@cyanheads/protein-mcp-server 0.8.2 → 0.8.3

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Files changed (45) hide show
  1. package/AGENTS.md +1 -1
  2. package/CLAUDE.md +1 -1
  3. package/README.md +10 -9
  4. package/changelog/0.8.x/0.8.2.md +7 -7
  5. package/changelog/0.8.x/0.8.3.md +23 -0
  6. package/dist/config/server-config.d.ts +2 -0
  7. package/dist/config/server-config.d.ts.map +1 -1
  8. package/dist/config/server-config.js +13 -1
  9. package/dist/config/server-config.js.map +1 -1
  10. package/dist/index.js +1 -1
  11. package/dist/index.js.map +1 -1
  12. package/dist/mcp-server/tools/definitions/analyze-collection.tool.js +2 -2
  13. package/dist/mcp-server/tools/definitions/analyze-collection.tool.js.map +1 -1
  14. package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts +10 -0
  15. package/dist/mcp-server/tools/definitions/compare-structures.tool.d.ts.map +1 -1
  16. package/dist/mcp-server/tools/definitions/compare-structures.tool.js +77 -11
  17. package/dist/mcp-server/tools/definitions/compare-structures.tool.js.map +1 -1
  18. package/dist/mcp-server/tools/definitions/find-similar.tool.d.ts.map +1 -1
  19. package/dist/mcp-server/tools/definitions/find-similar.tool.js +14 -6
  20. package/dist/mcp-server/tools/definitions/find-similar.tool.js.map +1 -1
  21. package/dist/mcp-server/tools/definitions/get-structure.tool.d.ts.map +1 -1
  22. package/dist/mcp-server/tools/definitions/get-structure.tool.js +84 -36
  23. package/dist/mcp-server/tools/definitions/get-structure.tool.js.map +1 -1
  24. package/dist/mcp-server/tools/definitions/search-structures.tool.d.ts.map +1 -1
  25. package/dist/mcp-server/tools/definitions/search-structures.tool.js +22 -17
  26. package/dist/mcp-server/tools/definitions/search-structures.tool.js.map +1 -1
  27. package/dist/mcp-server/tools/definitions/track-ligands.tool.d.ts.map +1 -1
  28. package/dist/mcp-server/tools/definitions/track-ligands.tool.js +5 -2
  29. package/dist/mcp-server/tools/definitions/track-ligands.tool.js.map +1 -1
  30. package/dist/services/alignment/alignment-service.d.ts +17 -4
  31. package/dist/services/alignment/alignment-service.d.ts.map +1 -1
  32. package/dist/services/alignment/alignment-service.js +31 -21
  33. package/dist/services/alignment/alignment-service.js.map +1 -1
  34. package/dist/services/rcsb/rcsb-service.d.ts +13 -3
  35. package/dist/services/rcsb/rcsb-service.d.ts.map +1 -1
  36. package/dist/services/rcsb/rcsb-service.js +35 -5
  37. package/dist/services/rcsb/rcsb-service.js.map +1 -1
  38. package/dist/services/rcsb/types.d.ts +21 -0
  39. package/dist/services/rcsb/types.d.ts.map +1 -1
  40. package/dist/services/shared/identifiers.d.ts +8 -1
  41. package/dist/services/shared/identifiers.d.ts.map +1 -1
  42. package/dist/services/shared/identifiers.js +12 -1
  43. package/dist/services/shared/identifiers.js.map +1 -1
  44. package/package.json +1 -1
  45. package/server.json +3 -3
package/AGENTS.md CHANGED
@@ -1,7 +1,7 @@
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  # Developer Protocol
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  **Server:** protein-mcp-server
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- **Version:** 0.8.2
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+ **Version:** 0.8.3
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.6`
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6
  **Engines:** Bun ≥1.4.0, Node ≥24.0.0
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  **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
package/CLAUDE.md CHANGED
@@ -1,7 +1,7 @@
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  # Developer Protocol
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3
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  **Server:** protein-mcp-server
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- **Version:** 0.8.2
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+ **Version:** 0.8.3
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.6`
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  **Engines:** Bun ≥1.4.0, Node ≥24.0.0
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  **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0
package/README.md CHANGED
@@ -7,7 +7,7 @@
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  <div align="center">
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- [![Version](https://img.shields.io/badge/Version-0.8.2-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0%2B-blueviolet.svg?style=flat-square)](https://bun.sh/)
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+ [![Version](https://img.shields.io/badge/Version-0.8.3-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/protein-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/protein-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/protein-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0%2B-blueviolet.svg?style=flat-square)](https://bun.sh/)
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  </div>
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@@ -58,8 +58,8 @@ All resource data is also reachable via tools — `pdb://{entry_id}` mirrors `pr
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  - Free-text, protein-sequence (triggers an mmseqs2 similarity search), and organism / method / resolution filters
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  - `content_type` scopes the search to `experimental`, `predicted`, or `all` (default) — `all` is a genuine union, so computed models appear alongside PDB entries
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- - Every hit names its `source`; experimental sequence hits expose a chainable PDB entry `id` plus the matched polymer `entityId`, with title, method, resolution, and organism enrichment; computed models retain their complete model ID and parsed UniProt accession
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- - `start` and `limit` page through ranked results; `nextStart` is returned while another page remains
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+ - Every hit names its `source`; sequence hits in either universe expose a chainable entry `id` plus the matched polymer `entityId`; experimental hits carry title, method, resolution, and organism enrichment, and AlphaFold models their parsed UniProt accession
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+ - `start` and `limit` page through ranked results; `nextStart` is returned while another page remains, and an empty page past the end names the offset in `notice` rather than reporting no matches
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  - Optional `facets` return a method / organism / release-year breakdown alongside the hits — each dimension may be listed once and reports how many matches carry no value for it; a capped dimension is named in `notice`, with `protein_analyze_collection` (larger `bucket_limit`) as the route to the long tail
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  - Chain hit IDs straight into `protein_get_structure`
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@@ -69,7 +69,8 @@ All resource data is also reachable via tools — `pdb://{entry_id}` mirrors `pr
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  - `source: experimental` batches PDB entry IDs (also resolving computed-model IDs like `AF_*`/`MA_*` from search, tagged `source: predicted` with their provider); `source: predicted` takes UniProt accessions for AlphaFold models with pLDDT/PAE; `source: best_available` takes UniProt accessions and returns the top federated model (highest-resolution experimental if one exists, else the best prediction)
