@cyanheads/protein-mcp-server 0.5.0 → 0.5.1
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 +2 -2
- package/changelog/0.5.x/0.5.1.md +14 -0
- package/dist/config/server-config.d.ts.map +1 -1
- package/dist/config/server-config.js +1 -1
- package/dist/config/server-config.js.map +1 -1
- package/dist/mcp-server/tools/definitions/_schemas.d.ts +12 -0
- package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/_schemas.js +20 -0
- 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 +16 -3
- package/dist/mcp-server/tools/definitions/analyze-collection.tool.js.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
package/AGENTS.md
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@@ -1,7 +1,7 @@
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# Developer Protocol
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**Server:** protein-mcp-server
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**Version:** 0.5.
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**Version:** 0.5.1
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.11.5`
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**Engines:** Bun ≥1.3.0, Node ≥24.0.0
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**MCP SDK:** `@modelcontextprotocol/sdk` ^1.30.0
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package/CLAUDE.md
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# Developer Protocol
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**Server:** protein-mcp-server
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**Version:** 0.5.
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**Version:** 0.5.1
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.11.5`
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**Engines:** Bun ≥1.3.0, Node ≥24.0.0
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**MCP SDK:** `@modelcontextprotocol/sdk` ^1.30.0
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package/README.md
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<div align="center">
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[](./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/)
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</div>
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@@ -111,7 +111,7 @@ Profile the PDB into distributions and trends over an optional scoping query —
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- One `group_by` dimension for a breakdown, or two distinct dimensions for a cross-tab (the first nests the second); a repeated dimension is rejected
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- `interval` sets the bin width for value histograms or the period for date histograms (`year` / `month` / `quarter`)
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- Scope with a free-text `query`, `organism`, `method`, or `max_resolution`; `content_type` selects the structure universe
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- `bucket_limit` caps buckets per dimension
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- `bucket_limit` caps buckets per dimension level, not per response — a cross-tab applies it separately to the parent dimension and to the nested child inside each parent bucket, so up to `bucket_limit × (1 + bucket_limit)` buckets come back. Each level flags its own truncation, and `bucketsReturned` gives the realized total
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- Every dimension reports `missingValueCount` — matches in scope carrying no value for that attribute, which therefore fall in no bucket (a `resolution` breakdown does not cover NMR entries, and neither `method` nor `resolution` covers computed models)
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---
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---
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summary: "protein_analyze_collection reports the realized bucket total, and bucket_limit's per-dimension-level semantics are now stated explicitly everywhere it's described."
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breaking: false
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---
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# 0.5.1 — 2026-08-16
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## Added
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- **`protein_analyze_collection` `bucketsReturned`**: new required enrichment field reporting the realized bucket total summed across every dimension level — the size a cross-tab returns isn't legible from `bucket_limit` alone ([#36](https://github.com/cyanheads/protein-mcp-server/issues/36)).
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## Changed
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- **`bucket_limit` semantics**: the input description, the tool description, `PROTEIN_FACET_BUCKET_CAP`'s config description, and the README now state that the cap applies per dimension level, not per response — a cross-tab can return up to `bucket_limit × (1 + bucket_limit)` buckets ([#36](https://github.com/cyanheads/protein-mcp-server/issues/36)).
