YAC5B,wEAAwE;YACxE,uEAAuE;YACvE,mCAAmC,CACtC;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC;aACR,KAAK,CACJ,mBAAmB,CAAC,QAAQ,CAC1B,qGAAqG,CACtG,CACF;aACA,QAAQ,CAAC,4CAA4C,CAAC;QACzD,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oCAAoC,CAAC;QACrE,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2DAA2D,CAAC;QACzF,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC3E,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,8DAA8D,CAAC;KAC/F,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;KAC/E;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,wDAAwD;YAC9D,QAAQ,EACN,oFAAoF;gBACpF,2DAA2D;SAC9D;QACD;YACE,MAAM,EAAE,UAAU;YAClB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,qCAAqC;YAC3C,QAAQ,EAAE,mEAAmE;SAC9E;QACD;YACE,MAAM,EAAE,mBAAmB;YAC3B,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,mCAAmC;YACzC,QAAQ,EACN,yFAAyF;SAC5F;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kBAAkB,EAAE;YAC/B,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,EAAE,EAAE,KAAK,CAAC,EAAE;YACZ,OAAO,EAAE,KAAK,CAAC,OAAO;YACtB,aAAa,EAAE,KAAK,CAAC,cAAc;YACnC,IAAI,EAAE,KAAK,CAAC,IAAI;SACjB,CAAC,CAAC;QACH,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,CAAC,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE,EAAE,CAAC;YAC/C,MAAM,GAAG,CAAC,IAAI,CAAC,UAAU,EAAE,2DAA2D,CAAC,CAAC;QAC1F,CAAC;QACD,IAAI,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE,IAAI,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,EAAE,CAAC;YAC7C,MAAM,GAAG,CAAC,IAAI,CACZ,mBAAmB,EACnB,8EAA8E,CAC/E,CAAC;QACJ,CAAC;QAED,MAAM,SAAS,GAAG,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE,CAAC;QACnC,MAAM,aAAa,GAAG,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC;QAC3C,IAAI,OAAe,CAAC;QACpB,IAAI,QAAyB,CAAC;QAE9B,IAAI,SAAS,EAAE,CAAC;YACd,MAAM,MAAM,GAAG,MAAM,OAAO;iBACzB,eAAe,CAAC,SAAS,EAAE,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,cAAc,EAAE,GAAG,CAAC;iBAChF,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,IAAI,2CAA2C,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBAC1D,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,YAAY,SAAS,yBAAyB,CAAC,CAAC;gBAC9E,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;YACL,QAAQ,GAAG,MAAM,CAAC,QAAQ,CAAC;YAC3B,0FAA0F;YAC1F,OAAO,GAAG,MAAM,CAAC,eAAe,IAAI,SAAS,CAAC;QAChD,CAAC;aAAM,CAAC;YACN,MAAM,eAAe,GAAG,aAAa,IAAI,EAAE,CAAC;YAC5C,MAAM,MAAM,GAAG,MAAM,OAAO;iBACzB,mBAAmB,CAAC,eAAe,EAAE,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,cAAc,EAAE,GAAG,CAAC;iBAC1F,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,2FAA2F;gBAC3F,IAAI,4BAA4B,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,KAAK,KAAK,CAAC,OAAO,EAAE,CAAC;oBACpE,MAAM,GAAG,CAAC,IAAI,CACZ,WAAW,EACX,gBAAgB,eAAe,kBAAkB,KAAK,CAAC,OAAO,GAAG,CAClE,CAAC;gBACJ,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;YACL,QAAQ,GAAG,MAAM,CAAC,QAAQ,CAAC;YAC3B,mFAAmF;YACnF,kFAAkF;YAClF,OAAO,GAAG,MAAM,CAAC,eAAe,IAAI,eAAe,CAAC;QACtD,CAAC;QAED,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC1B,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,MAAM,KAAK,CAAC,IAAI,eAAe,OAAO,QAAQ,KAAK,CAAC,OAAO,EAAE;gBAC3D,CAAC,KAAK,CAAC,cAAc,CAAC,CAAC,CAAC,cAAc,KAAK,CAAC,cAAc,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;gBAClE,qDAAqD,CACxD,CAAC;QACJ,CAAC;QACD,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC;QAElC,OAAO;YACL,QAAQ;YACR,UAAU,EAAE,QAAQ,CAAC,MAAM;YAC3B,OAAO;YACP,YAAY,EAAE,KAAK,CAAC,OAAO;YAC3B,SAAS,EAAE,KAAK,CAAC,IAAI;SACtB,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,KAAK,CAAC,IAAI,CAAC,kBAAkB,MAAM,CAAC,OAAO,KAAK,MAAM,CAAC,YAAY,GAAG,CAAC,CAAC;QACxE,KAAK,CAAC,IAAI,CAAC,aAAa,MAAM,CAAC,SAAS,iBAAiB,MAAM,CAAC,UAAU,IAAI,CAAC,CAAC;QAEhF,IAAI,MAAM,CAAC,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,KAAK,CAAC,IAAI,CAAC,sEAAsE,CAAC,CAAC;YACnF,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACpD,CAAC;QAED,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,QAAQ,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;YAChC,IAAI,CAAC,CAAC,aAAa;gBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,aAAa,EAAE,CAAC,CAAC;YACnE,IAAI,CAAC,CAAC,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;YACvD,IAAI,CAAC,CAAC,MAAM,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,yBAAyB,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YAClF,IAAI,CAAC,CAAC,OAAO,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,0BAA0B,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YACrF,IAAI,CAAC,CAAC,aAAa;gBAAE,KAAK,CAAC,IAAI,CAAC,6BAA6B,CAAC,CAAC,aAAa,EAAE,CAAC,CAAC;YAChF,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"}