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  - Per-ID partial success — unresolved IDs land in `failed[]`; `requested`/`processed` disclose IDs dropped beyond the batch cap, and every advisory (cap, failure, overflow) joins into one `notice`
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- - Records served by the RCSB entry endpoint also carry `polymerEntities` (both `authAsymIds` and `labelAsymIds`), `ligands`, `molecularWeight`, and `releaseDate`
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+ - Records fetched with `source: experimental`, computed models included, also carry `polymerEntities` (both `authAsymIds` and `labelAsymIds`), `ligands`, `molecularWeight`, and `releaseDate`
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+ - `coordinateUrls` lists only files that exist: BinaryCIF comes from RCSB's ModelServer, the PDB format is omitted for large mmCIF-only entries, and a computed model's files come from its provider (all three formats from AlphaFold DB, mmCIF from ModelArchive) — an AlphaFold model whose provider lookup fails keeps only its RCSB BinaryCIF, named in `notice`
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  - `include_coords` inlines coordinate content, subject to a response budget — an over-budget batch returns a per-structure size outline (re-call with `sections: [ids]`), and a single oversized file is withheld with a pointer to its `coordinateUrls`
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  - Every response carries an `attribution` block naming upstream data licenses and citations
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@@ -78,7 +79,7 @@ All resource data is also reachable via tools — `pdb://{entry_id}` mirrors `pr
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  ### `protein_find_similar` <sub>tool</sub>
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  - `by: sequence` runs a synchronous RCSB mmseqs2 search; `by: structure` runs an asynchronous Foldseek search against experimental and predicted databases — query from a raw sequence, a PDB ID, or a UniProt accession
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- - Both modes accept `start`/`limit` and report `totalCount`, echoing `start` and returning `nextStart` while another page remains
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+ - Both modes accept `start`/`limit` and report `totalCount`, echoing `start` and returning `nextStart` while another page remains; an empty page past the end names the offset in `notice`, distinct from a search with no matches
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  - Foldseek targets default to `pdb100` + `afdb50`; override via `databases` (e.g. `afdb-swissprot`, `BFVD`)
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  - An async job that exceeds the poll budget returns `status: computing` with a `ticketId` — re-call with `ticket_id` to resume; a completed structure search returns the same ticket so a new `start` pages the finished job
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  - Each mode reads only its own controls (`sequence`, `max_evalue`, `min_identity` under `by: sequence`; `ticket_id`, `databases` under `by: structure`) — a field the selected mode can't consume is rejected, not ignored
@@ -90,7 +91,7 @@ All resource data is also reachable via tools — `pdb://{entry_id}` mirrors `pr
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  - `mode: find_ligand` resolves a name or formula to chemical component IDs with formula, weight, SMILES, and InChIKey — ranked by deposition frequency, most-common match first
92
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  - A formula-shaped `query` matches on exact composition, spaced (`C29 H31 N7 O`) or unspaced; anything else (a component ID included) matches on name and synonyms
93
- - `mode: structures_with_ligand` returns PDB entries containing a ligand by exact component ID, with `start`/`limit` paging and `nextStart` while another page remains
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+ - `mode: structures_with_ligand` returns PDB entries containing a ligand by exact component ID, with `start`/`limit` paging and `nextStart` while another page remains; a page past the end names the offset in `notice` instead of reporting no entries
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  - `mode: binding_site` returns the protein residues lining a ligand's pocket in a structure, with contact distances
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  - Binding sites are experimental-only — computed from deposited coordinates; predicted models carry no bound ligands
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@@ -101,8 +102,8 @@ All resource data is also reachable via tools — `pdb://{entry_id}` mirrors `pr
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  - Aligns 2 to the configured cap (default 10, max 25) structures per call, via `tm-align`, `fatcat-rigid`, or `fatcat-flexible`; optional per-structure `chain` restricts the alignment to a single mmCIF label chain
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  - `reference: first` aligns every structure to the first; `reference: all_pairs` computes the full pairwise matrix; a structure repeated in `structures[]` is compared once
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  - Each pair is an independent async job with per-pair partial success — a pair still computing when the poll budget elapses returns `status: computing` with a job `uuid`; a failed pair degrades only its own row
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- - Re-call with a matching `{ a, b, uuid }` entry in `resume[]` to poll a computing pair instead of resubmitting
105
- - Returns TM-score, RMSD, and aligned-residue count per pair, plus each structure's `modeledResidues` and 0–100 `coverage`
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+ - Re-call with a matching `{ a, b, uuid }` entry in `resume[]` to poll a computing pair instead of resubmitting; a resumed pair reports `a`/`b` in the order its job was submitted, whatever the current `structures[]` order, and a resume under a different `method` is rejected
106
+ - Returns TM-score, RMSD, and aligned-residue count per pair, plus each structure's `modeledResidues` and 0–100 `coverage`, ordered `[a, b]`; TM-score is normalized by `a`'s length, so the same pair scores differently when reversed
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107
 
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  ---
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@@ -147,7 +148,7 @@ PDB / AlphaFold-specific:
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149
  - One federated surface over experimental (PDB) and predicted (AlphaFold / 3D-Beacons) structures — search, fetch, and compare treat both universes the same
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  - Keyless across every upstream — RCSB, AlphaFold DB, 3D-Beacons, UniProt, InterPro, and Foldseek, no API keys to provision
150
- - Corpus analytics run server-side on RCSB's facet engine — distributions, histograms, and cross-tabs in one call, no row pull and no SQL workspace
151
+ - Corpus analytics run on RCSB's facet engine — distributions, histograms, and cross-tabs come back as compact bucket counts, not the matching entries
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152
  - Async alignment and Foldseek jobs poll within a bounded budget and hand back a job ticket (`ticketId` / per-pair `uuid`) instead of blocking — re-call with `ticket_id` or a `resume[]` entry to poll the same job instead of resubmitting
152
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  Agent-friendly output:
@@ -1,5 +1,5 @@
1
1
  ---
2
- summary: "Adopts mcp-ts-core 0.13.6's argument-rejection recovery hints and pre-validation aliasing; rewrites server instructions for workflow chaining."