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@@ -1 +1 @@
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{"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,QAAA,MAAM,kBAAkB;;;;;;;;;;;;;;;
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{"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,QAAA,MAAM,kBAAkB;;;;;;;;;;;;;;;iBAoFtB,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CAkB9C"}
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.min(1)
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.max(500)
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.default(50)
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.describe('Default cap on buckets returned per protein_analyze_collection dimension.'),
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.describe('Default cap on buckets returned per protein_analyze_collection dimension level — applied separately to a cross-tab parent dimension and to the nested child inside each of its buckets.'),
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fanoutConcurrency: z.coerce
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.number()
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.int()
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{"version":3,"file":"server-config.js","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;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,iBAAiB,EAAE,CAAC;SACjB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,yBAAyB,CAAC;SAClC,QAAQ,CAAC,sCAAsC,CAAC;IACnD,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,uBAAuB,CAAC;SAChC,QAAQ,CAAC,kDAAkD,CAAC;IAC/D,gBAAgB,EAAE,CAAC;SAChB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,wBAAwB,CAAC;SACjC,QAAQ,CAAC,8CAA8C,CAAC;IAC3D,oBAAoB,EAAE,CAAC;SACpB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,4BAA4B,CAAC;SACrC,QAAQ,CAAC,kEAAkE,CAAC;IAC/E,cAAc,EAAE,CAAC;SACd,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,kDAAkD,CAAC;SAC3D,QAAQ,CAAC,sDAAsD,CAAC;IACnE,gBAAgB,EAAE,CAAC;SAChB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,6BAA6B,CAAC;SACtC,QAAQ,CAAC,4DAA4D,CAAC;IACzE,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,6BAA6B,CAAC;SACtC,QAAQ,CAAC,iEAAiE,CAAC;IAC9E,cAAc,EAAE,CAAC;SACd,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,0BAA0B,CAAC;SACnC,QAAQ,CAAC,oCAAoC,CAAC;IACjD,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,oCAAoC,CAAC;SAC7C,QAAQ,CAAC,qCAAqC,CAAC;IAClD,kBAAkB,EAAE,CAAC,CAAC,MAAM;SACzB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,GAAG,CAAC,IAAI,CAAC;SACT,OAAO,CAAC,MAAM,CAAC;SACf,QAAQ,CACP,yGAAyG,CAC1G;IACH,WAAW,EAAE,CAAC,CAAC,MAAM;SAClB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,GAAG,CAAC;SACR,OAAO,CAAC,EAAE,CAAC;SACX,QAAQ,CAAC,0EAA0E,CAAC;IACvF,oBAAoB,EAAE,CAAC,CAAC,MAAM;SAC3B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,EAAE,CAAC;SACP,OAAO,CAAC,EAAE,CAAC;SACX,QAAQ,CAAC,kFAAkF,CAAC;IAC/F,cAAc,EAAE,CAAC,CAAC,MAAM;SACrB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,GAAG,CAAC;SACR,OAAO,CAAC,EAAE,CAAC;SACX,QAAQ,
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{"version":3,"file":"server-config.js","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;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,iBAAiB,EAAE,CAAC;SACjB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,yBAAyB,CAAC;SAClC,QAAQ,CAAC,sCAAsC,CAAC;IACnD,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,uBAAuB,CAAC;SAChC,QAAQ,CAAC,kDAAkD,CAAC;IAC/D,gBAAgB,EAAE,CAAC;SAChB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,wBAAwB,CAAC;SACjC,QAAQ,CAAC,8CAA8C,CAAC;IAC3D,oBAAoB,EAAE,CAAC;SACpB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,4BAA4B,CAAC;SACrC,QAAQ,CAAC,kEAAkE,CAAC;IAC/E,cAAc,EAAE,CAAC;SACd,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,kDAAkD,CAAC;SAC3D,QAAQ,CAAC,sDAAsD,CAAC;IACnE,gBAAgB,EAAE,CAAC;SAChB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,6BAA6B,CAAC;SACtC,QAAQ,CAAC,4DAA4D,CAAC;IACzE,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,6BAA6B,CAAC;SACtC,QAAQ,CAAC,iEAAiE,CAAC;IAC9E,cAAc,EAAE,CAAC;SACd,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,0BAA0B,CAAC;SACnC,QAAQ,CAAC,oCAAoC,CAAC;IACjD,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,oCAAoC,CAAC;SAC7C,QAAQ,CAAC,qCAAqC,CAAC;IAClD,kBAAkB,EAAE,CAAC,CAAC,MAAM;SACzB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,GAAG,CAAC,IAAI,CAAC;SACT,OAAO,CAAC,MAAM,CAAC;SACf,QAAQ,CACP,yGAAyG,CAC1G;IACH,WAAW,EAAE,CAAC,CAAC,MAAM;SAClB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,GAAG,CAAC;SACR,OAAO,CAAC,EAAE,CAAC;SACX,QAAQ,CAAC,0EAA0E,CAAC;IACvF,oBAAoB,EAAE,CAAC,CAAC,MAAM;SAC3B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,EAAE,CAAC;SACP,OAAO,CAAC,EAAE,CAAC;SACX,QAAQ,CAAC,kFAAkF,CAAC;IAC/F,cAAc,EAAE,CAAC,CAAC,MAAM;SACrB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,GAAG,CAAC;SACR,OAAO,CAAC,EAAE,CAAC;SACX,QAAQ,CACP,yLAAyL,CAC1L;IACH,iBAAiB,EAAE,CAAC,CAAC,MAAM;SACxB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,GAAG,CAAC,CAAC,CAAC;SACN,GAAG,CAAC,EAAE,CAAC;SACP,OAAO,CAAC,CAAC,CAAC;SACV,QAAQ,CAAC,iEAAiE,CAAC;CAC/E,CAAC,CAAC;AAIH,IAAI,OAAiC,CAAC;AAEtC,MAAM,UAAU,eAAe;IAC7B,OAAO,KAAK,cAAc,CAAC,kBAAkB,EAAE;QAC7C,iBAAiB,EAAE,sBAAsB;QACzC,eAAe,EAAE,oBAAoB;QACrC,gBAAgB,EAAE,qBAAqB;QACvC,oBAAoB,EAAE,yBAAyB;QAC/C,cAAc,EAAE,kBAAkB;QAClC,gBAAgB,EAAE,oBAAoB;QACtC,eAAe,EAAE,mBAAmB;QACpC,cAAc,EAAE,kBAAkB;QAClC,eAAe,EAAE,mBAAmB;QACpC,kBAAkB,EAAE,+BAA+B;QACnD,WAAW,EAAE,uBAAuB;QACpC,oBAAoB,EAAE,gCAAgC;QACtD,cAAc,EAAE,0BAA0B;QAC1C,iBAAiB,EAAE,4BAA4B;KAChD,CAAC,CAAC;IACH,OAAO,OAAO,CAAC;AACjB,CAAC"}
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*/
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export declare function countBuckets(facets: FacetDimensionOutput[]): number;
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{"version":3,"file":"_schemas.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,KAAK,EAAe,cAAc,EAAE,MAAM,0BAA0B,CAAC;AAE5E;;;;;GAKG;AACH,eAAO,MAAM,mBAAmB;;;;CAIuC,CAAC;AAkDxE;;;GAGG;AACH,eAAO,MAAM,wBAAwB;;;;;;;;;;iBAgBwB,CAAC;AAE9D,qFAAqF;AACrF,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;iBAI0D,CAAC;AAE5F,MAAM,MAAM,oBAAoB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,oBAAoB,CAAC,CAAC;AAExE,MAAM,MAAM,wBAAwB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,wBAAwB,CAAC,CAAC;AAgChF;;;;GAIG;AACH,wBAAgB,aAAa,CAC3B,KAAK,EAAE,cAAc,EACrB,GAAG,EAAE,MAAM,EACX,KAAK,EAAE,MAAM,GACZ,oBAAoB,CAwBtB;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,YAAY,CAAC,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,CAOnE;AA0CD,iFAAiF;AACjF,wBAAgB,YAAY,CAAC,MAAM,EAAE,oBAAoB,EAAE,GAAG,MAAM,EAAE,CAoBrE;AAuDD;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAAC,MAAM,EAAE,oBAAoB,EAAE,EAAE,KAAK,EAAE,MAAM,GAAG,MAAM,EAAE,CAcvF;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"}
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/**
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* Buckets the response actually carries, summed over every dimension position:
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* its buckets.
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*
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* Counted after {@link toFacetOutput} has sliced each position to the cap, so it
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* is the realized size rather than what upstream aggregated. The cap bounds each
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+
* position independently — a cross-tab reaches `cap × (1 + cap)` buckets — and
|
|
150
|
+
* the per-position `truncated` flags do not compose into that size, so a caller
|
|
151
|
+
* cannot derive it from the levels.
