@cyanheads/protein-mcp-server 0.2.0 → 0.3.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/AGENTS.md +1 -1
- package/CLAUDE.md +1 -1
- package/README.md +21 -2
- package/changelog/0.2.x/0.2.1.md +16 -0
- package/changelog/0.3.x/0.3.0.md +20 -0
- package/dist/mcp-server/tools/definitions/_schemas.d.ts +11 -0
- package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/_schemas.js +25 -1
- package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts +1 -0
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.js +3 -1
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-similar.tool.js +7 -5
- package/dist/mcp-server/tools/definitions/find-similar.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts +22 -1
- package/dist/mcp-server/tools/definitions/get-annotations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-annotations.tool.js +118 -6
- package/dist/mcp-server/tools/definitions/get-annotations.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts +7 -0
- package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/get-structure.tool.js +32 -4
- package/dist/mcp-server/tools/definitions/get-structure.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts +1 -0
- package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-structures.tool.js +3 -1
- package/dist/mcp-server/tools/definitions/search-structures.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/track-ligands.tool.js +16 -4
- package/dist/mcp-server/tools/definitions/track-ligands.tool.js.map +1 -1
- package/dist/services/rcsb/rcsb-service.d.ts +9 -3
- package/dist/services/rcsb/rcsb-service.d.ts.map +1 -1
- package/dist/services/rcsb/rcsb-service.js +24 -11
- package/dist/services/rcsb/rcsb-service.js.map +1 -1
- package/dist/services/rcsb/types.d.ts +9 -0
- package/dist/services/rcsb/types.d.ts.map +1 -1
- package/dist/services/shared/attribution.d.ts +42 -0
- package/dist/services/shared/attribution.d.ts.map +1 -0
- package/dist/services/shared/attribution.js +111 -0
- package/dist/services/shared/attribution.js.map +1 -0
- package/package.json +1 -1
- package/server.json +3 -3
package/AGENTS.md
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
# Developer Protocol
|
|
2
2
|
|
|
3
3
|
**Server:** protein-mcp-server
|
|
4
|
-
**Version:** 0.
|
|
4
|
+
**Version:** 0.3.0
|
|
5
5
|
**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
|
|
6
6
|
**Engines:** Bun ≥1.3.0, Node ≥24.0.0
|
|
7
7
|
**MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
|
package/CLAUDE.md
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
# Developer Protocol
|
|
2
2
|
|
|
3
3
|
**Server:** protein-mcp-server
|
|
4
|
-
**Version:** 0.
|
|
4
|
+
**Version:** 0.3.0
|
|
5
5
|
**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.10`
|
|
6
6
|
**Engines:** Bun ≥1.3.0, Node ≥24.0.0
|
|
7
7
|
**MCP SDK:** `@modelcontextprotocol/sdk` ^1.29.0
|
package/README.md
CHANGED
|
@@ -7,7 +7,7 @@
|
|
|
7
7
|
|
|
8
8
|
<div align="center">
|
|
9
9
|
|
|
10
|
-
[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
|
|
11
11
|
|
|
12
12
|
</div>
|
|
13
13
|
|
|
@@ -62,6 +62,7 @@ Fetch structures with metadata and coordinate-file URLs, resolving across provid
|
|
|
62
62
|
- `source: best_available` takes UniProt accessions and returns the top federated model (experimental if one exists, else the best prediction)
|
|
63
63
|
- Per-ID partial success — unresolved IDs are listed in `failed[]`, not a batch-level error
|
|
64
64
|
- `include_coords` inlines coordinate content; when a batch overflows the response budget it returns a per-structure size outline, so you can re-call with `sections: [ids]` for specific structures
|
|
65
|
+
- Every response carries an `attribution` block naming the upstream data licenses and citations (see [Upstream data licensing](#upstream-data-licensing))
|
|
65
66
|
|
|
66
67
|
---
|
|
67
68
|
|
|
@@ -119,8 +120,10 @@ Sequence and functional annotation for a protein.
|
|
|
119
120
|
|
|
120
121
|
- UniProt features (domains, binding sites, PTMs) and natural sequence variants
|
|
121
122
|
- InterPro domain/family memberships (Pfam, PROSITE, …) with associated GO terms
|
|
122
|
-
- Provide a UniProt accession directly, or a PDB ID — resolved to
|
|
123
|
+
- Provide a UniProt accession directly, or a PDB ID — resolved to a UniProt accession via the structure's sequence cross-reference
|
|
124
|
+
- A multi-chain PDB entry can map to several accessions; the default is the deterministic lowest-author-chain pick, with the alternatives listed under `ambiguity`. Pass `chain` (an author chain ID, e.g. `A`) to select a specific one
|
|
123
125
|
- `include` scopes which annotation classes are fetched: `features`, `domains`, `variants`, or `all`
|
|
126
|
+
- Every response carries an `attribution` block naming the upstream data licenses and citations (see [Upstream data licensing](#upstream-data-licensing))
|
|
124
127
|
|
|
125
128
|
## Resources
|
|
126
129
|
|
|
@@ -340,6 +343,22 @@ bun run devcheck
|
|
|
340
343
|
bun run test
|
|
341
344
|
```
|
|
342
345
|
|
|
346
|
+
## Upstream data licensing
|
|
347
|
+
|
|
348
|
+
Structure and annotation data comes from public upstream databases, each under its own license. `protein_get_structure` and `protein_get_annotations` carry an `attribution` block on every response — the license, citation, and homepage for each source that contributed to that specific response — so the attribution obligation travels with the data to downstream consumers rather than living only here. CC BY / CC BY-SA sources require attribution on redistribution; CC0 sources are citation-only (attribution encouraged, not required).
|
|
349
|
+
|
|
350
|
+
| Source | Contributes to | License |
|
|
351
|
+
|:---|:---|:---|
|
|
352
|
+
| [RCSB PDB](https://www.rcsb.org/) | `protein_get_structure` — experimental records | CC0 1.0 Universal |
|
|
353
|
+
| [AlphaFold DB](https://alphafold.ebi.ac.uk/) | `protein_get_structure` — predicted models | CC BY 4.0 |
|
|
354
|
+
| [SWISS-MODEL](https://swissmodel.expasy.org/) | `protein_get_structure` — `best_available` models | CC BY-SA 4.0 |
|
|
355
|
+
| [BFVD](https://bfvd.steineggerlab.workers.dev/) | `protein_get_structure` — `best_available` models | CC BY 4.0 |
|
|
356
|
+
| [UniProt](https://www.uniprot.org/) | `protein_get_annotations` | CC BY 4.0 |
|
|
357
|
+
| [InterPro](https://www.ebi.ac.uk/interpro/) | `protein_get_annotations` — domain/family data | CC0 1.0 Universal |
|
|
358
|
+
| [GO](https://geneontology.org/) | `protein_get_annotations` — GO terms | CC BY 4.0 |
|
|
359
|
+
|
|
360
|
+
`best_available` federates predicted models through [3D-Beacons](https://3d-beacons.org/), so the `attribution` block credits the actual contributing provider (AlphaFold DB, SWISS-MODEL, BFVD, …); a provider without a curated license entry carries a `See provider terms` fallback pointing back to 3D-Beacons rather than a fabricated license. InterPro's own domain/family classifications are CC0; the GO terms carried alongside them are separately CC BY 4.0, so each is credited independently only when it actually contributes. Full citations for each source travel in the `attribution` block of the relevant tool responses. This covers upstream *data* licensing — the server's own code is licensed separately (see [License](#license)).
|
|
361
|
+
|
|
343
362
|
## License
|
|
344
363
|
|
|
345
364
|
Apache-2.0 — see [LICENSE](LICENSE) for details.
|
|
@@ -0,0 +1,16 @@
|
|
|
1
|
+
---
|
|
2
|
+
summary: "Nested cross-tab facet children now carry a truncated flag; declared error recovery hints reach the wire; protein_track_ligands binding_site honors limit."
|
|
3
|
+
breaking: false
|
|
4
|
+
security: false
|
|
5
|
+
---
|
|
6
|
+
|
|
7
|
+
# 0.2.1 — 2026-07-03
|
|
8
|
+
|
|
9
|
+
## Added
|
|
10
|
+
|
|
11
|
+
- **`protein_analyze_collection` / `protein_search_structures`** — nested cross-tab facet child dimensions now carry a `truncated` boolean when their bucket list is capped by `bucket_limit`; `renderFacets` appends `(truncated)` to the nested line in `content[]`. ([#13](https://github.com/cyanheads/protein-mcp-server/issues/13))
|
|
12
|
+
|
|
13
|
+
## Fixed
|
|
14
|
+
|
|
15
|
+
- **`protein_track_ligands` `binding_site`** — now caps returned instances to `limit` and emits a truncation notice, instead of returning every instance regardless of `limit`. ([#9](https://github.com/cyanheads/protein-mcp-server/issues/9))
|
|
16
|
+
- **Declared recovery hints** — `errors[].recovery` now reaches the wire (`data.recovery.hint`, mirrored into `content[]`) at throw sites across `protein_search_structures`, `protein_get_annotations`, `protein_get_structure`, `protein_find_similar`, `protein_track_ligands`, and `protein_analyze_collection`. ([#10](https://github.com/cyanheads/protein-mcp-server/issues/10))
|
|
@@ -0,0 +1,20 @@
|
|
|
1
|
+
---
|
|
2
|
+
summary: "protein_get_annotations disambiguates multi-chain PDB entries via a new chain input; protein_get_structure and protein_get_annotations both carry upstream data-source attribution (license + citation)."