2
+ summary: "Adopts mcp-ts-core 0.13.6: argument rejections carry recovery hints (0.13.3), tool arguments pass pre-validation aliasing (0.13.4), and tool-error text names its reason (0.13.5); server instructions rewritten for workflow chaining."
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  breaking: false
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  security: false
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5
  ---
@@ -9,9 +9,9 @@ security: false
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  ## Changed
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  - **Server instructions** — rewritten as three sentences addressed to the calling agent: where a workflow starts, what a PDB ID chains into, and how a running Foldseek search or structural alignment resumes.
12
- - **Argument-rejection recovery** — an unknown or mistyped tool argument now carries `data.reason: "invalid_arguments"` and a `Recovery:` hint naming the accepted keys or expected type; an omitted required enum field reads as missing rather than as a wrong choice.
13
- - **Argument pre-validation** — a differently-cased key naming exactly one declared parameter is rewritten (`pdbId` → `pdb_id`), and a JSON-stringified array argument is repaired and re-parsed once; an undeclared key is still rejected.
14
- - **Tool-error text** — closes with `(reason <reason>)`, adding `· retryable` or `· not retryable` when the reason declares it.
12
+ - **Argument-rejection recovery** (mcp-ts-core 0.13.3, [cyanheads/mcp-ts-core#445](https://github.com/cyanheads/mcp-ts-core/issues/445), [cyanheads/mcp-ts-core#378](https://github.com/cyanheads/mcp-ts-core/issues/378)) — an unknown or mistyped tool argument now carries `data.reason: "invalid_arguments"` and a `Recovery:` hint naming the accepted keys or expected type; an omitted required enum field reads as missing rather than as a wrong choice.
13
+ - **Argument pre-validation** (mcp-ts-core 0.13.4, [cyanheads/mcp-ts-core#452](https://github.com/cyanheads/mcp-ts-core/issues/452), [cyanheads/mcp-ts-core#234](https://github.com/cyanheads/mcp-ts-core/issues/234)) — a differently-cased key naming exactly one declared parameter is rewritten (`pdbId` → `pdb_id`), and a JSON-stringified array argument is repaired and re-parsed once; an undeclared key is still rejected.
14
+ - **Tool-error text** (mcp-ts-core 0.13.5, [cyanheads/mcp-ts-core#458](https://github.com/cyanheads/mcp-ts-core/issues/458)) — closes with `(reason <reason>)`, adding `· retryable` or `· not retryable` when the reason declares it.
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  - **Tool/field descriptions** — five definitions (`protein_analyze_collection`, `protein_compare_structures`, `protein_get_annotations`, `protein_search_structures`, `protein_track_ligands`) converted from `+`-joined strings to single string literals; advertised `tools/list` text is unchanged ([#38](https://github.com/cyanheads/protein-mcp-server/issues/38)).
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  - **Repo hygiene** — framework skills, the definition linter (config-driven truncation allowlist via `devcheck.config.json`), issue forms, and devcheck synced to the current template; adds `.github/workflows/codeql.yml`.
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@@ -19,6 +19,6 @@ security: false
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  - `@cyanheads/mcp-ts-core` ^0.13.2 → ^0.13.6
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  - `zod` ^4.6.4 → ^4.6.5
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- - `@biomejs/biome` 2.5.13 → 2.5.14
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- - `@types/node` 26.5.1 → 26.6.2
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- - `vitest` ^5.0.0 → ^5.0.1
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+ - `@biomejs/biome` 2.5.13 → 2.5.14 (dev)
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+ - `@types/node` 26.5.1 → 26.6.2 (dev)
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+ - `vitest` ^5.0.0 → ^5.0.1 (dev)
@@ -0,0 +1,23 @@
1
+ ---
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+ summary: "Fixes computed-model sequence-hit IDs, dead coordinate-file URLs, reversed alignment-resume labeling, and false zero-match notices past the last results page; tool descriptions reworded to drop implementation leaks."
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+ breaking: false
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+ security: false
5
+ ---
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+
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+ # 0.8.3 — 2026-09-22
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+
9
+ ## Added
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+
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+ - **`RCSB_MODELS_BASE_URL`** / **`MODELARCHIVE_BASE_URL`** — override the RCSB ModelServer (BinaryCIF) and ModelArchive coordinate-download bases, alongside the existing `RCSB_FILES_BASE_URL` (#61).
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+
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+ ## Changed
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+
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+ - **Tool descriptions** — nine clauses across four tools (`protein_analyze_collection`, `protein_compare_structures`, `protein_get_structure`, `protein_search_structures`) reworded to state only the caller-facing contract, dropping upstream call counts, the RCSB entry-endpoint name, an internal env-var name, and "an agent" phrasing; the server instructions and several neighboring field descriptions get the same treatment, and a new `description-hygiene` test guards every tool and resource description against regression (#55).