+{"version":3,"file":"get-homology.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-homology.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAG1E,MAAM,cAAc,GAAG,CAAC,aAAa,EAAE,YAAY,EAAE,KAAK,CAAU,CAAC;AAErE,MAAM,mBAAmB,GAAG,CAAC,CAAC,MAAM,CAAC;IACnC,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iEAAiE,CAAC;IAChG,aAAa,EAAE,CAAC;SACb,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,gEAAgE,CAAC;IAC7E,IAAI,EAAE,CAAC;SACJ,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,0EAA0E;QACxE,wDAAwD,CAC3D;IACH,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,wEAAwE;QACtE,kDAAkD,CACrD;IACH,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,iEAAiE;QAC/D,oEAAoE,CACvE;IACH,aAAa,EAAE,CAAC;SACb,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sEAAsE;QACpE,wCAAwC,CAC3C;CACJ,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,sBAAsB,EAAE;IAC7D,KAAK,EAAE,mBAAmB;IAC1B,WAAW,EACT,sGAAsG;QACtG,4GAA4G;QAC5G,wGAAwG;QACxG,6FAA6F;QAC7F,0GAA0G;QAC1G,gDAAgD;IAClD,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE,cAAc,EAAE,IAAI,EAAE;IAC9E,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,wDAAwD;YACtD,qEAAqE;YACrE,6BAA6B,CAChC;QACH,EAAE,EAAE,CAAC;aACF,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,iDAAiD;YAC/C,8DAA8D;YAC9D,iCAAiC,CACpC;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,OAAO,CAAC,cAAc,CAAC;aACvB,QAAQ,CACP,qFAAqF;YACnF,6EAA6E,CAChF;QACH,cAAc,EAAE,CAAC;aACd,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,+EAA+E;YAC7E,wDAAwD;YACxD,oDAAoD,CACvD;QACH,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,cAAc,CAAC;aACpB,OAAO,CAAC,aAAa,CAAC;aACtB,QAAQ,CACP,8BAA8B;YAC5B,wEAAwE;YACxE,uEAAuE;YACvE,mCAAmC,CACtC;QACH,WAAW,EAAE,CAAC;aACX,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CACP,gEAAgE;YAC9D,8EAA8E;YAC9E,gEAAgE;YAChE,sEAAsE,CACzE;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC;aACR,KAAK,CACJ,mBAAmB,CAAC,QAAQ,CAC1B,qGAAqG,CACtG,CACF;aACA,QAAQ,CACP,oEAAoE;YAClE,6DAA6D,CAChE;QACH,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,CACP,iEAAiE;YAC/D,+DAA+D,CAClE;QACH,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2DAA2D,CAAC;QACzF,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC3E,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,8DAA8D,CAAC;KAC/F,CAAC;IACF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,6DAA6D,CAAC;QAC1E,SAAS,EAAE,CAAC;aACT,OAAO,EAAE;aACT,QAAQ,EAAE;aACV,QAAQ,CAAC,uDAAuD,CAAC;QACpE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;QAC/F,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oDAAoD,CAAC;KAC1F;IAED,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,wDAAwD;YAC9D,QAAQ,EACN,oFAAoF;gBACpF,2DAA2D;SAC9D;QACD;YACE,MAAM,EAAE,UAAU;YAClB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,qCAAqC;YAC3C,QAAQ,EAAE,mEAAmE;SAC9E;QACD;YACE,MAAM,EAAE,mBAAmB;YAC3B,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,mCAAmC;YACzC,QAAQ,EACN,yFAAyF;SAC5F;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kBAAkB,EAAE;YAC/B,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,EAAE,EAAE,KAAK,CAAC,EAAE;YACZ,OAAO,EAAE,KAAK,CAAC,OAAO;YACtB,aAAa,EAAE,KAAK,CAAC,cAAc;YACnC,IAAI,EAAE,KAAK,CAAC,IAAI;SACjB,CAAC,CAAC;QACH,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,CAAC,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE,EAAE,CAAC;YAC/C,MAAM,GAAG,CAAC,IAAI,CAAC,UAAU,EAAE,2DAA2D,EAAE;gBACtF,GAAG,GAAG,CAAC,WAAW,CAAC,UAAU,CAAC;aAC/B,CAAC,CAAC;QACL,CAAC;QACD,IAAI,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE,IAAI,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,EAAE,CAAC;YAC7C,MAAM,GAAG,CAAC,IAAI,CACZ,mBAAmB,EACnB,8EAA8E,EAC9E,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,mBAAmB,CAAC,EAAE,CAC5C,CAAC;QACJ,CAAC;QAED,MAAM,SAAS,GAAG,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE,CAAC;QACnC,MAAM,aAAa,GAAG,KAAK,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC;QAC3C,IAAI,OAAe,CAAC;QACpB,IAAI,QAAyB,CAAC;QAE9B,IAAI,SAAS,EAAE,CAAC;YACd,MAAM,MAAM,GAAG,MAAM,OAAO;iBACzB,eAAe,CAAC,SAAS,EAAE,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,cAAc,EAAE,GAAG,CAAC;iBAChF,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,IAAI,2CAA2C,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBAC1D,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,YAAY,SAAS,yBAAyB,EAAE;wBAC1E,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;qBAChC,CAAC,CAAC;gBACL,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;YACL,QAAQ,GAAG,MAAM,CAAC,QAAQ,CAAC;YAC3B,0FAA0F;YAC1F,OAAO,GAAG,MAAM,CAAC,eAAe,IAAI,SAAS,CAAC;QAChD,CAAC;aAAM,CAAC;YACN,MAAM,eAAe,GAAG,aAAa,IAAI,EAAE,CAAC;YAC5C,MAAM,MAAM,GAAG,MAAM,OAAO;iBACzB,mBAAmB,CAAC,eAAe,EAAE,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,cAAc,EAAE,GAAG,CAAC;iBAC1F,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,2FAA2F;gBAC3F,IAAI,4BAA4B,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,KAAK,KAAK,CAAC,OAAO,EAAE,CAAC;oBACpE,MAAM,GAAG,CAAC,IAAI,CACZ,WAAW,EACX,gBAAgB,eAAe,kBAAkB,KAAK,CAAC,OAAO,GAAG,EACjE,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CACpC,CAAC;gBACJ,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;YACL,QAAQ,GAAG,MAAM,CAAC,QAAQ,CAAC;YAC3B,mFAAmF;YACnF,kFAAkF;YAClF,OAAO,GAAG,MAAM,CAAC,eAAe,IAAI,eAAe,CAAC;QACtD,CAAC;QAED,0EAA0E;QAC1E,6EAA6E;QAC7E,6EAA6E;QAC7E,MAAM,cAAc,GAAG,QAAQ,CAAC,MAAM,CAAC;QACvC,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC;QAEzF,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC1B,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,MAAM,KAAK,CAAC,IAAI,eAAe,OAAO,QAAQ,KAAK,CAAC,OAAO,EAAE;gBAC3D,CAAC,KAAK,CAAC,cAAc,CAAC,CAAC,CAAC,cAAc,KAAK,CAAC,cAAc,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;gBAClE,qDAAqD,CACxD,CAAC;QACJ,CAAC;aAAM,IAAI,QAAQ,CAAC,MAAM,GAAG,cAAc,EAAE,CAAC;YAC5C,GAAG,CAAC,MAAM,CAAC,SAAS,CAAC;gBACnB,KAAK,EAAE,QAAQ,CAAC,MAAM;gBACtB,GAAG,EAAE,KAAK,CAAC,WAAW;gBACtB,QAAQ,EACN,WAAW,QAAQ,CAAC,MAAM,OAAO,cAAc,aAAa;oBAC5D,mFAAmF;aACtF,CAAC,CAAC;QACL,CAAC;QAED,OAAO;YACL,QAAQ,EAAE,QAAQ;YAClB,UAAU,EAAE,cAAc;YAC1B,OAAO;YACP,YAAY,EAAE,KAAK,CAAC,OAAO;YAC3B,SAAS,EAAE,KAAK,CAAC,IAAI;SACtB,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,KAAK,CAAC,IAAI,CAAC,kBAAkB,MAAM,CAAC,OAAO,KAAK,MAAM,CAAC,YAAY,GAAG,CAAC,CAAC;QACxE,MAAM,KAAK,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC;QACrC,MAAM,UAAU,GACd,MAAM,CAAC,UAAU,GAAG,KAAK,CAAC,CAAC,CAAC,GAAG,KAAK,OAAO,MAAM,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC,UAAU,EAAE,CAAC;QAC1F,KAAK,CAAC,IAAI,CAAC,aAAa,MAAM,CAAC,SAAS,iBAAiB,UAAU,IAAI,CAAC,CAAC;QAEzE,IAAI,MAAM,CAAC,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,KAAK,CAAC,IAAI,CAAC,sEAAsE,CAAC,CAAC;YACnF,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACpD,CAAC;QAED,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,QAAQ,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;YAChC,IAAI,CAAC,CAAC,aAAa;gBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,aAAa,EAAE,CAAC,CAAC;YACnE,IAAI,CAAC,CAAC,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;YACvD,IAAI,CAAC,CAAC,MAAM,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,yBAAyB,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YAClF,IAAI,CAAC,CAAC,OAAO,IAAI,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,0BAA0B,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC;YACrF,IAAI,CAAC,CAAC,aAAa;gBAAE,KAAK,CAAC,IAAI,CAAC,6BAA6B,CAAC,CAAC,aAAa,EAAE,CAAC,CAAC;YAChF,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"}