|
|
152
|
+
*/
|
|
153
|
+
export function countBuckets(facets) {
|
|
154
|
+
let count = 0;
|
|
155
|
+
for (const f of facets) {
|
|
156
|
+
count += f.buckets.length;
|
|
157
|
+
for (const b of f.buckets)
|
|
158
|
+
count += b.child?.buckets.length ?? 0;
|
|
159
|
+
}
|
|
160
|
+
return count;
|
|
161
|
+
}
|
|
142
162
|
/**
|
|
143
163
|
* Render one bucket's `label: count` line, annotating numeric histogram buckets
|
|
144
164
|
* with their explicit half-open `[rangeFrom, rangeTo)` bin so the bare boundary
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"_schemas.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_schemas.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C;;;;;GAKG;AACH,MAAM,CAAC,MAAM,mBAAmB,GAAG;IACjC,YAAY,EAAE,CAAC,cAAc,CAAC;IAC9B,SAAS,EAAE,CAAC,eAAe,CAAC;IAC5B,GAAG,EAAE,CAAC,cAAc,EAAE,eAAe,CAAC;CAC+B,CAAC;AAExE,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;IAC9D,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,4JAA4J,CAC7J;IACH,OAAO,EAAE,CAAC;SACP,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,uJAAuJ,CACxJ;CACJ,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;IAC9F,iBAAiB,EAAE,CAAC;SACjB,MAAM,EAAE;SACR,QAAQ,CACP,kLAAkL,CACnL;CACJ,CAAC;KACD,QAAQ,CAAC,sDAAsD,CAAC,CAAC;AAEpE,kFAAkF;AAClF,MAAM,YAAY,GAAG,gBAAgB;KAClC,MAAM,CAAC;IACN,KAAK,EAAE,oBAAoB;SACxB,QAAQ,EAAE;SACV,QAAQ,CACP,ySAAyS,CAC1S;CACJ,CAAC;KACD,QAAQ,CAAC,gFAAgF,CAAC,CAAC;AAE9F;;;GAGG;AACH,MAAM,CAAC,MAAM,wBAAwB,GAAG,CAAC;KACtC,MAAM,CAAC;IACN,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,CAAC,gEAAgE,CAAC;IAC7E,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,QAAQ,CAAC,kDAAkD,CAAC;IAC/F,SAAS,EAAE,CAAC;SACT,OAAO,EAAE;SACT,QAAQ,EAAE;SACV,QAAQ,CAAC,kEAAkE,CAAC;IAC/E,iBAAiB,EAAE,CAAC;SACjB,MAAM,EAAE;SACR,QAAQ,CACP,qdAAqd,CACtd;CACJ,CAAC;KACD,QAAQ,CAAC,gDAAgD,CAAC,CAAC;AAE9D,qFAAqF;AACrF,MAAM,CAAC,MAAM,oBAAoB,GAAG,wBAAwB;KACzD,MAAM,CAAC;IACN,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,YAAY,CAAC,CAAC,QAAQ,CAAC,kDAAkD,CAAC;CAC5F,CAAC;KACD,QAAQ,CAAC,8EAA8E,CAAC,CAAC;AAM5F,2EAA2E;AAC3E,SAAS,SAAS,CAChB,CAAI;IAEJ,OAAO,CAAC,CAAC,SAAS,KAAK,SAAS,IAAI,CAAC,CAAC,OAAO,KAAK,SAAS;QACzD,CAAC,CAAC,EAAE,SAAS,EAAE,CAAC,CAAC,SAAS,EAAE,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE;QAChD,CAAC,CAAC,EAAE,CAAC;AACT,CAAC;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,SAAS,iBAAiB,CAAC,OAAqC,EAAE,KAAa;IAC7E,OAAO,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC;AAC3E,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,aAAa,CAC3B,KAAqB,EACrB,GAAW,EACX,KAAa;IAEb,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,SAAS,CAAC,CAAC,CAAC;YACf,GAAG,CAAC,CAAC,CAAC,KAAK;gBACT,CAAC,CAAC;oBACE,KAAK,EAAE;wBACL,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,SAAS;wBAC5B,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,OAAO;6BACrB,KAAK,CAAC,CAAC,EAAE,GAAG,CAAC;6BACb,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,GAAG,SAAS,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC;wBACxE,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;wBAC5D,iBAAiB,EAAE,iBAAiB,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC;qBAC/D;iBACF;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;QACzC,iBAAiB,EAAE,iBAAiB,CAAC,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC;KAC3D,CAAC;AACJ,CAAC;AAED;;;;;;;;;;GAUG;AACH,MAAM,UAAU,YAAY,CAAC,MAA8B;IACzD,IAAI,KAAK,GAAG,CAAC,CAAC;IACd,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,KAAK,IAAI,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC;QAC1B,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,OAAO;YAAE,KAAK,IAAI,CAAC,CAAC,KAAK,EAAE,OAAO,CAAC,MAAM,IAAI,CAAC,CAAC;IACnE,CAAC;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;;;GAIG;AACH,SAAS,YAAY,CAAC,CAKrB;IACC,MAAM,KAAK,GACT,CAAC,CAAC,SAAS,KAAK,SAAS,IAAI,CAAC,CAAC,OAAO,KAAK,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;IAC/F,OAAO,GAAG,CAAC,CAAC,KAAK,GAAG,KAAK,KAAK,CAAC,CAAC,KAAK,EAAE,CAAC;AAC1C,CAAC;AAED;;;;;GAKG;AACH,MAAM,oBAAoB,GAAG,oDAAoD,CAAC;AAElF,2GAA2G;AAC3G,MAAM,0BAA0B,GAAG,yBAAyB,CAAC;AAE7D;;;;GAIG;AACH,SAAS,cAAc,CAAC,CAAiE;IACvF,MAAM,KAAK,GAAG;QACZ,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,EAAE;QAC9B,CAAC,CAAC,iBAAiB,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,iBAAiB,gBAAgB,CAAC,CAAC,CAAC,EAAE;KACtE,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;IAClB,OAAO,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,KAAK,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;AAC1D,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,CAAC,CAAC,EAAE,CAAC,CAAC;QACvD,IAAI,CAAC,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC3B,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC;YACjC,SAAS;QACX,CAAC;QACD,KAAK,MAAM,CAAC,IAAI,CAAC,CAAC,OAAO,EAAE,CAAC;YAC1B,KAAK,CAAC,IAAI,CAAC,KAAK,YAAY,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;YACnC,MAAM,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC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@@ -72,5 +72,6 @@ export declare const analyzeCollection: import("@cyanheads/mcp-ts-core").ToolDef