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+
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+ ## Fixed
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+
19
+ - **`protein_search_structures`** — a computed-model (`AF_`/`MA_`) sequence hit now resolves to a chainable entry `id`, with the matched polymer moved to the existing `entityId` field; previously the raw entity-suffixed ID was returned as `id` and failed to resolve in `protein_get_structure` (#60).
20
+ - **`protein_get_structure` `coordinateUrls`** — BinaryCIF now resolves via `models.rcsb.org` instead of the 404ing `files.rcsb.org`; `pdb` is omitted for entries with no legacy-PDB-compatible file; a computed model fetched via `source: "experimental"` gets its provider's coordinate URLs (AlphaFold DB or ModelArchive) instead of a dead RCSB link, falling back to the record's RCSB BinaryCIF URL (named in `notice`) when that provider lookup fails; `include_coords` inlines from the corrected URLs and names a record with no text-format file in `notice` rather than skipping it silently (#61).
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+ - **`protein_find_similar` `by: "structure"`** — a PDB ID query uploads the entry's mmCIF file instead of its PDB-format file, so large entries archived as mmCIF only no longer fail to download (#61).
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+ - **`protein_compare_structures` resume** — a resumed pair's `a`/`b`, `modeledResidues`, `coverage`, and `tmScore` now follow the alignment job's own submitted order rather than this call's `structures[]` order; a resume under a different `method` is rejected with `resume_method_mismatch`, and a ticket whose job aligned a different pair with `resume_job_mismatch`. The still-computing notice now notes that an expired job reads the same as a running one, so a pair that stays computing across several resumes should be resubmitted (#62).
23
+ - **Pagination past the last page** — `protein_search_structures`, `protein_find_similar` (`by: "sequence"`), and `protein_track_ligands` (`structures_with_ligand`) now report an offset-past-the-end notice instead of falsely claiming no matches when `start` exceeds a nonzero total (#66).
@@ -9,9 +9,11 @@ declare const ServerConfigSchema: z.ZodObject<{
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  rcsbSearchBaseUrl: z.ZodDefault<z.ZodString>;
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  rcsbDataBaseUrl: z.ZodDefault<z.ZodString>;
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  rcsbFilesBaseUrl: z.ZodDefault<z.ZodString>;
12
+ rcsbModelsBaseUrl: z.ZodDefault<z.ZodString>;
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  rcsbAlignmentBaseUrl: z.ZodDefault<z.ZodString>;
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  beaconsBaseUrl: z.ZodDefault<z.ZodString>;
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  alphafoldBaseUrl: z.ZodDefault<z.ZodString>;
16
+ modelArchiveBaseUrl: z.ZodDefault<z.ZodString>;
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  foldseekBaseUrl: z.ZodDefault<z.ZodString>;
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  uniprotBaseUrl: z.ZodDefault<z.ZodString>;
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  interproBaseUrl: z.ZodDefault<z.ZodString>;
@@ -1 +1 @@
1
- {"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"}
1
+ {"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;;;;;;;;;;;;;;;;;iBA8FtB,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CAoB9C"}
@@ -21,7 +21,12 @@ const ServerConfigSchema = z.object({
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  .string()
22
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  .url()
23
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  .default('https://files.rcsb.org')
24
- .describe('Base URL for RCSB coordinate-file downloads.'),
24
+ .describe('Base URL for RCSB mmCIF and PDB-format coordinate-file downloads.'),
25
+ rcsbModelsBaseUrl: z
26
+ .string()
27
+ .url()
28
+ .default('https://models.rcsb.org')
29
+ .describe('Base URL for RCSB BinaryCIF coordinate downloads (ModelServer).'),
25
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  rcsbAlignmentBaseUrl: z
26
31
  .string()
27
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  .url()
@@ -37,6 +42,11 @@ const ServerConfigSchema = z.object({
37
42
  .url()
38
43
  .default('https://alphafold.ebi.ac.uk')
39
44
  .describe('Base URL for the AlphaFold Protein Structure Database API.'),
45
+ modelArchiveBaseUrl: z
46
+ .string()
47
+ .url()
48
+ .default('https://modelarchive.org')
49
+ .describe('Base URL for ModelArchive computed-model coordinate downloads.'),
40
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  foldseekBaseUrl: z
41
51
  .string()
42
52
  .url()
@@ -93,9 +103,11 @@ export function getServerConfig() {
93
103
  rcsbSearchBaseUrl: 'RCSB_SEARCH_BASE_URL',
94
104
  rcsbDataBaseUrl: 'RCSB_DATA_BASE_URL',
95
105
  rcsbFilesBaseUrl: 'RCSB_FILES_BASE_URL',
106
+ rcsbModelsBaseUrl: 'RCSB_MODELS_BASE_URL',
96
107
  rcsbAlignmentBaseUrl: 'RCSB_ALIGNMENT_BASE_URL',
97
108
  beaconsBaseUrl: 'BEACONS_BASE_URL',
98
109
  alphafoldBaseUrl: 'ALPHAFOLD_BASE_URL',
110
+ modelArchiveBaseUrl: 'MODELARCHIVE_BASE_URL',
99
111
  foldseekBaseUrl: 'FOLDSEEK_BASE_URL',
100
112
  uniprotBaseUrl: 'UNIPROT_BASE_URL',
101
113