|
|
3
|
+
breaking: false
|
|
4
|
+
security: false
|
|
5
|
+
---
|
|
6
|
+
|
|
7
|
+
# 0.3.0 — 2026-07-03
|
|
8
|
+
|
|
9
|
+
## Added
|
|
10
|
+
|
|
11
|
+
- **`protein_get_annotations` `chain`** — optional author chain ID (`auth_asym_id`) input disambiguates a multi-chain PDB entry to a specific UniProt accession; ignored when `uniprot` is supplied directly. ([#12](https://github.com/cyanheads/protein-mcp-server/issues/12))
|
|
12
|
+
- **`protein_get_annotations` `ambiguity`** — new optional output field listing every distinct UniProt mapping (chains, accession, protein name) and a notice, present when a PDB ID resolves to more than one accession and no `chain` was given. ([#12](https://github.com/cyanheads/protein-mcp-server/issues/12))
|
|
13
|
+
- **`chain_not_found`** — new declared error reason on `protein_get_annotations` for a supplied `chain` that matches no UniProt-mapped polymer entity in the resolved entry. ([#12](https://github.com/cyanheads/protein-mcp-server/issues/12))
|
|
14
|
+
- **`attribution`** — new output field on `protein_get_structure` and `protein_get_annotations`: license, citation, and homepage for every upstream source that contributed to the response (RCSB PDB, AlphaFold DB, SWISS-MODEL, BFVD, UniProt, InterPro, GO). `best_available` credits the real federated 3D-Beacons provider; an uncurated provider gets an honest "See provider terms" fallback rather than a fabricated license. ([#7](https://github.com/cyanheads/protein-mcp-server/issues/7))
|
|
15
|
+
- **README** — "Upstream data licensing" section documenting each source's license. ([#7](https://github.com/cyanheads/protein-mcp-server/issues/7))
|
|
16
|
+
|
|
17
|
+
## Changed
|
|
18
|
+
|
|
19
|
+
- **`RcsbService.resolveUniprot()`** → `resolveUniprotEntities()` — returns entity-grained `UniProtXref[]` (chains, accession, protein name) instead of a flat accession list. ([#12](https://github.com/cyanheads/protein-mcp-server/issues/12))
|
|
20
|
+
- **`protein_get_annotations` unqualified PDB resolution** — now picks the deterministic lowest-author-chain accession instead of an order dependent on upstream GraphQL entity ordering. ([#12](https://github.com/cyanheads/protein-mcp-server/issues/12))
|
|
@@ -19,6 +19,7 @@ export declare const facetDimensionSchema: z.ZodObject<{
|
|
|
19
19
|
label: z.ZodString;
|
|
20
20
|
count: z.ZodNumber;
|
|
21
21
|
}, z.core.$strip>>;
|
|
22
|
+
truncated: z.ZodOptional<z.ZodBoolean>;
|
|
22
23
|
}, z.core.$strip>>>;
|
|
23
24
|
}, z.core.$strip>>;
|
|
24
25
|
truncated: z.ZodOptional<z.ZodBoolean>;
|
|
@@ -28,4 +29,14 @@ export type FacetDimensionOutput = z.infer<typeof facetDimensionSchema>;
|
|
|
28
29
|
export declare function toFacetOutput(facet: FacetDimension, cap: number): FacetDimensionOutput;
|
|
29
30
|
/** Render a list of facet dimensions to markdown lines for `format()` parity. */
|
|
30
31
|
export declare function renderFacets(facets: FacetDimensionOutput[]): string[];
|
|
32
|
+
/** License + citation for one upstream data source that contributed to a response. */
|
|
33
|
+
export declare const attributionSchema: z.ZodObject<{
|
|
34
|
+
source: z.ZodString;
|
|
35
|
+
license: z.ZodString;
|
|
36
|
+
citation: z.ZodString;
|
|
37
|
+
homepage: z.ZodString;
|
|
38
|
+
}, z.core.$strip>;
|
|
39
|
+
export type AttributionOutput = z.infer<typeof attributionSchema>;
|
|
40
|
+
/** Render an attribution list to one compact markdown line per source for `format()` parity. */
|
|
41
|
+
export declare function renderAttribution(attributions: AttributionOutput[]): string[];
|
|
31
42
|
//# sourceMappingURL=_schemas.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"_schemas.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;
|
|
1
|
+
{"version":3,"file":"_schemas.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAoC/D,yCAAyC;AACzC,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;iBAW4B,CAAC;AAE9D,MAAM,MAAM,oBAAoB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAExE,oFAAoF;AACpF,wBAAgB,aAAa,CAAC,KAAK,EAAE,cAAc,EAAE,GAAG,EAAE,MAAM,GAAG,oBAAoB,CAmBtF;AAED,iFAAiF;AACjF,wBAAgB,YAAY,CAAC,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,EAAE,CAarE;AAED,sFAAsF;AACtF,eAAO,MAAM,iBAAiB;;;;;iBAWmD,CAAC;AAElF,MAAM,MAAM,iBAAiB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC;AAElE,gGAAgG;AAChG,wBAAgB,iBAAiB,CAAC,YAAY,EAAE,iBAAiB,EAAE,GAAG,MAAM,EAAE,CAM7E"}
|
|
@@ -18,6 +18,10 @@ const childDimensionSchema = z
|
|
|
18
18
|
.object({
|
|
19
19
|
dimension: z.string().describe('Nested dimension name.'),
|
|
20
20
|
buckets: z.array(leafBucketSchema).describe('Nested buckets within the parent bucket.'),
|
|
21
|
+
truncated: z
|
|
22
|
+
.boolean()
|
|
23
|
+
.optional()
|
|
24
|
+
.describe('True when this nested bucket list was capped by the per-dimension bucket limit.'),
|
|
21
25
|
})
|
|
22
26
|
.describe('A nested cross-tab dimension within a parent bucket.');
|
|
23
27
|
/** A top-level facet bucket, optionally carrying a nested cross-tab dimension. */
|
|
@@ -57,6 +61,7 @@ export function toFacetOutput(facet, cap) {
|
|
|
57
61
|
children: b.children.map((c) => ({
|
|
58
62
|
dimension: c.dimension,
|
|
59
63
|
buckets: c.buckets.slice(0, cap).map((cb) => ({ label: cb.label, count: cb.count })),
|
|
64
|
+
...(c.buckets.length > cap ? { truncated: true } : {}),
|
|
60
65
|
})),
|
|
61
66
|
}
|
|
62
67
|
: {}),
|
|
@@ -73,10 +78,29 @@ export function renderFacets(facets) {
|
|
|
73
78
|
lines.push(`- ${b.label}: ${b.count}`);
|
|
74
79
|
for (const c of b.children ?? []) {
|
|
75
80
|
const inner = c.buckets.map((cb) => `${cb.label}: ${cb.count}`).join(', ');
|
|
76
|
-
lines.push(` - ${c.dimension} → ${inner}`);
|
|
81
|
+
lines.push(` - ${c.dimension} → ${inner}${c.truncated ? ' (truncated)' : ''}`);
|
|
77
82
|
}
|
|
78
83
|
}
|
|
79
84
|
}
|
|
80
85
|
return lines;
|
|
81
86
|
}
|
|
87
|
+
/** License + citation for one upstream data source that contributed to a response. */
|
|
88
|
+
export const attributionSchema = z
|
|
89
|
+
.object({
|
|
90
|
+
source: z
|
|
91
|
+
.string()
|
|
92
|
+