package/dist/mcp-server/tools/definitions/get-sequence.tool.d.ts

@@ -7,9 +7,9 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const ensemblGetSequence: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     id: z.ZodString;
     type: z.ZodDefault<z.ZodEnum<{
-        genomic: "genomic";
         cdna: "cdna";
         cds: "cds";
+        genomic: "genomic";
         protein: "protein";
     }>>;
     species: z.ZodOptional<z.ZodString>;

package/dist/mcp-server/tools/definitions/get-sequence.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get-sequence.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-sequence.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAKjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA8L7B,CAAC"}
+{"version":3,"file":"get-sequence.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-sequence.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAKjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAoM7B,CAAC"}

package/dist/mcp-server/tools/definitions/get-sequence.tool.js

@@ -112,14 +112,16 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
             const species = input.species?.trim() || (isPrefixedRegion ? input.id.slice(0, firstColon) : undefined);
             const region = isPrefixedRegion ? input.id.slice(firstColon + 1) : input.id;
             if (!species) {
-                throw ctx.fail('missing_species', `Region ${input.id} needs a species — set species (e.g. homo_sapiens) or use the species:chr:start-end id form.`);
+                throw ctx.fail('missing_species', `Region ${input.id} needs a species — set species (e.g. homo_sapiens) or use the species:chr:start-end id form.`, { ...ctx.recoveryFor('missing_species') });
             }
             const seq = await service
                 .getSequenceByRegion(species, region, input.expand_5prime, input.expand_3prime, ctx)
                 .catch((err) => {
                 const msg = err instanceof Error ? err.message : String(err);
                 if (/not found|invalid|no stable id/i.test(msg)) {
-                    throw ctx.fail('not_found', `Region ${input.id} not found: ${msg}`);
+                    throw ctx.fail('not_found', `Region ${input.id} not found: ${msg}`, {
+                        ...ctx.recoveryFor('not_found'),
+                    });
                 }
                 throw err;
             });
@@ -134,10 +136,12 @@ export const ensemblGetSequence = tool('ensembl_get_sequence', {
                 /requesting a gene and type not equal/i.test(msg) ||
                 /multiple sequences detected/i.test(msg)) {
                 throw ctx.fail('type_mismatch', `Cannot request type "${input.type}" from a gene ID — use a transcript or protein stable ID instead. ` +
-                    `Call ensembl_lookup_gene with expand_transcripts=true to get transcript IDs.`);
+                    `Call ensembl_lookup_gene with expand_transcripts=true to get transcript IDs.`, { ...ctx.recoveryFor('type_mismatch') });
             }
             if (/not found|no stable id/i.test(msg)) {
-                throw ctx.fail('not_found', `ID ${input.id} not found in Ensembl.`);
+                throw ctx.fail('not_found', `ID ${input.id} not found in Ensembl.`, {
+                    ...ctx.recoveryFor('not_found'),
+                });
             }
             throw err;
         });