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readonly truncated: z.ZodOptional<z.ZodBoolean>;
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readonly shown: z.ZodOptional<z.ZodNumber>;
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readonly cap: z.ZodOptional<z.ZodNumber>;
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+
readonly bucketsReturned: z.ZodNumber;
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}>;
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//# sourceMappingURL=analyze-collection.tool.d.ts.map
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@@ -1 +1 @@
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-
{"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;
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1
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+
{"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;AAyBjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA0L5B,CAAC"}
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@@ -11,7 +11,7 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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11
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import { getServerConfig } from '../../../config/server-config.js';
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import { buildFacetSpec, FACET_DIMENSION_NAMES, } from '../../../services/rcsb/facets.js';
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import { getRcsbService } from '../../../services/rcsb/rcsb-service.js';
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-
import { CONTENT_TYPE_SCOPES, coverageNotices, facetDimensionSchema, renderFacets, toFacetOutput, } from './_schemas.js';
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+
import { CONTENT_TYPE_SCOPES, countBuckets, coverageNotices, facetDimensionSchema, renderFacets, toFacetOutput, } from './_schemas.js';
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15
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/**
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* Dimensions RCSB cannot aggregate over computed models: an AlphaFold /
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* ModelArchive record carries no experimental method or resolution, so the
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@@ -25,7 +25,9 @@ export const analyzeCollection = tool('protein_analyze_collection', {
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25
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'organism, or polymer composition; resolution and molecular-weight histograms; release-year timelines; ' +
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26
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'and multidimensional cross-tabs (e.g. method × release_year). Aggregation runs server-side at RCSB — ' +
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'one call returns compact buckets, no row pull. Pass one group_by dimension for a single breakdown, or ' +
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-
'two distinct dimensions for a cross-tab (the first nests the second).'
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+
'two distinct dimensions for a cross-tab (the first nests the second). bucket_limit caps each dimension ' +
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+
'level separately rather than the response, so a cross-tab returns up to that many nested buckets under ' +
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'each of its capped parent buckets; bucketsReturned reports the realized total.',
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annotations: { readOnlyHint: true, openWorldHint: true },
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30
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errors: [
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{
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@@ -82,7 +84,10 @@ export const analyzeCollection = tool('protein_analyze_collection', {
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.min(1)
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.max(500)
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.optional()
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-
.describe('Max buckets per dimension.