  interproBaseUrl: 'INTERPRO_BASE_URL',
@@ -1 +1 @@
1
- {"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"}
1
+ {"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,mEAAmE,CAAC;IAChF,iBAAiB,EAAE,CAAC;SACjB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,yBAAyB,CAAC;SAClC,QAAQ,CAAC,iEAAiE,CAAC;IAC9E,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,mBAAmB,EAAE,CAAC;SACnB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,OAAO,CAAC,0BAA0B,CAAC;SACnC,QAAQ,CAAC,gEAAgE,CAAC;IAC7E,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,iBAAiB,EAAE,sBAAsB;QACzC,oBAAoB,EAAE,yBAAyB;QAC/C,cAAc,EAAE,kBAAkB;QAClC,gBAAgB,EAAE,oBAAoB;QACtC,mBAAmB,EAAE,uBAAuB;QAC5C,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"}
package/dist/index.js CHANGED
@@ -48,7 +48,7 @@ await createApp({
48
48
  'server/discover': { ttlMs: 3_600_000, cacheScope: 'public' },
49
49
  'resources/read': { ttlMs: 3_600_000, cacheScope: 'public' },
50
50
  },
51
- instructions: 'Find structures with protein_search_structures, then pass the returned IDs to protein_get_structure for metadata and coordinate URLs, or pass UniProt accessions there for AlphaFold predictions and the best available model. A PDB ID also chains into protein_get_annotations, protein_track_ligands, protein_find_similar, and protein_compare_structures for annotations, binding sites, homologs, and structural alignment, while protein_analyze_collection profiles the whole PDB without pulling rows. A Foldseek search or structural alignment still running when the poll budget elapses returns status "computing" with a ticket (protein_find_similar) or a job UUID (protein_compare_structures); re-call with it to resume that job rather than resubmitting.',
51
+ instructions: 'Find structures with protein_search_structures, then pass the returned IDs to protein_get_structure for metadata and coordinate URLs, or pass UniProt accessions there for AlphaFold predictions and the best available model. A PDB ID also chains into protein_get_annotations, protein_track_ligands, protein_find_similar, and protein_compare_structures for annotations, binding sites, homologs, and structural alignment, while protein_analyze_collection profiles the whole PDB as aggregate counts. A Foldseek search or structural alignment still running when the poll budget elapses returns status "computing" with a ticket (protein_find_similar) or a job UUID (protein_compare_structures); re-call with it to resume that job rather than resubmitting.',
52
52
  setup(core) {
53
53
  const serverConfig = getServerConfig();
54
54
  initRcsbService(core.config, core.storage, serverConfig);
package/dist/index.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;;GAKG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,iBAAiB,EAAE,kBAAkB,EAAE,MAAM,6CAA6C,CAAC;AACpG,OAAO,EACL,iBAAiB,EACjB,iBAAiB,EACjB,WAAW,EACX,cAAc,EACd,YAAY,EACZ,gBAAgB,EAChB,YAAY,GACb,MAAM,yCAAyC,CAAC;AACjD,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAC3E,OAAO,EAAE,mBAAmB,EAAE,MAAM,yCAAyC,CAAC;AAC9E,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAC;AAClE,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAE3E,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,oBAAoB;IAC1B,KAAK,EAAE,oBAAoB;IAC3B,KAAK,EAAE;QACL,gBAAgB;QAChB,YAAY;QACZ,WAAW;QACX,YAAY;QACZ,iBAAiB;QACjB,iBAAiB;QACjB,cAAc;KACf;IACD,SAAS,EAAE,CAAC,kBAAkB,EAAE,iBAAiB,CAAC;IAClD,OAAO,EAAE,EAAE;IACX,qFAAqF;IACrF,OAAO,EAAE,EAAE,WAAW,EAAE,KAAK,EAAE;IAC/B,4EAA4E;IAC5E,WAAW,EAAE,WAAW;IACxB;;;;;;;OAOG;IACH,UAAU,EAAE;QACV,YAAY,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QACxD,gBAAgB,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC5D,0BAA0B,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QACtE,iBAAiB,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC7D,gBAAgB,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;KAC7D;IACD,YAAY,EACV,+uBAA+uB;IACjvB,KAAK,CAAC,IAAI;QACR,MAAM,YAAY,GAAG,eAAe,EAAE,CAAC;QACvC,eAAe,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QACzD,oBAAoB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC9D,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC5D,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC5D,oBAAoB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC9D,mBAAmB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;IAC/D,CAAC;CACF,CAAC,CAAC"}
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;;GAKG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,iBAAiB,EAAE,kBAAkB,EAAE,MAAM,6CAA6C,CAAC;AACpG,OAAO,EACL,iBAAiB,EACjB,iBAAiB,EACjB,WAAW,EACX,cAAc,EACd,YAAY,EACZ,gBAAgB,EAChB,YAAY,GACb,MAAM,yCAAyC,CAAC;AACjD,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAC3E,OAAO,EAAE,mBAAmB,EAAE,MAAM,yCAAyC,CAAC;AAC9E,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAC;AAClE,OAAO,EAAE,kBAAkB,EAAE,MAAM,uCAAuC,CAAC;AAE3E,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,oBAAoB;IAC1B,KAAK,EAAE,oBAAoB;IAC3B,KAAK,EAAE;QACL,gBAAgB;QAChB,YAAY;QACZ,WAAW;QACX,YAAY;QACZ,iBAAiB;QACjB,iBAAiB;QACjB,cAAc;KACf;IACD,SAAS,EAAE,CAAC,kBAAkB,EAAE,iBAAiB,CAAC;IAClD,OAAO,EAAE,EAAE;IACX,qFAAqF;IACrF,OAAO,EAAE,EAAE,WAAW,EAAE,KAAK,EAAE;IAC/B,4EAA4E;IAC5E,WAAW,EAAE,WAAW;IACxB;;;;;;;OAOG;IACH,UAAU,EAAE;QACV,YAAY,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QACxD,gBAAgB,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC5D,0BAA0B,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QACtE,iBAAiB,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;QAC7D,gBAAgB,EAAE,EAAE,KAAK,EAAE,SAAS,EAAE,UAAU,EAAE,QAAQ,EAAE;KAC7D;IACD,YAAY,EACV,8uBAA8uB;IAChvB,KAAK,CAAC,IAAI;QACR,MAAM,YAAY,GAAG,eAAe,EAAE,CAAC;QACvC,eAAe,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QACzD,oBAAoB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC9D,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC5D,kBAAkB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC5D,oBAAoB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QAC9D,mBAAmB,CAAC,IAAI,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;IAC/D,CAAC;CACF,CAAC,CAAC"}