package/dist/mcp-server/tools/definitions/get-sequence.tool.js.map

@@ -1 +1 @@
-{"version":3,"file":"get-sequence.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-sequence.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,cAAc,GAAG,CAAC,SAAS,EAAE,MAAM,EAAE,KAAK,EAAE,SAAS,CAAU,CAAC;AAEtE,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,sBAAsB,EAAE;IAC7D,KAAK,EAAE,cAAc;IACrB,WAAW,EACT,oGAAoG;QACpG,oGAAoG;QACpG,sGAAsG;QACtG,6FAA6F;QAC7F,oFAAoF;QACpF,8FAA8F;QAC9F,8GAA8G;QAC9G,wGAAwG;QACxG,2CAA2C;IAC7C,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,+EAA+E;YAC7E,0FAA0F;YAC1F,0EAA0E,CAC7E;QACH,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,cAAc,CAAC;aACpB,OAAO,CAAC,SAAS,CAAC;aAClB,QAAQ,CACP,6BAA6B;YAC3B,yDAAyD;YACzD,yDAAyD;YACzD,iFAAiF;YACjF,4DAA4D,CAC/D;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,0DAA0D;YACxD,wFAAwF;YACxF,4DAA4D;YAC5D,6EAA6E,CAChF;QACH,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,mFAAmF;YACjF,kEAAkE,CACrE;QACH,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,qFAAqF;YACnF,kEAAkE,CACrE;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;QACvE,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,0DAA0D,CAAC;QACrF,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,QAAQ,CACP,wFAAwF;YACtF,wDAAwD;YACxD,sEAAsE,CACzE;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,CACP,qGAAqG;YACnG,yEAAyE,CAC5E;QACH,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iDAAiD,CAAC;KAC/F,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,mDAAmD;YACzD,QAAQ,EACN,oEAAoE;gBACpE,wDAAwD;SAC3D;QACD;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,wEAAwE;YAC9E,QAAQ,EACN,kGAAkG;gBAClG,4FAA4F;gBAC5F,mEAAmE;SACtE;QACD;YACE,MAAM,EAAE,iBAAiB;YACzB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,0DAA0D;YAChE,QAAQ,EACN,sEAAsE;gBACtE,oDAAoD;SACvD;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,mBAAmB,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;QACtE,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,qCAAqC;QACrC,sFAAsF;QACtF,iFAAiF;QACjF,+EAA+E;QAC/E,iFAAiF;QACjF,+EAA+E;QAC/E,2DAA2D;QAC3D,MAAM,gBAAgB,GAAG,2BAA2B,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QACpE,MAAM,YAAY,GAAG,kBAAkB,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAEvD,IAAI,gBAAgB,IAAI,YAAY,EAAE,CAAC;YACrC,8EAA8E;YAC9E,8EAA8E;YAC9E,qDAAqD;YACrD,MAAM,UAAU,GAAG,KAAK,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;YACzC,MAAM,OAAO,GACX,KAAK,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAC,gBAAgB,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;YAC1F,MAAM,MAAM,GAAG,gBAAgB,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;YAC5E,IAAI,CAAC,OAAO,EAAE,CAAC;gBACb,MAAM,GAAG,CAAC,IAAI,CACZ,iBAAiB,EACjB,UAAU,KAAK,CAAC,EAAE,8FAA8F,CACjH,CAAC;YACJ,CAAC;YACD,MAAM,GAAG,GAAG,MAAM,OAAO;iBACtB,mBAAmB,CAAC,OAAO,EAAE,MAAM,EAAE,KAAK,CAAC,aAAa,EAAE,KAAK,CAAC,aAAa,EAAE,GAAG,CAAC;iBACnF,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,IAAI,iCAAiC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBAChD,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,UAAU,KAAK,CAAC,EAAE,eAAe,GAAG,EAAE,CAAC,CAAC;gBACtE,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;YACL,OAAO,GAAG,CAAC;QACb,CAAC;QAED,iBAAiB;QACjB,MAAM,GAAG,GAAG,MAAM,OAAO;aACtB,eAAe,CAAC,KAAK,CAAC,EAAE,CAAC,IAAI,EAAE,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,aAAa,EAAE,KAAK,CAAC,aAAa,EAAE,GAAG,CAAC;aAC3F,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YAC7D,IACE,sDAAsD,CAAC,IAAI,CAAC,GAAG,CAAC;gBAChE,uCAAuC,CAAC,IAAI,CAAC,GAAG,CAAC;gBACjD,8BAA8B,CAAC,IAAI,CAAC,GAAG,CAAC,EACxC,CAAC;gBACD,MAAM,GAAG,CAAC,IAAI,CACZ,eAAe,EACf,wBAAwB,KAAK,CAAC,IAAI,oEAAoE;oBACpG,8EAA8E,CACjF,CAAC;YACJ,CAAC;YACD,IAAI,yBAAyB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,MAAM,KAAK,CAAC,EAAE,wBAAwB,CAAC,CAAC;YACtE,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC,CAAC,CAAC;QACL,OAAO,GAAG,CAAC;IACb,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,KAAK,CAAC,IAAI,CAAC,gBAAgB,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;QACxC,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC;QAC3D,KAAK,CAAC,IAAI,CAAC,aAAa,MAAM,CAAC,IAAI,kBAAkB,MAAM,CAAC,MAAM,CAAC,cAAc,EAAE,IAAI,IAAI,EAAE,CAAC,CAAC;QAC/F,IAAI,MAAM,CAAC,WAAW;YAAE,KAAK,CAAC,IAAI,CAAC,oBAAoB,MAAM,CAAC,WAAW,EAAE,CAAC,CAAC;QAC7E,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,6DAA6D;QAC7D,IAAI,MAAM,CAAC,GAAG,CAAC,MAAM,GAAG,GAAG,EAAE,CAAC;YAC5B,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;YAClB,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC;YACrC,KAAK,CAAC,IAAI,CAAC,MAAM,MAAM,CAAC,MAAM,CAAC,cAAc,EAAE,oBAAoB,CAAC,CAAC;YACrE,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACpB,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;YAClB,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YACvB,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACpB,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
+{"version":3,"file":"get-sequence.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-sequence.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,cAAc,GAAG,CAAC,SAAS,EAAE,MAAM,EAAE,KAAK,EAAE,SAAS,CAAU,CAAC;AAEtE,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,sBAAsB,EAAE;IAC7D,KAAK,EAAE,cAAc;IACrB,WAAW,EACT,oGAAoG;QACpG,oGAAoG;QACpG,sGAAsG;QACtG,6FAA6F;QAC7F,oFAAoF;QACpF,8FAA8F;QAC9F,8GAA8G;QAC9G,wGAAwG;QACxG,2CAA2C;IAC7C,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,+EAA+E;YAC7E,0FAA0F;YAC1F,0EAA0E,CAC7E;QACH,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,cAAc,CAAC;aACpB,OAAO,CAAC,SAAS,CAAC;aAClB,QAAQ,CACP,6BAA6B;YAC3B,yDAAyD;YACzD,yDAAyD;YACzD,iFAAiF;YACjF,4DAA4D,CAC/D;QACH,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,0DAA0D;YACxD,wFAAwF;YACxF,4DAA4D;YAC5D,6EAA6E,CAChF;QACH,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,mFAAmF;YACjF,kEAAkE,CACrE;QACH,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,qFAAqF;YACnF,kEAAkE,CACrE;KACJ,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;QACvE,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,0DAA0D,CAAC;QACrF,GAAG,EAAE,CAAC;aACH,MAAM,EAAE;aACR,QAAQ,CACP,wFAAwF;YACtF,wDAAwD;YACxD,sEAAsE,CACzE;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,CACP,qGAAqG;YACnG,yEAAyE,CAC5E;QACH,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iDAAiD,CAAC;KAC/F,CAAC;IAEF,MAAM,EAAE;QACN;YACE,MAAM,EAAE,WAAW;YACnB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,mDAAmD;YACzD,QAAQ,EACN,oEAAoE;gBACpE,wDAAwD;SAC3D;QACD;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,wEAAwE;YAC9E,QAAQ,EACN,kGAAkG;gBAClG,4FAA4F;gBAC5F,mEAAmE;SACtE;QACD;YACE,MAAM,EAAE,iBAAiB;YACzB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,0DAA0D;YAChE,QAAQ,EACN,sEAAsE;gBACtE,oDAAoD;SACvD;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,mBAAmB,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,EAAE,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;QACtE,MAAM,OAAO,GAAG,iBAAiB,EAAE,CAAC;QAEpC,qCAAqC;QACrC,sFAAsF;QACtF,iFAAiF;QACjF,+EAA+E;QAC/E,iFAAiF;QACjF,+EAA+E;QAC/E,2DAA2D;QAC3D,MAAM,gBAAgB,GAAG,2BAA2B,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QACpE,MAAM,YAAY,GAAG,kBAAkB,