.describe('Contributing data-source display name (e.g. "RCSB PDB", "AlphaFold DB", "SWISS-MODEL", "UniProt"). Open-ended — best_available structures are federated through 3D-Beacons providers.'),
|
|
93
|
+
license: z.string().describe('License the source data is released under (e.g. "CC BY 4.0").'),
|
|
94
|
+
citation: z.string().describe('Primary-literature citation to credit the source.'),
|
|
95
|
+
homepage: z.string().describe('Source homepage (absolute URL).'),
|
|
96
|
+
})
|
|
97
|
+
.describe('Upstream data-source attribution: license, citation, and homepage.');
|
|
98
|
+
/** Render an attribution list to one compact markdown line per source for `format()` parity. */
|
|
99
|
+
export function renderAttribution(attributions) {
|
|
100
|
+
const lines = [];
|
|
101
|
+
for (const a of attributions) {
|
|
102
|
+
lines.push(`- **${a.source}** (${a.license}) — ${a.citation} — ${a.homepage}`);
|
|
103
|
+
}
|
|
104
|
+
return lines;
|
|
105
|
+
}
|
|
82
106
|
//# sourceMappingURL=_schemas.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"_schemas.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,kCAAkC;AAClC,MAAM,gBAAgB,GAAG,CAAC;KACvB,MAAM,CAAC;IACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;IACpF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;CAC/D,CAAC;KACD,QAAQ,CAAC,yDAAyD,CAAC,CAAC;AAEvE,kEAAkE;AAClE,MAAM,oBAAoB,GAAG,CAAC;KAC3B,MAAM,CAAC;IACN,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;IACxD,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,QAAQ,CAAC,0CAA0C,CAAC;
|
|
1
|
+
{"version":3,"file":"_schemas.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,kCAAkC;AAClC,MAAM,gBAAgB,GAAG,CAAC;KACvB,MAAM,CAAC;IACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;IACpF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;CAC/D,CAAC;KACD,QAAQ,CAAC,yDAAyD,CAAC,CAAC;AAEvE,kEAAkE;AAClE,MAAM,oBAAoB,GAAG,CAAC;KAC3B,MAAM,CAAC;IACN,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;IACxD,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,QAAQ,CAAC,0CAA0C,CAAC;IACvF,SAAS,EAAE,CAAC;SACT,OAAO,EAAE;SACT,QAAQ,EAAE;SACV,QAAQ,CAAC,iFAAiF,CAAC;CAC/F,CAAC;KACD,QAAQ,CAAC,sDAAsD,CAAC,CAAC;AAEpE,kFAAkF;AAClF,MAAM,YAAY,GAAG,CAAC;KACnB,MAAM,CAAC;IACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wDAAwD,CAAC;IACpF,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;IAC9D,QAAQ,EAAE,CAAC;SACR,KAAK,CAAC,oBAAoB,CAAC;SAC3B,QAAQ,EAAE;SACV,QAAQ,CACP,uFAAuF,CACxF;CACJ,CAAC;KACD,QAAQ,CAAC,gFAAgF,CAAC,CAAC;AAE9F,yCAAyC;AACzC,MAAM,CAAC,MAAM,oBAAoB,GAAG,CAAC;KAClC,MAAM,CAAC;IACN,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,CAAC,gEAAgE,CAAC;IAC7E,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,QAAQ,CAAC,kDAAkD,CAAC;IAC3F,SAAS,EAAE,CAAC;SACT,OAAO,EAAE;SACT,QAAQ,EAAE;SACV,QAAQ,CAAC,kEAAkE,CAAC;CAChF,CAAC;KACD,QAAQ,CAAC,gDAAgD,CAAC,CAAC;AAI9D,oFAAoF;AACpF,MAAM,UAAU,aAAa,CAAC,KAAqB,EAAE,GAAW;IAC9D,MAAM,SAAS,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,GAAG,GAAG,CAAC;IAC7C,OAAO;QACL,SAAS,EAAE,KAAK,CAAC,SAAS;QAC1B,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC/C,KAAK,EAAE,CAAC,CAAC,KAAK;YACd,KAAK,EAAE,CAAC,CAAC,KAAK;YACd,GAAG,CAAC,CAAC,CAAC,QAAQ;gBACZ,CAAC,CAAC;oBACE,QAAQ,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;wBAC/B,SAAS,EAAE,CAAC,CAAC,SAAS;wBACtB,OAAO,EAAE,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC;wBACpF,GAAG,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;qBACvD,CAAC,CAAC;iBACJ;gBACH,CAAC,CAAC,EAAE,CAAC;SACR,CAAC,CAAC;QACH,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;KAC1C,CAAC;AACJ,CAAC;AAED,iFAAiF;AACjF,MAAM,UAAU,YAAY,CAAC,MAA8B;IACzD,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,SAAS,KAAK,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;QACvE,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,OAAO,EAAE,CAAC;YAC1B,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,KAAK,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;YACvC,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,QAAQ,IAAI,EAAE,EAAE,CAAC;gBACjC,MAAM,KAAK,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,GAAG,EAAE,CAAC,KAAK,KAAK,EAAE,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;gBAC3E,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,SAAS,MAAM,KAAK,GAAG,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAClF,CAAC;QACH,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED,sFAAsF;AACtF,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC;KAC/B,MAAM,CAAC;IACN,MAAM,EAAE,CAAC;SACN,MAAM,EAAE;SACR,QAAQ,CACP,uLAAuL,CACxL;IACH,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+DAA+D,CAAC;IAC7F,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;IAClF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;CACjE,CAAC;KACD,QAAQ,CAAC,oEAAoE,CAAC,CAAC;AAIlF,gGAAgG;AAChG,MAAM,UAAU,iBAAiB,CAAC,YAAiC;IACjE,MAAM,KAAK,GAAa,EAAE,CAAC;IAC3B,KAAK,MAAM,CAAC,IAAI,YAAY,EAAE,CAAC;QAC7B,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,MAAM,OAAO,CAAC,CAAC,OAAO,OAAO,CAAC,CAAC,QAAQ,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;IACjF,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC"}
|
|
@@ -45,6 +45,7 @@ export declare const analyzeCollection: import("@cyanheads/mcp-ts-core").ToolDef
|
|
|
45
45
|
label: z.ZodString;
|
|
46
46
|
count: z.ZodNumber;
|
|
47
47
|
}, z.core.$strip>>;
|
|
48
|
+
truncated: z.ZodOptional<z.ZodBoolean>;
|
|
48
49
|
}, z.core.$strip>>>;
|
|
49
50
|
}, z.core.$strip>>;
|
|
50
51
|
truncated: z.ZodOptional<z.ZodBoolean>;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"analyze-collection.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAOjE,eAAO,MAAM,iBAAiB
|
|
1
|
+
{"version":3,"file":"analyze-collection.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAOjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAyH5B,CAAC"}
|
|
@@ -86,7 +86,9 @@ export const analyzeCollection = tool('protein_analyze_collection', {
|
|
|
86
86
|
: 'experimental';
|
|
87
87
|
const [primary, secondary] = input.group_by;
|
|
88
88
|
if (!primary)
|
|
89
|
-
throw ctx.fail('unknown_dimension', 'group_by requires at least one dimension.'
|
|
89
|
+
throw ctx.fail('unknown_dimension', 'group_by requires at least one dimension.', {
|
|
90
|
+
...ctx.recoveryFor('unknown_dimension'),
|
|
91
|
+
});
|
|
90
92
|
const spec = buildFacetSpec(primary, input.interval, secondary);
|
|
91
93
|
const { total, facets } = await rcsb.analyzeFacets({
|
|
92
94
|
...(input.query ? { text: input.query } : {}),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"analyze-collection.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,qBAAqB,EAAE,MAAM,2BAA2B,CAAC;AAClF,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,OAAO,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AAElF,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IAClE,KAAK,EAAE,wCAAwC;IAC/C,WAAW,EACT,kGAAkG;QAClG,wGAAwG;QACxG,uGAAuG;QACvG,wGAAwG;QACxG,mDAAmD;IACrD,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,mBAAmB;YAC3B,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,0DAA0D;YAChE,QAAQ,EACN,2GAA2G;SAC9G;KACF;IAED,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC;aACpC,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,iFAAiF,CAAC;QAC9F,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,0EAA0E,CAAC;QACvF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QAC3E,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QAC7E,cAAc,EAAE,CAAC;aACd,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,EAAE;aACV,QAAQ,CAAC,wCAAwC,CAAC;QACrD,YAAY,EAAE,CAAC;aACZ,IAAI,CAAC,CAAC,cAAc,EAAE,WAAW,EAAE,KAAK,CAAC,CAAC;aAC1C,OAAO,CAAC,cAAc,CAAC;aACvB,QAAQ,CAAC,4DAA4D,CAAC;QACzE,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC;YACL,CAAC;iBACE,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,8DAA8D,CAAC;YAC3E,CAAC,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,OAAO,EAAE,SAAS,CAAC,CAAC,CAAC,QAAQ,CAAC,0CAA0C,CAAC;SAC1F,CAAC;aACD,QAAQ,EAAE;aACV,QAAQ,CACP,mGAAmG,CACpG;QACH,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,6EAA6E,CAAC;KAC3F,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;QACrE,MAAM,EAAE,CAAC,CAAC,KAAK,CAAC,oBAAoB,CAAC,CAAC,QAAQ,CAAC,6BAA6B,CAAC;KAC9E,CAAC;IAEF,UAAU,EAAE;QACV,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+CAA+C,CAAC;QACtF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;KAC/F;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,GAAG,GAAG,eAAe,EAAE,CAAC;QAC9B,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,IAAI,GAAG,CAAC,cAAc,CAAC;QACrD,MAAM,WAAW,GACf,KAAK,CAAC,YAAY,KAAK,KAAK;YAC1B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,KAAK,CAAC,YAAY,KAAK,WAAW;gBAClC,CAAC,CAAC,eAAe;gBACjB,CAAC,CAAC,cAAc,CAAC;QAEvB,MAAM,CAAC,OAAO,EAAE,SAAS,CAAC,GAAG,KAAK,CAAC,QAAQ,CAAC;QAC5C,IAAI,CAAC,OAAO;
|
|
1
|
+
{"version":3,"file":"analyze-collection.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/analyze-collection.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,qBAAqB,EAAE,MAAM,2BAA2B,CAAC;AAClF,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,OAAO,EAAE,oBAAoB,EAAE,YAAY,EAAE,aAAa,EAAE,MAAM,eAAe,CAAC;AAElF,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,4BAA4B,EAAE;IAClE,KAAK,EAAE,wCAAwC;IAC/C,WAAW,EACT,kGAAkG;QAClG,wGAAwG;QACxG,uGAAuG;QACvG,wGAAwG;QACxG,mDAAmD;IACrD,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,mBAAmB;YAC3B,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,0DAA0D;YAChE,QAAQ,EACN,2GAA2G;SAC9G;KACF;IAED,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC;aACpC,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,iFAAiF,CAAC;QAC9F,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,0EAA0E,CAAC;QACvF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QAC3E,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QAC7E,cAAc,EAAE,CAAC;aACd,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,EAAE;aACV,QAAQ,CAAC,wCAAwC,CAAC;QACrD,YAAY,EAAE,CAAC;aACZ,IAAI,CAAC,CAAC,cAAc,EAAE,WAAW,EAAE,KAAK,CAAC,CAAC;aAC1C,OAAO,CAAC,cAAc,CAAC;aACvB,QAAQ,CAAC,4DAA4D,CAAC;QACzE,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC;YACL,CAAC;iBACE,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,8DAA8D,CAAC;YAC3E,CAAC,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,OAAO,EAAE,SAAS,CAAC,CAAC,CAAC,QAAQ,CAAC,0CAA0C,CAAC;SAC1F,CAAC;aACD,QAAQ,EAAE;aACV,QAAQ,CACP,mGAAmG,CACpG;QACH,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,6EAA6E,CAAC;KAC3F,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;QACrE,MAAM,EAAE,CAAC,CAAC,KAAK,CAAC,oBAAoB,CAAC,CAAC,QAAQ,CAAC,6BAA6B,CAAC;KAC9E,CAAC;IAEF,UAAU,EAAE;QACV,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+CAA+C,CAAC;QACtF,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sDAAsD,CAAC;KAC/F;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,GAAG,GAAG,eAAe,EAAE,CAAC;QAC9B,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,IAAI,GAAG,CAAC,cAAc,CAAC;QACrD,MAAM,WAAW,GACf,KAAK,CAAC,YAAY,KAAK,KAAK;YAC1B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,KAAK,CAAC,YAAY,KAAK,WAAW;gBAClC,CAAC,CAAC,eAAe;gBACjB,CAAC,CAAC,cAAc,CAAC;QAEvB,MAAM,CAAC,OAAO,EAAE,SAAS,CAAC,GAAG,KAAK,CAAC,QAAQ,CAAC;QAC5C,IAAI,CAAC,OAAO;YACV,MAAM,GAAG,CAAC,IAAI,CAAC,mBAAmB,EAAE,2CAA2C,EAAE;gBAC/E,GAAG,GAAG,CAAC,WAAW,CAAC,mBAAmB,CAAC;aACxC,CAAC,CAAC;QACL,MAAM,IAAI,GAAG,cAAc,CAAC,OAAO,EAAE,KAAK,CAAC,QAAQ,EAAE,SAAS,CAAC,CAAC;QAEhE,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,CAChD;YACE,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC7C,GAAG,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,KAAK,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACvD,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACjD,GAAG,CAAC,OAAO,KAAK,CAAC,cAAc,KAAK,QAAQ;gBAC1C,CAAC,CAAC,EAAE,aAAa,EAAE,KAAK,CAAC,cAAc,EAAE;gBACzC,CAAC,CAAC,EAAE,CAAC;YACP,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;SACxC,EACD,CAAC,IAAI,CAAC,EACN,GAAG,CACJ,CAAC;QAEF,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,aAAa,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC;QACrD,IAAI,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,EAAE,CAAC;YACjC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,mCAAmC,GAAG,sEAAsE,CAC7G,CAAC;QACJ,CAAC;QACD,MAAM,SAAS,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,QAAQ,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;QAC9E,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC;YAAE,GAAG,CAAC,MAAM,CAAC,EAAE,KAAK,EAAE,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QAEvE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC;IAChC,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,CAAC,2BAA2B,MAAM,CAAC,KAAK,UAAU,CAAC,CAAC;QAC5E,KAAK,CAAC,IAAI,CAAC,GAAG,YAAY,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC;QAC3C,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
|
|
@@ -253,16 +253,18 @@ async function resolveSequence(input, ctx) {
|
|
|
253
253
|
if (input.pdb_id) {
|
|
254
254
|
const seq = await getRcsbService().getSequence(input.pdb_id, ctx);
|
|
255
255
|
if (!seq)
|
|
256
|
-
throw ctx.fail('no_sequence', `No protein sequence found for PDB entry ${input.pdb_id.toUpperCase()}
|
|
256
|
+
throw ctx.fail('no_sequence', `No protein sequence found for PDB entry ${input.pdb_id.toUpperCase()}.`, { ...ctx.recoveryFor('no_sequence') });
|
|
257
257
|
return seq.sequence;
|
|
258
258
|
}
|
|
259
259
|
if (input.uniprot) {
|
|
260
260
|
const seq = await getUniProtService().getSequence(input.uniprot, ctx);
|
|
261
261
|
if (!seq)
|
|
262
|
-
throw ctx.fail('no_sequence', `No sequence found for UniProt accession ${input.uniprot.toUpperCase()}
|
|
262
|
+
throw ctx.fail('no_sequence', `No sequence found for UniProt accession ${input.uniprot.toUpperCase()}.`, { ...ctx.recoveryFor('no_sequence') });
|
|
263
263
|
return seq;
|
|
264
264
|
}
|
|
265
|
-
throw ctx.fail('missing_query', 'Provide a sequence, pdb_id, or uniprot to search from.'
