@cyanheads/pubmed-mcp-server 2.6.3 → 2.6.5
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/CLAUDE.md +32 -12
- package/README.md +1 -1
- package/dist/mcp-server/prompts/definitions/research-plan.prompt.d.ts.map +1 -1
- package/dist/mcp-server/prompts/definitions/research-plan.prompt.js +1 -1
- package/dist/mcp-server/prompts/definitions/research-plan.prompt.js.map +1 -1
- package/dist/mcp-server/resources/definitions/database-info.resource.d.ts +1 -1
- package/dist/mcp-server/resources/definitions/database-info.resource.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/_error-contracts.d.ts +38 -0
- package/dist/mcp-server/tools/definitions/_error-contracts.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/_error-contracts.js +42 -0
- package/dist/mcp-server/tools/definitions/_error-contracts.js.map +1 -0
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js +13 -4
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +21 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +11 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +21 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +13 -3
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +21 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js +18 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +8 -3
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.js +12 -10
- package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +4 -4
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +4 -3
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +26 -15
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.js +3 -3
- package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.js +14 -36
- package/dist/services/ncbi/api-client.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +24 -19
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/request-queue.d.ts.map +1 -1
- package/dist/services/ncbi/request-queue.js +9 -9
- package/dist/services/ncbi/request-queue.js.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts +2 -2
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.js +50 -29
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.js +22 -18
- package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
- package/package.json +6 -3
- package/server.json +3 -3
package/CLAUDE.md
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# Agent Protocol
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**Server:** @cyanheads/pubmed-mcp-server
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**Version:** 2.6.
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**Version:** 2.6.5
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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> **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
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1. **Re-run the `setup` skill** — ensures CLAUDE.md, skills, structure, and metadata are populated and up to date with the current codebase
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2. **Run the `design-mcp-server` skill** — if the tool/resource surface hasn't been mapped yet, work through domain design
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3. **Add tools/resources/prompts** — scaffold new definitions using the `add-tool`, `add-resource`, `add-prompt` skills
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3. **Add tools/resources/prompts** — scaffold new definitions using the `add-tool`, `add-app-tool`, `add-resource`, `add-prompt` skills
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4. **Add services** — scaffold domain service integrations using the `add-service` skill
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5. **Add tests** — scaffold tests for existing definitions using the `add-test` skill
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6. **Field-test definitions** — exercise tools/resources/prompts with real inputs using the `field-test` skill, get a report of issues and pain points
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7. **Run `devcheck`** — lint, format, typecheck, and security audit
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8. **Run the `security-pass` skill** — audit handlers for MCP-specific security gaps: output injection, scope blast radius, input sinks, tenant isolation
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9. **Run the `polish-docs-meta` skill** — finalize README, CHANGELOG, metadata, and agent protocol for shipping
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10. **Run the `maintenance` skill** —
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10. **Run the `maintenance` skill** — investigate changelogs, adopt upstream changes, and sync skills after `bun update --latest`
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Tailor suggestions to what's actually missing or stale — don't recite the full list every time.
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## Errors
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Handlers throw — the framework catches, classifies, and formats.
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Handlers throw — the framework catches, classifies, and formats.
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**Recommended: typed error contract.** Declare `errors: [{ reason, code, when, retryable? }]` on `tool()` / `resource()` to advertise the failure surface in `tools/list` (under `_meta['mcp-ts-core/errors']`) and receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`) bubble freely and don't need declaring.
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```ts
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errors: [
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{ reason: 'no_match', code: JsonRpcErrorCode.NotFound, when: 'No requested PMID returned data' },
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],
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async handler(input, ctx) {
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const articles = await ncbi.fetch(input.pmids);
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if (articles.length === 0) throw ctx.fail('no_match', `None of ${input.pmids.length} PMIDs returned data`);
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return { articles };
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}
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```
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**Fallback (no contract entry fits):** error factories or plain `Error`.
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```ts
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// Error factories — explicit code, concise
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import { notFound, serializationError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
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throw notFound('Item not found', { itemId });
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throw serviceUnavailable('API unavailable', { url }, { cause: err });
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throw serializationError('Invalid XML response', { endpoint });
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// Plain Error — framework auto-classifies from message patterns
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throw new Error('Item not found'); // → NotFound
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throw new Error('Invalid query format'); // → ValidationError
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//
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// McpError — full control when the code is dynamic
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import { McpError, JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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throw new McpError(JsonRpcErrorCode.DatabaseError, 'Connection failed', { pool: 'primary' });
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```
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For HTTP responses, prefer `httpErrorFromResponse(response, { service, data })` from `/utils` over hand-rolled status ladders — covers the full 4xx/5xx → `JsonRpcErrorCode` table and captures body + `Retry-After`.
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**Service-layer:** services don't have `ctx.fail`. To carry a contract `reason` from a service throw, pass `data: { reason: 'X' }` to the factory — the auto-classifier preserves `data` on the wire so clients see the same `error.data.reason` they'd see from `ctx.fail`.