@@ -31,7 +31,7 @@ const ZERO_MATCH_NOTICE = {
31
31
  };
32
32
  export const analyzeCollection = tool('protein_analyze_collection', {
33
33
  title: 'protein-mcp-server: analyze collection',
34
- description: 'Profile the PDB into distributions and trends over an optional scoping query: counts by method, organism, or polymer composition; resolution and molecular-weight histograms; release-year timelines; and multidimensional cross-tabs (e.g. method × release_year). Aggregation runs server-side at RCSB one call returns compact buckets, no row pull. Pass one group_by dimension for a single breakdown, or two distinct dimensions for a cross-tab (the first nests the second). bucket_limit caps each dimension level separately rather than the response, so a cross-tab returns up to that many nested buckets under each of its capped parent buckets; bucketsReturned reports the realized total.',
34
+ description: 'Profile the PDB into distributions and trends over an optional scoping query: counts by method, organism, or polymer composition; resolution and molecular-weight histograms; release-year timelines; and multidimensional cross-tabs (e.g. method × release_year). Aggregation runs at RCSB, so the response carries compact counts per bucket rather than the matching entries. Pass one group_by dimension for a single breakdown, or two distinct dimensions for a cross-tab (the first nests the second). bucket_limit caps each dimension level separately rather than the response, so a cross-tab returns up to that many nested buckets under each of its capped parent buckets; bucketsReturned reports the realized total.',
35
35
  annotations: { readOnlyHint: true, openWorldHint: true },
36
36
  errors: [
37
37
  {
@@ -92,7 +92,7 @@ export const analyzeCollection = tool('protein_analyze_collection', {
92
92
  .min(1)
93
93
  .max(500)
94
94
  .optional()
95
- .describe('Max buckets per dimension level, not per response. A cross-tab applies the cap separately to the parent dimension and to the nested child inside each parent bucket, so up to bucket_limit × (1 + bucket_limit) buckets can come back — 2550 at the default 50. The realized count comes back as bucketsReturned. Defaults to the server PROTEIN_FACET_BUCKET_CAP.'),
95
+ .describe('Max buckets per dimension level, not per response. A cross-tab applies the cap separately to the parent dimension and to the nested child inside each parent bucket, so up to bucket_limit × (1 + bucket_limit) buckets can come back — 2550 at the default 50. The realized count comes back as bucketsReturned. Defaults to the configured server cap.'),
96
96
  }),
97
97
  output: z.object({
98
98
  total: z.number().describe('Total entries in the scoped collection.'),
@@ -1 +1 @@
1
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@@ -59,6 +59,16 @@ export declare const compareStructures: import("@cyanheads/mcp-ts-core").ToolDef
59
59
  readonly code: JsonRpcErrorCode.InvalidParams;
60
60
  readonly when: "Every entry in structures[] denotes the same structure, leaving no pair to align.";
61
61
  readonly recovery: "Pass at least two different structures (entry ID, or entry ID + chain); a structure repeated in the list is compared once.";
62
+ }, {
63
+ readonly reason: "resume_method_mismatch";
64
+ readonly code: JsonRpcErrorCode.InvalidParams;
65
+ readonly when: "A resumed alignment job completed under a different method than this call's method input.";
66
+ readonly recovery: "Re-call with the method the job ran (named in the message), or drop that resume entry to submit a fresh alignment with the new method.";
67
+ }, {
68
+ readonly reason: "resume_job_mismatch";
69
+ readonly code: JsonRpcErrorCode.InvalidParams;
70
+ readonly when: "A resume entry's uuid belongs to an alignment job for a different structure pair than its a/b labels.";
71
+ readonly recovery: "Copy each resume entry's uuid from the same pairs[] row as its a and b, or drop the entry to submit a fresh alignment for that pair.";
62
72
  }], {
63
73
  readonly pairsTotal: z.ZodNumber;
64
74
  readonly computing: z.ZodNumber;
@@ -1 +1 @@
1
- {"version":3,"file":"compare-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/compare-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqHjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwJ5B,CAAC"}
1
+ {"version":3,"file":"compare-structures.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/compare-structures.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6HjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA0L5B,CAAC"}
@@ -57,7 +57,7 @@ const inputSchema = z.object({
57
57
  })
58
58
  .describe('A prior pair to resume by UUID instead of resubmitting.'))