|
|
265
|
+
throw ctx.fail('missing_query', 'Provide a sequence, pdb_id, or uniprot to search from.', {
|
|
266
|
+
...ctx.recoveryFor('missing_query'),
|
|
267
|
+
});
|
|
266
268
|
}
|
|
267
269
|
/** Resolve a query coordinate file (PDB-format text) from a PDB ID or UniProt accession. */
|
|
268
270
|
async function resolveCoordinateFile(input, ctx) {
|
|
@@ -275,14 +277,14 @@ async function resolveCoordinateFile(input, ctx) {
|
|
|
275
277
|
if (input.uniprot && isUniProtAccession(input.uniprot)) {
|
|
276
278
|
const model = await getAlphaFoldService().getPrediction(input.uniprot, ctx);
|
|
277
279
|
if (!model?.pdbUrl) {
|
|
278
|
-
throw ctx.fail('no_sequence', `No predicted model with coordinates found for ${input.uniprot.toUpperCase()}
|
|
280
|
+
throw ctx.fail('no_sequence', `No predicted model with coordinates found for ${input.uniprot.toUpperCase()}.`, { ...ctx.recoveryFor('no_sequence') });
|
|
279
281
|
}
|
|
280
282
|
return {
|
|
281
283
|
content: await fetchCoordinateText(model.pdbUrl, ctx),
|
|
282
284
|
fileName: `${input.uniprot.toUpperCase()}.pdb`,
|
|
283
285
|
};
|
|
284
286
|
}
|
|
285
|
-
throw ctx.fail('missing_query', 'by:structure requires a pdb_id or uniprot accession to derive coordinates.');
|
|
287
|
+
throw ctx.fail('missing_query', 'by:structure requires a pdb_id or uniprot accession to derive coordinates.', { ...ctx.recoveryFor('missing_query') });
|
|
286
288
|
}
|
|
287
289
|
function fetchCoordinateText(url, ctx) {
|
|
288
290
|
return fetchText(url, ctx, {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"find-similar.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-similar.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAuB,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,mBAAmB,EAAE,MAAM,2CAA2C,CAAC;AAChF,OAAO,EAAwB,kBAAkB,EAAE,MAAM,yCAAyC,CAAC;AACnG,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,OAAO,EAAE,SAAS,EAAE,MAAM,2BAA2B,CAAC;AACtD,OAAO,EAAE,SAAS,EAAE,OAAO,EAAE,kBAAkB,EAAE,MAAM,kCAAkC,CAAC;AAC1F,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,oBAAoB,GAAG,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;AAClD,MAAM,aAAa,GAAG,OAAO,CAAC;AAE9B,MAAM,WAAW,GAAG,CAAC,CAAC,MAAM,CAAC;IAC3B,EAAE,EAAE,CAAC;SACF,IAAI,CAAC,CAAC,UAAU,EAAE,WAAW,CAAC,CAAC;SAC/B,QAAQ,CAAC,8DAA8D,CAAC;IAC3E,QAAQ,EAAE,CAAC;SACR,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,8DAA8D,CAAC;IAC3E,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;IAChF,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;IACtF,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sNAAsN,CACvN;IACH,SAAS,EAAE,CAAC;SACT,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;SACjB,QAAQ,EAAE;SACV,QAAQ,CACP,+FAA+F,CAChG;IACH,UAAU,EAAE,CAAC;SACV,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,EAAE;SACV,QAAQ,CAAC,2CAA2C,CAAC;IACxD,YAAY,EAAE,CAAC;SACZ,MAAM,EAAE;SACR,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,CAAC,CAAC;SACN,QAAQ,EAAE;SACV,QAAQ,CAAC,yDAAyD,CAAC;IACtE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,iCAAiC,CAAC;CAChG,CAAC,CAAC;AAEH,MAAM,YAAY,GAAG,CAAC,CAAC,MAAM,CAAC;IAC5B,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,UAAU,EAAE,WAAW,CAAC,CAAC,CAAC,QAAQ,CAAC,yBAAyB,CAAC;IACzE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6DAA6D,CAAC;IAC1F,MAAM,EAAE,CAAC;SACN,IAAI,CAAC,CAAC,UAAU,EAAE,WAAW,CAAC,CAAC;SAC/B,QAAQ,CAAC,8EAA8E,CAAC;IAC3F,QAAQ,EAAE,CAAC;SACR,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,8DAA8D,CAAC;IAC3E,IAAI,EAAE,CAAC;SACJ,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4DAA4D,CAAC;QACrF,MAAM,EAAE,CAAC;aACN,IAAI,CAAC,CAAC,cAAc,EAAE,WAAW,CAAC,CAAC;aACnC,QAAQ,CAAC,4DAA4D,CAAC;QACzE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,8BAA8B,CAAC;QACrE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QAC7E,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,4DAA4D,CAAC;QACzE,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,qDAAqD,CAAC;QAClE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;QAClF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;QACrF,gBAAgB,EAAE,CAAC;aAChB,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,+CAA+C,CAAC;KAC7D,CAAC;SACD,QAAQ,CAAC,0DAA0D,CAAC,CACxE;SACA,QAAQ,CAAC,+BAA+B,CAAC;CAC7C,CAAC,CAAC;AAEH,MAAM,eAAe,GAAG;IACtB,UAAU,EAAE,CAAC;SACV,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,yDAAyD,CAAC;IACtE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iDAAiD,CAAC;CAC1F,CAAC;AASF,MAAM,CAAC,MAAM,WAAW,GAAG,IAAI,CAAC,sBAAsB,EAAE;IACtD,KAAK,EAAE,kCAAkC;IACzC,WAAW,EACT,2FAA2F;QAC3F,wGAAwG;QACxG,qGAAqG;QACrG,wGAAwG;QACxG,yGAAyG;QACzG,gGAAgG;IAClG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,oDAAoD;YAC1D,QAAQ,EAAE,gFAAgF;SAC3F;QACD;YACE,MAAM,EAAE,aAAa;YACrB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,8EAA8E;YACpF,QAAQ,EACN,+FAA+F;SAClG;QACD;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;YACzC,IAAI,EAAE,mEAAmE;YACzE,SAAS,EAAE,IAAI;YACf,QAAQ,EACN,uGAAuG;SAC1G;QACD;YACE,MAAM,EAAE,kBAAkB;YAC1B,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,kFAAkF;YACxF,QAAQ,EACN,mIAAmI;SACtI;KACF;IAED,KAAK,EAAE,WAAW;IAClB,MAAM,EAAE,YAAY;IACpB,UAAU,EAAE,eAAe;IAE3B,OAAO,CAAC,KAAK,EAAE,GAAG;QAChB,MAAM,GAAG,GAAG,eAAe,EAAE,CAAC;QAC9B,IAAI,KAAK,CAAC,EAAE,KAAK,UAAU;YAAE,OAAO,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,cAAc,EAAE,GAAG,CAAC,CAAC;QAChF,OAAO,YAAY,CAAC,KAAK,EAAE,GAAG,CAAC,kBAAkB,EAAE,GAAG,CAAC,CAAC;IAC1D,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,CAAC,MAAM,MAAM,CAAC,MAAM,QAAQ,MAAM,CAAC,EAAE,OAAO,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC;QACrF,IAAI,MAAM,CAAC,QAAQ;YACjB,KAAK,CAAC,IAAI,CAAC,eAAe,MAAM,CAAC,QAAQ,sCAAsC,CAAC,CAAC;QACnF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;YAC5B,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC;YAC5C,IAAI,CAAC,CAAC,KAAK;gBAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;YACjC,MAAM,KAAK,GAAG;gBACZ,OAAO,CAAC,CAAC,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,IAAI;gBAC5D,OAAO,CAAC,CAAC,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,IAAI;gBAChE,OAAO,CAAC,CAAC,QAAQ,KAAK,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI;gBACrE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI;gBAC3C,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI;gBACjD,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,gBAAgB,EAAE,CAAC,CAAC,CAAC,IAAI;aACjE,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;YAClB,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC;gBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC;QACtD,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;AAEH,KAAK,UAAU,WAAW,CACxB,KAAuB,EACvB,WAAmB,EACnB,GAAQ;IAER,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;IAC9B,MAAM,QAAQ,GAAG,MAAM,eAAe,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;IAEnD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,cAAc,CACtC,QAAQ,EACR;QACE,GAAG,CAAC,OAAO,KAAK,CAAC,UAAU,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QAChF,GAAG,CAAC,OAAO,KAAK,CAAC,YAAY,