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See framework CLAUDE.md and the `api-errors` skill for the full auto-classification table, all factories, and the contract reference.
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---
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| `security-pass` | Audit server for MCP-flavored security gaps: output injection, scope blast radius, input sinks, tenant isolation |
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| `devcheck` | Lint, format, typecheck, audit |
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| `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
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| `maintenance` | Investigate changelogs, adopt upstream changes, sync skills after `bun update --latest` |
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| `maintenance` | Investigate changelogs, adopt upstream changes, and sync skills after `bun update --latest` |
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| `release-and-publish` | Ship a release: verification gate, push commits+tags, publish to npm / MCP Registry / GHCR |
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| `api-auth` | Auth modes, scopes, JWT/OAuth |
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| `api-config` | AppConfig, parseConfig, env vars |
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package/README.md
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<div align="center">
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[](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](./CHANGELOG.md) [](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [](https://modelcontextprotocol.io/)
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[](./LICENSE) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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{"version":3,"file":"research-plan.prompt.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/prompts/definitions/research-plan.prompt.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAU,CAAC,EAAE,MAAM,wBAAwB,CAAC;
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{"version":3,"file":"research-plan.prompt.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/prompts/definitions/research-plan.prompt.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAU,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAgJnD,eAAO,MAAM,kBAAkB;;;;;;;;;kBA6B7B,CAAC"}
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includeAgentPrompts: z
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.enum(['true', 'false'])
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.default('false')
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.describe('Include
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.describe('Include inline guidance blocks under each phase with execution-time hints ("true" or "false")'),
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});
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function agentBlock(text, include) {
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return include ? `\n> **Agent guidance:** ${text}\n` : '';
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{"version":3,"file":"research-plan.prompt.js","sourceRoot":"","sources":["../../../../src/mcp-server/prompts/definitions/research-plan.prompt.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAEnD,MAAM,UAAU,GAAG,CAAC,CAAC,MAAM,CAAC;IAC1B,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;IAC3C,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;IAClD,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;IACpE,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;IAC3D,mBAAmB,EAAE,CAAC;SACnB,IAAI,CAAC,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;SACvB,OAAO,CAAC,OAAO,CAAC;SAChB,QAAQ,