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAEvD,IAAI,gBAAgB,IAAI,YAAY,EAAE,CAAC;YACrC,8EAA8E;YAC9E,8EAA8E;YAC9E,qDAAqD;YACrD,MAAM,UAAU,GAAG,KAAK,CAAC,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC;YACzC,MAAM,OAAO,GACX,KAAK,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAC,gBAAgB,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;YAC1F,MAAM,MAAM,GAAG,gBAAgB,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;YAC5E,IAAI,CAAC,OAAO,EAAE,CAAC;gBACb,MAAM,GAAG,CAAC,IAAI,CACZ,iBAAiB,EACjB,UAAU,KAAK,CAAC,EAAE,8FAA8F,EAChH,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,iBAAiB,CAAC,EAAE,CAC1C,CAAC;YACJ,CAAC;YACD,MAAM,GAAG,GAAG,MAAM,OAAO;iBACtB,mBAAmB,CAAC,OAAO,EAAE,MAAM,EAAE,KAAK,CAAC,aAAa,EAAE,KAAK,CAAC,aAAa,EAAE,GAAG,CAAC;iBACnF,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;gBACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;gBAC7D,IAAI,iCAAiC,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;oBAChD,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,UAAU,KAAK,CAAC,EAAE,eAAe,GAAG,EAAE,EAAE;wBAClE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;qBAChC,CAAC,CAAC;gBACL,CAAC;gBACD,MAAM,GAAG,CAAC;YACZ,CAAC,CAAC,CAAC;YACL,OAAO,GAAG,CAAC;QACb,CAAC;QAED,iBAAiB;QACjB,MAAM,GAAG,GAAG,MAAM,OAAO;aACtB,eAAe,CAAC,KAAK,CAAC,EAAE,CAAC,IAAI,EAAE,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,aAAa,EAAE,KAAK,CAAC,aAAa,EAAE,GAAG,CAAC;aAC3F,KAAK,CAAC,CAAC,GAAY,EAAE,EAAE;YACtB,MAAM,GAAG,GAAG,GAAG,YAAY,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YAC7D,IACE,sDAAsD,CAAC,IAAI,CAAC,GAAG,CAAC;gBAChE,uCAAuC,CAAC,IAAI,CAAC,GAAG,CAAC;gBACjD,8BAA8B,CAAC,IAAI,CAAC,GAAG,CAAC,EACxC,CAAC;gBACD,MAAM,GAAG,CAAC,IAAI,CACZ,eAAe,EACf,wBAAwB,KAAK,CAAC,IAAI,oEAAoE;oBACpG,8EAA8E,EAChF,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,eAAe,CAAC,EAAE,CACxC,CAAC;YACJ,CAAC;YACD,IAAI,yBAAyB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,GAAG,CAAC,IAAI,CAAC,WAAW,EAAE,MAAM,KAAK,CAAC,EAAE,wBAAwB,EAAE;oBAClE,GAAG,GAAG,CAAC,WAAW,CAAC,WAAW,CAAC;iBAChC,CAAC,CAAC;YACL,CAAC;YACD,MAAM,GAAG,CAAC;QACZ,CAAC,CAAC,CAAC;QACL,OAAO,GAAG,CAAC;IACb,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,KAAK,CAAC,IAAI,CAAC,gBAAgB,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;QACxC,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,KAAK,SAAS,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,IAAI,CAAC;QAC3D,KAAK,CAAC,IAAI,CAAC,aAAa,MAAM,CAAC,IAAI,kBAAkB,MAAM,CAAC,MAAM,CAAC,cAAc,EAAE,IAAI,IAAI,EAAE,CAAC,CAAC;QAC/F,IAAI,MAAM,CAAC,WAAW;YAAE,KAAK,CAAC,IAAI,CAAC,oBAAoB,MAAM,CAAC,WAAW,EAAE,CAAC,CAAC;QAC7E,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,6DAA6D;QAC7D,IAAI,MAAM,CAAC,GAAG,CAAC,MAAM,GAAG,GAAG,EAAE,CAAC;YAC5B,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;YAClB,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC;YACrC,KAAK,CAAC,IAAI,CAAC,MAAM,MAAM,CAAC,MAAM,CAAC,cAAc,EAAE,oBAAoB,CAAC,CAAC;YACrE,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACpB,CAAC;aAAM,CAAC;YACN,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;YAClB,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;YACvB,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACpB,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/tools/definitions/get-xrefs.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get-xrefs.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-xrefs.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyBjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;EAmH1B,CAAC"}
+{"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;;;;;;;;;;;;;;;;;;;;EAqH1B,CAAC"}