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,KAAK,CAAC,YAAY,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QACtF,KAAK,EAAE,KAAK,CAAC,KAAK;KACnB,EACD,GAAG,CACJ,CAAC;IAEF,MAAM,QAAQ,GAAG,CAAC,GAAG,IAAI,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,WAAW,CAAC,CAAC;IAC7F,MAAM,QAAQ,GAAG,IAAI,GAAG,EAAqB,CAAC;IAC9C,IAAI,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,KAAK,MAAM,IAAI,IAAI,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,GAAG,CAAC;YAAE,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,CAAC;IACvF,CAAC;IAED,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;IAC/B,IAAI,MAAM,CAAC,IAAI,CAAC,MAAM,KAAK,CAAC;QAC1B,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,4EAA4E,CAAC,CAAC;IAElG,OAAO;QACL,EAAE,EAAE,UAAU;QACd,MAAM,EAAE,cAAc;QACtB,MAAM,EAAE,UAAU;QAClB,IAAI,EAAE,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;YAC1B,MAAM,IAAI,GAAG,QAAQ,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;YAC3C,OAAO;gBACL,EAAE,EAAE,CAAC,CAAC,EAAE;gBACR,MAAM,EAAE,cAAuB;gBAC/B,KAAK,EAAE,CAAC,CAAC,KAAK;gBACd,GAAG,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,IAAI,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;gBAC7C,GAAG,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;aAC/D,CAAC;QACJ,CAAC,CAAC;KACH,CAAC;AACJ,CAAC;AAED,KAAK,UAAU,YAAY,CACzB,KAAuB,EACvB,SAAiB,EACjB,GAAQ;IAER,MAAM,QAAQ,GAAG,kBAAkB,EAAE,CAAC;IACtC,IAAI,OAAwB,CAAC;IAC7B,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;QACpB,kFAAkF;QAClF,OAAO,GAAG,MAAM,QAAQ,CAAC,MAAM,CAC7B,EAAE,QAAQ,EAAE,KAAK,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,SAAS,EAAE,EAC5D,GAAG,CACJ,CAAC;IACJ,CAAC;SAAM,CAAC;QACN,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,MAAM,qBAAqB,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;QACtE,OAAO,GAAG,MAAM,QAAQ,CAAC,MAAM,CAC7B;YACE,WAAW,EAAE,OAAO;YACpB,QAAQ;YACR,SAAS,EACP,KAAK,CAAC,SAAS,IAAI,KAAK,CAAC,SAAS,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,oBAAoB;YACxF,IAAI,EAAE,aAAa;YACnB,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,SAAS;SACV,EACD,GAAG,CACJ,CAAC;IACJ,CAAC;IAED,IAAI,OAAO,CAAC,MAAM,KAAK,WAAW,EAAE,CAAC;QACnC,MAAM,GAAG,CAAC,IAAI,CACZ,kBAAkB,EAClB,mBAAmB,OAAO,CAAC,QAAQ,yBAAyB,EAC5D,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,kBAAkB,CAAC,EAAE,CAC3C,CAAC;IACJ,CAAC;IACD,IAAI,OAAO,CAAC,MAAM,KAAK,QAAQ,EAAE,CAAC;QAChC,MAAM,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,2BAA2B,OAAO,CAAC,KAAK,EAAE,EAAE;YAC1E,QAAQ,EAAE;gBACR,IAAI,EAAE,8EAA8E;aACrF;SACF,CAAC,CAAC;IACL,CAAC;IACD,IAAI,OAAO,CAAC,MAAM,KAAK,WAAW,EAAE,CAAC;QACnC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,wCAAwC,OAAO,CAAC,QAAQ,0DAA0D,OAAO,CAAC,QAAQ,cAAc,CACjJ,CAAC;QACF,OAAO;YACL,EAAE,EAAE,WAAW;YACf,MAAM,EAAE,UAAU;YAClB,MAAM,EAAE,WAAW;YACnB,QAAQ,EAAE,OAAO,CAAC,QAAQ;YAC1B,IAAI,EAAE,EAAE;SACT,CAAC;IACJ,CAAC;IAED,IAAI,OAAO,CAAC,IAAI,CAAC,MAAM,KAAK,CAAC;QAC3B,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,mEAAmE,CAAC,CAAC;IACzF,OAAO;QACL,EAAE,EAAE,WAAW;QACf,MAAM,EAAE,UAAU;QAClB,MAAM,EAAE,UAAU;QAClB,IAAI,EAAE,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC7B,EAAE,EAAE,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,gBAAgB,IAAI,CAAC,CAAC,MAAM;YAC7C,MAAM,EAAE,CAAC,CAAC,UAAU,KAAK,WAAW,CAAC,CAAC,CAAE,WAAqB,CAAC,CAAC,CAAE,cAAwB;YACzF,GAAG,CAAC,OAAO,CAAC,CAAC,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC1D,GAAG,CAAC,OAAO,CAAC,CAAC,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC7D,GAAG,CAAC,OAAO,CAAC,CAAC,gBAAgB,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,CAAC,CAAC,gBAAgB,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACnF,QAAQ,EAAE,CAAC,CAAC,QAAQ;YACpB,GAAG,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,gBAAgB,EAAE,CAAC,CAAC,gBAAgB,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;SACxE,CAAC,CAAC;KACJ,CAAC;AACJ,CAAC;AAED,qFAAqF;AACrF,KAAK,UAAU,eAAe,CAAC,KAAuB,EAAE,GAAQ;IAC9D,IAAI,KAAK,CAAC,QAAQ;QAAE,OAAO,KAAK,CAAC,QAAQ,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;IAC9D,IAAI,KAAK,CAAC,MAAM,EAAE,CAAC;QACjB,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;QAClE,IAAI,CAAC,GAAG;YACN,MAAM,GAAG,CAAC,IAAI,CACZ,aAAa,EACb,2CAA2C,KAAK,CAAC,MAAM,CAAC,WAAW,EAAE,GAAG,CACzE,CAAC;QACJ,OAAO,GAAG,CAAC,QAAQ,CAAC;IACtB,CAAC;IACD,IAAI,KAAK,CAAC,OAAO,EAAE,CAAC;QAClB,MAAM,GAAG,GAAG,MAAM,iBAAiB,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC;QACtE,IAAI,CAAC,GAAG;YACN,MAAM,GAAG,CAAC,IAAI,CACZ,aAAa,EACb,2CAA2C,KAAK,CAAC,OAAO,CAAC,WAAW,EAAE,GAAG,CAC1E,CAAC;QACJ,OAAO,GAAG,CAAC;IACb,CAAC;IACD,MAAM,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,wDAAwD,CAAC,CAAC;AAC5F,CAAC;AAED,4FAA4F;AAC5F,KAAK,UAAU,qBAAqB,CAClC,KAAuB,EACvB,GAAQ;IAER,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;IAC9B,IAAI,KAAK,CAAC,MAAM,IAAI,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,EAAE,CAAC;QAC1C,MAAM,EAAE,GAAG,KAAK,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC;QACtC,MAAM,OAAO,GAAG,MAAM,mBAAmB,CAAC,IAAI,CAAC,iBAAiB,CAAC,EAAE,EAAE,KAAK,CAAC,EAAE,GAAG,CAAC,CAAC;QAClF,OAAO,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC;IAC5C,CAAC;IACD,IAAI,KAAK,CAAC,OAAO,IAAI,kBAAkB,CAAC,KAAK,CAAC,OAAO,CAAC,EAAE,CAAC;QACvD,MAAM,KAAK,GAAG,MAAM,mBAAmB,EAAE,CAAC,aAAa,CAAC,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC;QAC5E,IAAI,CAAC,KAAK,EAAE,MAAM,EAAE,CAAC;YACnB,MAAM,GAAG,CAAC,IAAI,CACZ,aAAa,EACb,iDAAiD,KAAK,CAAC,OAAO,CAAC,WAAW,EAAE,GAAG,CAChF,CAAC;QACJ,CAAC;QACD,OAAO;YACL,OAAO,EAAE,MAAM,mBAAmB,CAAC,KAAK,CAAC,MAAM,EAAE,GAAG,CAAC;YACrD,QAAQ,EAAE,GAAG,KAAK,CAAC,OAAO,CAAC,WAAW,EAAE,MAAM;SAC/C,CAAC;IACJ,CAAC;IACD,MAAM,GAAG,CAAC,IAAI,CACZ,eAAe,EACf,4EAA4E,CAC7E,CAAC;AACJ,CAAC;AAED,SAAS,mBAAmB,CAAC,GAAW,EAAE,GAAQ;IAChD,OAAO,SAAS,CAAC,GAAG,EAAE,GAAG,EAAE;QACzB,SAAS,EAAE,8BAA8B;QACzC,KAAK,EAAE,iBAAiB;QACxB,WAAW,EAAE,GAAG;QAChB,UAAU,EAAE,CAAC;KACd,CAAC,CAAC;AACL,CAAC"}
|
|
1
|
+
{"version":3,"file":"find-similar.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-similar.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAuB,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACtE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,mBAAmB,EAAE,MAAM,2CAA2C,CAAC;AAChF,OAAO,EAAwB,kBAAkB,EAAE,MAAM,yCAAyC,CAAC;AACnG,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,OAAO,EAAE,SAAS,EAAE,MAAM,2BAA2B,CAAC;AACtD,OAAO,EAAE,SAAS,EAAE,OAAO,EAAE,kBAAkB,EAAE,MAAM,kCAAkC,CAAC;AAC1F,OAAO,EAAE,iBAAiB,EAAE,MAAM,uCAAuC,CAAC;AAE1E,MAAM,oBAAoB,GAAG,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;AAClD,MAAM,aAAa,GAAG,OAAO,CAAC;AAE9B,MAAM,WAAW,GAAG,CAAC,CAAC,MAAM,CAAC;IAC3B,EAAE,EAAE,CAAC;SACF,IAAI,CAAC,CAAC,UAAU,EAAE,WAAW,CAAC,CAAC;SAC/B,QAAQ,CAAC,8DAA8D,CAAC;IAC3E,QAAQ,EAAE,CAAC;SACR,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,8DAA8D,CAAC;IAC3E,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;IAChF,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;IACtF,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,sNAAsN,CACvN;IACH,SAAS,EAAE,CAAC;SACT,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;SACjB,QAAQ,EAAE;SACV,QAAQ,CACP,+FAA