59
59
  .optional()
60
- .describe("Resume tickets from a prior call: for each pair whose labels match an entry here, poll the existing UUID instead of submitting a new alignment job. Copy a, b, and uuid verbatim from a prior response's pairs[]; keep structures and reference unchanged."),
60
+ .describe("Resume tickets from a prior call: for each pair whose labels match an entry here, poll the existing UUID instead of submitting a new alignment job. Copy a, b, and uuid verbatim from a prior response's pairs[]; keep structures, reference, and method unchanged. The order of structures may change — a resumed pair keeps the orientation its job was submitted in."),
61
61
  });
62
62
  const outputSchema = z.object({
63
63
  method: z.string().describe('Alignment method used.'),
@@ -65,13 +65,15 @@ const outputSchema = z.object({
65
65
  pairs: z
66
66
  .array(z
67
67
  .object({
68
- a: z.string().describe('First structure of the pair (entry[.chain]).'),
68
+ a: z
69
+ .string()
70
+ .describe("First structure of the pair (entry[.chain]), as the alignment job was submitted — for a resumed pair that can differ from this call's structures[] order."),
69
71
  b: z.string().describe('Second structure of the pair (entry[.chain]).'),
70
72
  status: z.enum(['complete', 'computing', 'failed']).describe('Outcome for this pair.'),
71
73
  tmScore: z
72
74
  .number()
73
75
  .optional()
74
- .describe('TM-score (0–1; higher is more similar). Length-normalized, so it can be sensitive to terminal length differences between the two structures — a one-residue overhang can flip the greedy superposition into a worse local optimum, dropping the score sharply. Cross-check rmsd and alignedResidues to spot such cases.'),
76
+ .describe("TM-score (0–1; higher is more similar). Length-normalized by structure a's modeled length, so the same pair aligned b-first can score very differently (0.17 vs 0.40 for a 141- vs a 46-residue chain). It can also be sensitive to terminal length differences between the two structures — a one-residue overhang can flip the greedy superposition into a worse local optimum, dropping the score sharply. Cross-check rmsd and alignedResidues to spot such cases."),
75
77
  rmsd: z.number().optional().describe('RMSD in Å over aligned residues.'),
76
78
  alignedResidues: z.number().optional().describe('Number of aligned residue pairs.'),
77
79
  modeledResidues: z
@@ -95,7 +97,7 @@ const outputSchema = z.object({
95
97
  });
96
98
  export const compareStructures = tool('protein_compare_structures', {
97
99
  title: 'protein-mcp-server: compare structures',
98
- description: `Structurally align multiple structures (up to the configured batch cap) via the RCSB Structural Comparison service (TM-align / jFATCAT). reference:"first" aligns every structure to the first; reference:"all_pairs" computes the full pairwise matrix. Each pair is an independent async alignment job, fanned out with a concurrency cap and per-pair partial success — a pair still computing when the budget elapses returns status "computing" with its job UUID, and a failed pair degrades its row without sinking the others. Re-call with a matching entry in resume[] to poll a computing pair's UUID instead of resubmitting. Returns TM-score, RMSD, and aligned-residue count per pair, plus each structure's modeled-residue count and alignment coverage. TM-score is length-normalized and can shift sharply between structures that differ only by a terminal residue or two — the greedy superposition can settle into a worse local optimum — so read tmScore alongside rmsd, alignedResidues, modeledResidues and coverage, the columns that make such cases diagnosable.`,
100
+ description: `Structurally align multiple structures (up to the configured batch cap) via the RCSB Structural Comparison service (TM-align / jFATCAT). reference:"first" aligns every structure to the first; reference:"all_pairs" computes the full pairwise matrix. Each pair is an independent async alignment job with per-pair partial success — a pair still computing when the budget elapses returns status "computing" with its job UUID, and a failed pair degrades its row without sinking the others. Re-call with a matching entry in resume[] to poll a computing pair's UUID instead of resubmitting; a resumed pair reports a and b in the order its job was submitted, and a resume under a different method is rejected. Returns TM-score, RMSD, and aligned-residue count per pair, plus each structure's modeled-residue count and alignment coverage. TM-score is length-normalized and can shift sharply between structures that differ only by a terminal residue or two — the greedy superposition can settle into a worse local optimum — so read tmScore alongside rmsd, alignedResidues, modeledResidues and coverage, the columns that make such cases diagnosable.`,
99
101
  annotations: { readOnlyHint: true, openWorldHint: true },
100
102
  errors: [
101
103
  {
@@ -110,13 +112,28 @@ export const compareStructures = tool('protein_compare_structures', {
110
112
  when: 'Every entry in structures[] denotes the same structure, leaving no pair to align.',
111
113
  recovery: 'Pass at least two different structures (entry ID, or entry ID + chain); a structure repeated in the list is compared once.',
112
114
  },
115
+ {
116
+ reason: 'resume_method_mismatch',
117
+ code: JsonRpcErrorCode.InvalidParams,
118
+ when: "A resumed alignment job completed under a different method than this call's method input.",
119
+ recovery: 'Re-call with the method the job ran (named in the message), or drop that resume entry to submit a fresh alignment with the new method.',
120
+ },
121
+ {
122
+ reason: 'resume_job_mismatch',
123
+ code: JsonRpcErrorCode.InvalidParams,
124
+ when: "A resume entry's uuid belongs to an alignment job for a different structure pair than its a/b labels.",
125
+ recovery: "Copy each resume entry's uuid from the same pairs[] row as its a and b, or drop the entry to submit a fresh alignment for that pair.",
126
+ },
113
127
  ],
114
128
  input: inputSchema,
115
129
  output: outputSchema,
116
130
  enrichment: {
117
131
  pairsTotal: z.number().describe('Number of pairs compared.'),
118
132
  computing: z.number().describe('Number of pairs still computing.'),
119
- notice: z.string().optional().describe('Advisory note (pending pairs, failures).'),
133
+ notice: z
134
+ .string()
135
+ .optional()
136
+ .describe('Advisory note: pairs still computing or failed (with how to resume them), structures beyond the batch cap that were ignored, and repeated structures compared once.'),
120
137
  },
121
138
  async handler(input, ctx) {
122
139
  const cfg = getServerConfig();
@@ -151,12 +168,23 @@ export const compareStructures = tool('protein_compare_structures', {
151
168
  }
152
169
  }
153
170
  const alignment = getAlignmentService();
171
+ // A resumed job whose own record contradicts this call is a client error, but
172
+ // it only surfaces once that job completes. Record the first one and throw
173
+ // after the fanout settles, so no sibling pair is left polling in the background.