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+
.describe('Max buckets per dimension level, not per response. A cross-tab applies the cap separately to the ' +
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+
'parent dimension and to the nested child inside each parent bucket, so up to ' +
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89
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+
'bucket_limit × (1 + bucket_limit) buckets can come back — 2550 at the default 50. The realized ' +
|
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90
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+
'count comes back as bucketsReturned. Defaults to the server PROTEIN_FACET_BUCKET_CAP.'),
|
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86
91
|
}),
|
|
87
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|
output: z.object({
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88
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|
total: z.number().describe('Total entries in the scoped collection.'),
|
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@@ -100,6 +105,11 @@ export const analyzeCollection = tool('protein_analyze_collection', {
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100
105
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.describe('True when a dimension had more buckets than the applied cap.'),
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shown: z.number().optional().describe('Buckets returned for the capped dimension.'),
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|
cap: z.number().optional().describe('Per-dimension bucket cap that was applied.'),
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|
+
bucketsReturned: z
|
|
109
|
+
.number()
|
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110
|
+
.describe('Buckets in this response, summed over every dimension level: the top-level buckets plus, for a ' +
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111
|
+
'cross-tab, the nested child buckets under each of them. Since bucket_limit caps each level ' +
|
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112
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+
'separately, this is the size those caps actually produced — always present, cross-tab or not.'),
|
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|
},
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|
async handler(input, ctx) {
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105
115
|
const cfg = getServerConfig();
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@@ -127,6 +137,9 @@ export const analyzeCollection = tool('protein_analyze_collection', {
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127
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|
contentType: CONTENT_TYPE_SCOPES[input.content_type],
|
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128
138
|
}, [spec], ctx);
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129
139
|
const out = facets.map((f) => toFacetOutput(f, cap, total));
|
|
140
|
+
// The cap bounds each dimension level, so a cross-tab's size is the product of
|
|
141
|
+
// two capped lists rather than one. Report what the response actually holds.
|
|
142
|
+
ctx.enrich({ bucketsReturned: countBuckets(out) });
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130
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|
// Every advisory writes the same `notice` field (ctx.enrich.truncated routes
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131
144
|
// through it and is last-wins), and a cross-tab under predicted content can
|
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132
145
|
// trip several at once — collect the fragments and emit them as ONE notice.
|
|
@@ -1 +1 @@
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1
|
-
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/protein-mcp-server",
|
|
3
|
-
"version": "0.5.
|
|
3
|
+
"version": "0.5.1",
|
|
4
4
|
"mcpName": "io.github.cyanheads/protein-mcp-server",
|
|
5
5
|
"description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
|
|
6
6
|
"type": "module",
|
package/server.json
CHANGED
|
@@ -6,7 +6,7 @@
|
|
|
6
6
|
"url": "https://github.com/cyanheads/protein-mcp-server",
|
|
7
7
|
"source": "github"
|
|
8
8
|
},
|
|
9
|
-
"version": "0.5.
|
|
9
|
+
"version": "0.5.1",
|
|
10
10
|
"remotes": [
|
|
11
11
|
{
|
|
12
12
|
"type": "streamable-http",
|
|
@@ -19,7 +19,7 @@
|
|
|
19
19
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
20
20
|
"identifier": "@cyanheads/protein-mcp-server",
|
|
21
21
|
"runtimeHint": "node",
|
|
22
|
-
"version": "0.5.
|
|
22
|
+
"version": "0.5.1",
|
|
23
23
|
"packageArguments": [
|
|
24
24
|
{
|
|
25
25
|
"type": "positional",
|
|
@@ -48,7 +48,7 @@
|
|
|
48
48
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
49
49
|
"identifier": "@cyanheads/protein-mcp-server",
|
|
50
50
|
"runtimeHint": "node",
|
|
51
|
-
"version": "0.5.
|
|
51
|
+
"version": "0.5.1",
|
|
52
52
|
"packageArguments": [
|
|
53
53
|
{
|
|
54
54
|
"type": "positional",
|