+F,CAChG;IACH,UAAU,EAAE,CAAC;SACV,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,EAAE;SACV,QAAQ,CAAC,2CAA2C,CAAC;IACxD,YAAY,EAAE,CAAC;SACZ,MAAM,EAAE;SACR,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,CAAC,CAAC;SACN,QAAQ,EAAE;SACV,QAAQ,CAAC,yDAAyD,CAAC;IACtE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,iCAAiC,CAAC;CAChG,CAAC,CAAC;AAEH,MAAM,YAAY,GAAG,CAAC,CAAC,MAAM,CAAC;IAC5B,EAAE,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,UAAU,EAAE,WAAW,CAAC,CAAC,CAAC,QAAQ,CAAC,yBAAyB,CAAC;IACzE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6DAA6D,CAAC;IAC1F,MAAM,EAAE,CAAC;SACN,IAAI,CAAC,CAAC,UAAU,EAAE,WAAW,CAAC,CAAC;SAC/B,QAAQ,CAAC,8EAA8E,CAAC;IAC3F,QAAQ,EAAE,CAAC;SACR,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,8DAA8D,CAAC;IAC3E,IAAI,EAAE,CAAC;SACJ,KAAK,CACJ,CAAC;SACE,MAAM,CAAC;QACN,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,4DAA4D,CAAC;QACrF,MAAM,EAAE,CAAC;aACN,IAAI,CAAC,CAAC,cAAc,EAAE,WAAW,CAAC,CAAC;aACnC,QAAQ,CAAC,4DAA4D,CAAC;QACzE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,8BAA8B,CAAC;QACrE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QAC7E,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,4DAA4D,CAAC;QACzE,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,qDAAqD,CAAC;QAClE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;QAClF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;QACrF,gBAAgB,EAAE,CAAC;aAChB,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,+CAA+C,CAAC;KAC7D,CAAC;SACD,QAAQ,CAAC,0DAA0D,CAAC,CACxE;SACA,QAAQ,CAAC,+BAA+B,CAAC;CAC7C,CAAC,CAAC;AAEH,MAAM,eAAe,GAAG;IACtB,UAAU,EAAE,CAAC;SACV,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,yDAAyD,CAAC;IACtE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iDAAiD,CAAC;CAC1F,CAAC;AASF,MAAM,CAAC,MAAM,WAAW,GAAG,IAAI,CAAC,sBAAsB,EAAE;IACtD,KAAK,EAAE,kCAAkC;IACzC,WAAW,EACT,2FAA2F;QAC3F,wGAAwG;QACxG,qGAAqG;QACrG,wGAAwG;QACxG,yGAAyG;QACzG,gGAAgG;IAClG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,aAAa;YACpC,IAAI,EAAE,oDAAoD;YAC1D,QAAQ,EAAE,gFAAgF;SAC3F;QACD;YACE,MAAM,EAAE,aAAa;YACrB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,8EAA8E;YACpF,QAAQ,EACN,+FAA+F;SAClG;QACD;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;YACzC,IAAI,EAAE,mEAAmE;YACzE,SAAS,EAAE,IAAI;YACf,QAAQ,EACN,uGAAuG;SAC1G;QACD;YACE,MAAM,EAAE,kBAAkB;YAC1B,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,kFAAkF;YACxF,QAAQ,EACN,mIAAmI;SACtI;KACF;IAED,KAAK,EAAE,WAAW;IAClB,MAAM,EAAE,YAAY;IACpB,UAAU,EAAE,eAAe;IAE3B,OAAO,CAAC,KAAK,EAAE,GAAG;QAChB,MAAM,GAAG,GAAG,eAAe,EAAE,CAAC;QAC9B,IAAI,KAAK,CAAC,EAAE,KAAK,UAAU;YAAE,OAAO,WAAW,CAAC,KAAK,EAAE,GAAG,CAAC,cAAc,EAAE,GAAG,CAAC,CAAC;QAChF,OAAO,YAAY,CAAC,KAAK,EAAE,GAAG,CAAC,kBAAkB,EAAE,GAAG,CAAC,CAAC;IAC1D,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,CAAC,MAAM,MAAM,CAAC,MAAM,QAAQ,MAAM,CAAC,EAAE,OAAO,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC;QACrF,IAAI,MAAM,CAAC,QAAQ;YACjB,KAAK,CAAC,IAAI,CAAC,eAAe,MAAM,CAAC,QAAQ,sCAAsC,CAAC,CAAC;QACnF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;YAC5B,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,MAAM,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC;YAC5C,IAAI,CAAC,CAAC,KAAK;gBAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC;YACjC,MAAM,KAAK,GAAG;gBACZ,OAAO,CAAC,CAAC,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,IAAI;gBAC5D,OAAO,CAAC,CAAC,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,IAAI;gBAChE,OAAO,CAAC,CAAC,QAAQ,KAAK,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI;gBACrE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI;gBAC3C,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,iBAAiB,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,IAAI;gBACjD,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,gBAAgB,EAAE,CAAC,CAAC,CAAC,IAAI;aACjE,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;YAClB,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC;gBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC;QACtD,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;AAEH,KAAK,UAAU,WAAW,CACxB,KAAuB,EACvB,WAAmB,EACnB,GAAQ;IAER,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;IAC9B,MAAM,QAAQ,GAAG,MAAM,eAAe,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;IAEnD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,cAAc,CACtC,QAAQ,EACR;QACE,GAAG,CAAC,OAAO,KAAK,CAAC,UAAU,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QAChF,GAAG,CAAC,OAAO,KAAK,CAAC,YAAY,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,KAAK,CAAC,YAAY,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;QACtF,KAAK,EAAE,KAAK,CAAC,KAAK;KACnB,EACD,GAAG,CACJ,CAAC;IAEF,MAAM,QAAQ,GAAG,CAAC,GAAG,IAAI,GAAG,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,WAAW,CAAC,CAAC;IAC7F,MAAM,QAAQ,GAAG,IAAI,GAAG,EAAqB,CAAC;IAC9C,IAAI,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACxB,KAAK,MAAM,IAAI,IAAI,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,GAAG,CAAC;YAAE,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,CAAC;IACvF,CAAC;IAED,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;IAC/B,IAAI,MAAM,CAAC,IAAI,CAAC,MAAM,KAAK,CAAC;QAC1B,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,4EAA4E,CAAC,CAAC;IAElG,OAAO;QACL,EAAE,EAAE,UAAU;QACd,MAAM,EAAE,cAAc;QACtB,MAAM,EAAE,UAAU;QAClB,IAAI,EAAE,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;YAC1B,MAAM,IAAI,GAAG,QAAQ,CAAC,GAAG,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;YAC3C,OAAO;gBACL,EAAE,EAAE,CAAC,CAAC,EAAE;gBACR,MAAM,EAAE,cAAuB;gBAC/B,KAAK,EAAE,CAAC,CAAC,KAAK;gBACd,GAAG,CAAC,IAAI,EAAE,KAAK,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,IAAI,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;gBAC7C,GAAG,CAAC,IAAI,EAAE,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;aAC/D,CAAC;QACJ,CAAC,CAAC;KACH,CAAC;AACJ,CAAC;AAED,KAAK,UAAU,YAAY,CACzB,KAAuB,EACvB,SAAiB,EACjB,GAAQ;IAER,MAAM,QAAQ,GAAG,kBAAkB,EAAE,CAAC;IACtC,IAAI,OAAwB,CAAC;IAC7B,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;QACpB,kFAAkF;QAClF,OAAO,GAAG,MAAM,QAAQ,CAAC,MAAM,CAC7B,EAAE,QAAQ,EAAE,KAAK,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,SAAS,EAAE,EAC5D,GAAG,CACJ,CAAC;IACJ,CAAC;SAAM,CAAC;QACN,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,MAAM,qBAAqB,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC;QACtE,OAAO,GAAG,MAAM,QAAQ,CAAC,MAAM,CAC7B;YACE,WAAW,EAAE,OAAO;YACpB,QAAQ;YACR,SAAS,EACP,KAAK,CAAC,SAAS,IAAI,KAAK,CAAC,SAAS,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,SAAS,CAAC,CAAC,CAAC,oBAAoB;YACxF,IAAI,EAAE,aAAa;YACnB,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,SAAS;SACV,EACD,GAAG,CACJ,CAAC;IACJ,CAAC;IAED,IAAI,OAAO,CAAC,MAAM,KAAK,WAAW,EAAE,CAAC;QACnC,MAAM,GAAG,CAAC,IAAI,CACZ,kBAAkB,EAClB,mBAAmB,OAAO,CAAC,QAAQ,yBAAyB,EAC5D,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,kBAAkB,CAAC,EAAE,CAC3C,CAAC;IACJ,CAAC;IACD,IAAI,OAAO,CAAC,MAAM,KAAK,QAAQ,EAAE,CAAC;QAChC,MAAM,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,2BAA2B,OAAO,CAAC,KAAK,EAAE,EAAE;YAC1E,QAAQ,EAAE;gBACR,IAAI,EAAE,8EAA8E;aACrF;SACF,CAAC,CAAC;IACL,CAAC;IACD,IAAI,OAAO,CAAC,MAAM,KAAK,WAAW,EAAE,CAAC;QACnC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,wCAAwC,OAAO,CAAC,QAAQ,0DAA0D,OAAO,CAAC,QAAQ,cAAc,CACjJ,CAAC;QACF,OAAO;YACL,EAAE,EAAE,WAAW;YACf,MAAM,EAAE,UAAU;YAClB,MAAM,EAAE,WAAW;YACnB,QAAQ,EAAE,OAAO,CAAC,QAAQ;YAC1B,IAAI,EAAE,EAAE;SACT,CAAC;IACJ,CAAC;IAED,IAAI,OAAO,CAAC,IAAI,CAAC,MAAM,KAAK,CAAC;QAC3B,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,mEAAmE,CAAC,CAAC;IACzF,OAAO;QACL,EAAE,EAAE,WAAW;QACf,MAAM,EAAE,UAAU;QAClB,MAAM,EAAE,UAAU;QAClB,IAAI,EAAE,OAAO,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC7B,EAAE,EAAE,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,gBAAgB,IAAI,CAAC,CAAC,MAAM;YAC7C,MAAM,EAAE,CAAC,CAAC,UAAU,KAAK,WAAW,CAAC,CAAC,CAAE,WAAqB,CAAC,CAAC,CAAE,cAAwB;YACzF,GAAG,CAAC,OAAO,CAAC,CAAC,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC1D,GAAG,CAAC,OAAO,CAAC,CAAC,MAAM,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YAC7D,GAAG,CAAC,OAAO,CAAC,CAAC,gBAAgB,KAAK,QAAQ,CAAC,CAAC,CAAC,EAAE,QAAQ,EAAE,CAAC,CAAC,gBAAgB,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;YACnF,QAAQ,EAAE,CAAC,CAAC,QAAQ;YACpB,GAAG,CAAC,CAAC,CAAC,gBAAgB,CAAC,CAAC,CAAC,EAAE,gBAAgB,EAAE,CAAC,CAAC,gBAAgB,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;SACxE,CAAC,CAAC;KACJ,CAAC;AACJ,CAAC;AAED,qFAAqF;AACrF,KAAK,UAAU,eAAe,CAAC,KAAuB,EAAE,GAAQ;IAC9D,IAAI,KAAK,CAAC,QAAQ;QAAE,OAAO,KAAK,CAAC,QAAQ,CAAC,OAAO,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;IAC9D,IAAI,KAAK,CAAC,MAAM,EAAE,CAAC;QACjB,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,MAAM,EAAE,GAAG,CAAC,CAAC;QAClE,IAAI,CAAC,GAAG;YACN,MAAM,GAAG,CAAC,IAAI,CACZ,aAAa,EACb,2CAA2C,KAAK,CAAC,MAAM,CAAC,WAAW,EAAE,GAAG,EACxE,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,aAAa,CAAC,EAAE,CACtC,CAAC;QACJ,OAAO,GAAG,CAAC,QAAQ,CAAC;IACtB,CAAC;IACD,IAAI,KAAK,CAAC,OAAO,EAAE,CAAC;QAClB,MAAM,GAAG,GAAG,MAAM,iBAAiB,EAAE,CAAC,WAAW,CAAC,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC;QACtE,IAAI,CAAC,GAAG;YACN,MAAM,GAAG,CAAC,IAAI,CACZ,aAAa,EACb,2CAA2C,KAAK,CAAC,OAAO,CAAC,WAAW,EAAE,GAAG,EACzE,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,aAAa,CAAC,EAAE,CACtC,CAAC;QACJ,OAAO,GAAG,CAAC;IACb,CAAC;IACD,MAAM,GAAG,CAAC,IAAI,CAAC,eAAe,EAAE,wDAAwD,EAAE;QACxF,GAAG,GAAG,CAAC,WAAW,CAAC,eAAe,CAAC;KACpC,CAAC,CAAC;AACL,CAAC;AAED,4FAA4F;AAC5F,KAAK,UAAU,qBAAqB,CAClC,KAAuB,EACvB,GAAQ;IAER,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;IAC9B,IAAI,KAAK,CAAC,MAAM,IAAI,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,EAAE,CAAC;QAC1C,MAAM,EAAE,GAAG,KAAK,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC;QACtC,MAAM,OAAO,GAAG,MAAM,mBAAmB,CAAC,IAAI,CAAC,iBAAiB,CAAC,EAAE,EAAE,KAAK,CAAC,EAAE,GAAG,CAAC,CAAC;QAClF,OAAO,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,EAAE,MAAM,EAAE,CAAC;IAC5C,CAAC;IACD,IAAI,KAAK,CAAC,OAAO,IAAI,kBAAkB,CAAC,KAAK,CAAC,OAAO,CAAC,EAAE,CAAC;QACvD,MAAM,KAAK,GAAG,MAAM,mBAAmB,EAAE,CAAC,aAAa,CAAC,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC;QAC5E,IAAI,CAAC,KAAK,EAAE,MAAM,EAAE,CAAC;YACnB,MAAM,GAAG,CAAC,IAAI,CACZ,aAAa,EACb,iDAAiD,KAAK,CAAC,OAAO,CAAC,WAAW,EAAE,GAAG,EAC/E,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,aAAa,CAAC,EAAE,CACtC,CAAC;QACJ,CAAC;QACD,OAAO;YACL,OAAO,EAAE,MAAM,mBAAmB,CAAC,KAAK,CAAC,MAAM,EAAE,GAAG,CAAC;YACrD,QAAQ,EAAE,GAAG,KAAK,CAAC,OAAO,CAAC,WAAW,EAAE,MAAM;SAC/C,CAAC;IACJ,CAAC;IACD,MAAM,GAAG,CAAC,IAAI,CACZ,eAAe,EACf,4EAA4E,EAC5E,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,eAAe,CAAC,EAAE,CACxC,CAAC;AACJ,CAAC;AAED,SAAS,mBAAmB,CAAC,GAAW,EAAE,GAAQ;IAChD,OAAO,SAAS,CAAC,GAAG,EAAE,GAAG,EAAE;QACzB,SAAS,EAAE,8BAA8B;QACzC,KAAK,EAAE,iBAAiB;QACxB,WAAW,EAAE,GAAG;QAChB,UAAU,EAAE,CAAC;KACd,CAAC,CAAC;AACL,CAAC"}
|
|
@@ -2,7 +2,8 @@
|
|
|
2
2
|
* @fileoverview protein_get_annotations — sequence & functional annotation for a
|
|
3
3
|
* protein: UniProt features (domains, binding sites, PTMs, variants) and InterPro
|
|
4
4
|
* domain/family memberships with GO terms. Keyed by UniProt accession; resolves a
|
|
5
|
-
* PDB ID to its accession when needed
|
|
5
|
+
* PDB ID to its accession when needed — deterministically by default, by author
|
|
6
|
+
* chain when a multi-chain entry is ambiguous. Carries upstream data attribution.
|
|
6
7
|
* @module mcp-server/tools/definitions/get-annotations.tool
|
|
7
8
|
*/
|
|
8
9
|
import { z } from '@cyanheads/mcp-ts-core';
|
|
@@ -10,6 +11,7 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
|
|
|
10
11
|
export declare const getAnnotations: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
|
|
11
12
|
uniprot: z.ZodOptional<z.ZodString>;
|
|
12
13
|
pdb_id: z.ZodOptional<z.ZodString>;
|
|
14
|
+
chain: z.ZodOptional<z.ZodString>;
|
|
13
15
|
include: z.ZodDefault<z.ZodEnum<{
|
|
14
16
|
all: "all";
|
|
15
17
|
features: "features";
|
|
@@ -46,11 +48,30 @@ export declare const getAnnotations: import("@cyanheads/mcp-ts-core").ToolDefini
|
|
|
46
48
|
category: z.ZodOptional<z.ZodString>;
|
|
47
49
|
}, z.core.$strip>>;
|
|
48
50
|
}, z.core.$strip>>>;
|
|
51
|
+
ambiguity: z.ZodOptional<z.ZodObject<{
|
|
52
|
+
accessions: z.ZodArray<z.ZodObject<{
|
|
53
|
+
chain: z.ZodArray<z.ZodString>;
|
|
54
|
+
accession: z.ZodString;
|
|
55
|
+
proteinName: z.ZodOptional<z.ZodString>;
|
|
56
|
+
}, z.core.$strip>>;
|
|
57
|
+
notice: z.ZodString;
|
|
58
|
+
}, z.core.$strip>>;
|
|
59
|
+
attribution: z.ZodArray<z.ZodObject<{
|
|
60
|
+
source: z.ZodString;
|
|
61
|
+
license: z.ZodString;
|
|
62
|
+
citation: z.ZodString;
|
|
63
|
+
homepage: z.ZodString;
|
|
64
|
+
}, z.core.$strip>>;
|
|
49
65
|
}, z.core.$strip>, readonly [{
|
|
50
66
|
readonly reason: "no_uniprot_mapping";
|
|
51
67
|
readonly code: JsonRpcErrorCode.NotFound;
|
|
52
68
|
readonly when: "A PDB ID has no UniProt cross-reference (e.g. nucleic-acid-only entry), or neither uniprot nor pdb_id was provided.";
|
|
53
69
|
readonly recovery: "Pass a UniProt accession directly, or use protein_search_structures to find a structure with a modeled protein chain.";
|
|
70
|
+
}, {
|
|
71
|
+
readonly reason: "chain_not_found";
|
|
72
|
+
readonly code: JsonRpcErrorCode.NotFound;
|
|
73
|
+
readonly when: "A supplied chain matches no UniProt-mapped polymer entity in the resolved PDB entry.";
|
|
74
|
+
readonly recovery: "Omit chain for the deterministic default mapping, or pass an author chain ID the entry exposes (see polymerEntities[].chains in the pdb://{entry_id} resource).";
|
|
54
75
|
}], {
|
|
55
76
|
readonly resolvedFrom: z.ZodOptional<z.ZodString>;
|
|
56
77
|
readonly notice: z.ZodOptional<z.ZodString>;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"get-annotations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-annotations.tool.ts"],"names":[],"mappings":"AAAA
|
|
1
|
+
{"version":3,"file":"get-annotations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-annotations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwEjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6NzB,CAAC"}
|