174
+ let rejection;
154
175
  const rows = await mapWithConcurrency(pairs, cfg.fanoutConcurrency, async ([a, b]) => {
155
176
  const resumeUuid = resumeByPair.get(pairKey(label(a), label(b)));
156
177
  const outcome = resumeUuid
157
178
  ? await alignment.resumePair(resumeUuid, timeoutMs, ctx)
158
179
  : await alignment.comparePair(toCompare(a), toCompare(b), method, timeoutMs, ctx);
159
- const base = { a: label(a), b: label(b) };
180
+ let base = { a: label(a), b: label(b) };
181
+ if (outcome.status === 'complete' && resumeUuid && outcome.job) {
182
+ const oriented = orientResumedJob(outcome.job, base, method, resumeUuid);
183
+ if ('reason' in oriented)
184
+ rejection ??= oriented;
185
+ else
186
+ base = oriented;
187
+ }
160
188
  if (outcome.status === 'complete') {
161
189
  return {
162
190
  ...base,
@@ -180,12 +208,17 @@ export const compareStructures = tool('protein_compare_structures', {
180
208
  }
181
209
  return { ...base, status: 'failed', error: outcome.error };
182
210
  });
211
+ if (rejection) {
212
+ throw ctx.fail(rejection.reason, rejection.message, {
213
+ ...ctx.recoveryFor(rejection.reason),
214
+ });
215
+ }
183
216
  const computing = rows.filter((r) => r.status === 'computing').length;
184
217
  const failed = rows.filter((r) => r.status === 'failed').length;
185
218
  ctx.enrich({ pairsTotal: rows.length, computing });
186
219
  if (computing > 0 || failed > 0) {
187
220
  notices.push(`${computing} pair(s) still computing${failed > 0 ? `, ${failed} failed` : ''}. ` +
188
- `Re-call with a resume entry per pair (copy a, b, uuid from the pairs above) to poll existing jobs — cold alignment jobs typically finish within 30–60 s.`);
221
+ `Re-call with a resume entry per pair (copy a, b, uuid from the pairs above) to poll existing jobs — cold alignment jobs typically finish within 30–60 s. The alignment service answers an expired job the same way as a running one, so a pair that stays computing across several resumes should be resubmitted without its resume entry.`);
189
222
  }
190
223
  if (notices.length > 0)
191
224
  ctx.enrich.notice(notices.join(' '));
@@ -221,9 +254,9 @@ export const compareStructures = tool('protein_compare_structures', {
221
254
  * keyed exactly as {@link pairKey} normalizes labels. Two entries for one
222
255
  * structure yield pairs that are indistinguishable under that key — `(A,B)` and
223
256
  * `(B,A)` collapse to one — so a single resume ticket would be applied to two
224
- * separate alignment jobs, silently discarding one. Case-folding the whole label
225
- * follows the same normalization: distinguishing chains `A` and `a` here would
226
- * hand the resume lookup two pairs it cannot tell apart.
257
+ * separate alignment jobs, silently discarding one. The entry ID is case-folded
258
+ * and the chain suffix kept as-is, matching that normalization: chains `A` and
259
+ * `a` are distinct chains and stay distinct here too.
227
260
  */
228
261
  function dedupeStructures(structures) {
229
262
  const seen = new Set();
@@ -266,7 +299,7 @@ function toCompare(s) {
266
299
  return { entryId: s.pdb_id, ...(s.chain ? { asymId: s.chain } : {}) };
267
300
  }
268
301
  function label(s) {
269
- return s.chain ? `${s.pdb_id.toUpperCase()}.${s.chain}` : s.pdb_id.toUpperCase();
302
+ return compareLabel(toCompare(s));
270
303
  }
271
304
  /**
272
305
  * Canonical, order-insensitive key for a pair of structure labels, so a resume
@@ -283,4 +316,37 @@ function normalizeLabel(value) {
283
316
  function pairKey(a, b) {
284
317
  return [normalizeLabel(a), normalizeLabel(b)].sort().join('\u0000');
285
318
  }
319
+ /**
320
+ * Orient a completed resumed pair by the job's own record rather than this
321
+ * call's `structures[]` order. Resume matching is order-insensitive, but every
322
+ * per-structure value (and the TM-score, normalized by the first structure) is
323
+ * ordered as the job was submitted — so the row's `a`/`b` follow the job. The
324
+ * method can't be remapped: a job that ran a different one is rejected, as is a
325
+ * ticket whose job aligned a different pair. A record missing either echo keeps
326
+ * the current order.
327
+ */
328
+ function orientResumedJob(job, current, method, uuid) {
329
+ if (job.method && job.method !== method) {
330
+ return {
331
+ reason: 'resume_method_mismatch',
332
+ message: `Alignment job ${uuid} for ${current.a} ↔ ${current.b} ran ${job.method}, not the requested ${method}.`,
333
+ };
334
+ }
335
+ if (!job.structures)
336
+ return current;
337
+ const first = compareLabel(job.structures[0]);
338
+ const second = compareLabel(job.structures[1]);
339
+ if (pairKey(first, second) !== pairKey(current.a, current.b)) {
340
+ return {
341
+ reason: 'resume_job_mismatch',
342
+ message: `Alignment job ${uuid} aligned ${first} ↔ ${second}, not ${current.a} ↔ ${current.b}.`,
343
+ };
344
+ }
345
+ return normalizeLabel(first) === normalizeLabel(current.a)
346
+ ? current
347
+ : { a: current.b, b: current.a };
348
+ }
349
+ function compareLabel(s) {
350
+ return s.asymId ? `${s.entryId.toUpperCase()}.${s.asymId}` : s.entryId.toUpperCase();
351
+ }
286
352
  //# sourceMappingURL=compare-structures.tool.js.map
@@ -1 +1 @@
1
- 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