package/dist/mcp-server/tools/definitions/get-xrefs.tool.js

@@ -75,7 +75,9 @@ export const ensemblGetXrefs = tool('ensembl_get_xrefs', {
             .catch((err) => {
             const msg = err instanceof Error ? err.message : String(err);
             if (/not found/i.test(msg)) {
-                throw ctx.fail('not_found', `ID "${input.id}" not found in Ensembl.`);
+                throw ctx.fail('not_found', `ID "${input.id}" not found in Ensembl.`, {
+                    ...ctx.recoveryFor('not_found'),
+                });
             }
             throw err;
         });

package/dist/mcp-server/tools/definitions/get-xrefs.tool.js.map

@@ -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,CAAC,CAAC;YACxE,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"}
+{"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"}

package/dist/mcp-server/tools/definitions/list-species.tool.d.ts

@@ -5,11 +5,11 @@
 import { z } from '@cyanheads/mcp-ts-core';
 export declare const ensemblListSpecies: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     division: z.ZodOptional<z.ZodEnum<{
-        EnsemblVertebrates: "EnsemblVertebrates";
-        EnsemblPlants: "EnsemblPlants";
         EnsemblFungi: "EnsemblFungi";
         EnsemblMetazoa: "EnsemblMetazoa";
+        EnsemblPlants: "EnsemblPlants";
         EnsemblProtists: "EnsemblProtists";
+        EnsemblVertebrates: "EnsemblVertebrates";
     }>>;
     nameContains: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>, z.ZodObject<{

package/dist/mcp-server/tools/definitions/lookup-gene.tool.d.ts.map

@@ -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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAsP5B,CAAC"}
+{"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAmQ5B,CAAC"}

package/dist/mcp-server/tools/definitions/lookup-gene.tool.js

@@ -156,7 +156,9 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
             input.symbols?.length,
         ].filter(Boolean).length;
         if (inputCount > 1) {
-            throw ctx.fail('conflicting_input', 'Provide exactly one of: symbol, id, ids, or symbols.');
+            throw ctx.fail('conflicting_input', 'Provide exactly one of: symbol, id, ids, or symbols.', {
+                ...ctx.recoveryFor('conflicting_input'),
+            });
         }
         // --- Batch by IDs ---
         if (input.ids?.length) {
@@ -190,10 +192,12 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
                 .catch((err) => {
                 const msg = err instanceof Error ? err.message : String(err);
                 if (/not found|no stable id|no results|no valid lookup/i.test(msg)) {
-                    throw ctx.fail('not_found', `Gene symbol "${input.symbol}" not found in ${speciesStr}.`);
+                    throw ctx.fail('not_found', `Gene symbol "${input.symbol}" not found in ${speciesStr}.`, { ...ctx.recoveryFor('not_found') });
                 }
                 if (/species|invalid|unrecognized/i.test(msg)) {
-                    throw ctx.fail('invalid_species', `Species "${speciesStr}" not recognized by Ensembl.`);
+                    throw ctx.fail('invalid_species', `Species "${speciesStr}" not recognized by Ensembl.`, {
+                        ...ctx.recoveryFor('invalid_species'),
+                    });
                 }
                 throw err;
             });
@@ -206,13 +210,17 @@ export const ensemblLookupGene = tool('ensembl_lookup_gene', {
                 .catch((err) => {
                 const msg = err instanceof Error ? err.message : String(err);
                 if (/not found|no stable id/i.test(msg)) {
-                    throw ctx.fail('not_found', `Gene ID "${input.id}" not found in Ensembl.`);
+                    throw ctx.fail('not_found', `Gene ID "${input.id}" not found in Ensembl.`, {
+                        ...ctx.recoveryFor('not_found'),
+                    });
                 }
                 throw err;
             });
             return { gene };
         }
-        throw ctx.fail('no_input', 'Provide symbol (with species), id, ids, or symbols.');
+        throw ctx.fail('no_input', 'Provide symbol (with species), id, ids, or symbols.', {
+            ...ctx.recoveryFor('no_input'),
+        });
     },
     format: (result) => {
         const lines = [];