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{"version":3,"file":"research-plan.prompt.js","sourceRoot":"","sources":["../../../../src/mcp-server/prompts/definitions/research-plan.prompt.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAEnD,MAAM,UAAU,GAAG,CAAC,CAAC,MAAM,CAAC;IAC1B,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;IAC3C,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;IAClD,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;IACpE,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;IAC3D,mBAAmB,EAAE,CAAC;SACnB,IAAI,CAAC,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;SACvB,OAAO,CAAC,OAAO,CAAC;SAChB,QAAQ,CACP,+FAA+F,CAChG;CACJ,CAAC,CAAC;AAEH,SAAS,UAAU,CAAC,IAAY,EAAE,OAAgB;IAChD,OAAO,OAAO,CAAC,CAAC,CAAC,2BAA2B,IAAI,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;AAC5D,CAAC;AAED,SAAS,SAAS,CAAC,IAAgC;IACjD,MAAM,EAAE,GAAG,IAAI,CAAC,QAAQ;SACrB,KAAK,CAAC,GAAG,CAAC;SACV,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;SACpB,MAAM,CAAC,OAAO,CAAC,CAAC;IACnB,MAAM,MAAM,GAAG,EAAE,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC7B,MAAM,GAAG,GAAG,IAAI,CAAC,QAAQ,IAAI,eAAe,CAAC;IAC7C,MAAM,EAAE,GAAG,IAAI,CAAC,mBAAmB,KAAK,MAAM,CAAC;IAE/C,MAAM,KAAK,GAAa,EAAE,CAAC;IAE3B,KAAK,CAAC,IAAI,CAAC,oBAAoB,IAAI,CAAC,KAAK,EAAE,CAAC,CAAC;IAC7C,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACf,KAAK,CAAC,IAAI,CAAC,aAAa,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC;IACrC,KAAK,CAAC,IAAI,CAAC,iBAAiB,MAAM,EAAE,CAAC,CAAC;IACtC,KAAK,CAAC,IAAI,CAAC,iBAAiB,GAAG,EAAE,CAAC,CAAC;IACnC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAEf,UAAU;IACV,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IAClB,KAAK,CAAC,IAAI,CAAC,mCAAmC,CAAC,CAAC;IAChD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACf,KAAK,CAAC,IAAI,CAAC,wCAAwC,CAAC,CAAC;IACrD,KAAK,CAAC,IAAI,CAAC,yDAAyD,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC;IAClF,KAAK,CAAC,IAAI,CAAC,2DAA2D,CAAC,CAAC;IACxE,KAAK,CAAC,IAAI,CAAC,mDAAmD,CAAC,CAAC;IAChE,KAAK,CAAC,IAAI,CACR,UAAU,CACR,8FAA8F,EAC9F,EAAE,CACH,CACF,CAAC;IACF,KAAK,CAAC,IAAI,CAAC,2BAA2B,CAAC,CAAC;IACxC,KAAK,CAAC,IAAI,CAAC,iDAAiD,MAAM,EAAE,CAAC,CAAC;IACtE,KAAK,CAAC,IAAI,CAAC,qCAAqC,CAAC,CAAC;IAClD,KAAK,CAAC,IAAI,CAAC,qEAAqE,CAAC,CAAC;IAClF,KAAK,CAAC,IAAI,CAAC,2EAA2E,CAAC,CAAC;IACxF,KAAK,CAAC,IAAI,CACR,UAAU,CACR,qGAAqG,EACrG,EAAE,CACH,CACF,CAAC;IACF,KAAK,CAAC,IAAI,CAAC,6BAA6B,CAAC,CAAC;IAC1C,KAAK,CAAC,IAAI,CAAC,+CAA+C,CAAC,CAAC;IAC5D,KAAK,CAAC,IAAI,CAAC,iEAAiE,CAAC,CAAC;IAC9E,KAAK,CAAC,IAAI,CAAC,yEAAyE,CAAC,CAAC;IACtF,KAAK,CAAC,IAAI,CAAC,kEAAkE,CAAC,CAAC;IAC/E,KAAK,CAAC,IAAI,CAAC,kEAAkE,CAAC,CAAC;IAC/E,KAAK,CAAC,IAAI,CACR,UAAU,CAAC,6EAA6E,EAAE,EAAE,CAAC,CAC9F,CAAC;IAEF,UAAU;IACV,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IAClB,KAAK,CAAC,IAAI,CAAC,0CAA0C,CAAC,CAAC;IACvD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACf,KAAK,CAAC,IAAI,CAAC,yBAAyB,CAAC,CAAC;IACtC,KAAK,CAAC,IAAI,CAAC,uDAAuD,CAAC,CAAC;IACpE,KAAK,CAAC,IAAI,CAAC,gEAAgE,CAAC,CAAC;IAC7E,KAAK,CAAC,IAAI,CAAC,qDAAqD,CAAC,CAAC;IAClE,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,6DAA6D,EAAE,EAAE,CAAC,CAAC,CAAC;IAC1F,KAAK,CAAC,IAAI,CAAC,yCAAyC,CAAC,CAAC;IACtD,KAAK,CAAC,IAAI,CAAC,+CAA+C,CAAC,CAAC;IAC5D,KAAK,CAAC,IAAI,CAAC,4DAA4D,CAAC,CAAC;IACzE,KAAK,CAAC,IAAI,CAAC,wEAAwE,CAAC,CAAC;IACrF,KAAK,CAAC,IAAI,CAAC,wDAAwD,CAAC,CAAC;IACrE,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,8DAA8D,EAAE,EAAE,CAAC,CAAC,CAAC;IAE3F,UAAU;IACV,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IAClB,KAAK,CAAC,IAAI,CAAC,uCAAuC,CAAC,CAAC;IACpD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACf,KAAK,CAAC,IAAI,CAAC,8CAA8C,CAAC,CAAC;IAC3D,KAAK,CAAC,IAAI,CAAC,2EAA2E,CAAC,CAAC;IACxF,KAAK,CAAC,IAAI,CAAC,uDAAuD,CAAC,CAAC;IACpE,KAAK,CAAC,IAAI,CAAC,oEAAoE,CAAC,CAAC;IACjF,KAAK,CAAC,IAAI,CAAC,qDAAqD,CAAC,CAAC;IAClE,KAAK,CAAC,IAAI,CACR,UAAU,CACR,yFAAyF,EACzF,EAAE,CACH,CACF,CAAC;IACF,KAAK,CAAC,IAAI,CAAC,4CAA4C,CAAC,CAAC;IACzD,KAAK,CAAC,IAAI,CAAC,oDAAoD,CAAC,CAAC;IACjE,KAAK,CAAC,IAAI,CAAC,4EAA4E,CAAC,CAAC;IACzF,KAAK,CAAC,IAAI,CAAC,2DAA2D,CAAC,CAAC;IACxE,KAAK,CAAC,IAAI,CAAC,8DAA8D,CAAC,CAAC;IAC3E,KAAK,CAAC,IAAI,CACR,UAAU,CACR,uFAAuF,EACvF,EAAE,CACH,CACF,CAAC;IAEF,UAAU;IACV,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IAClB,KAAK,CAAC,IAAI,CAAC,2BAA2B,CAAC,CAAC;IACxC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACf,KAAK,CAAC,IAAI,CAAC,sCAAsC,CAAC,CAAC;IACnD,KAAK,CAAC,IAAI,CAAC,sEAAsE,CAAC,CAAC;IACnF,KAAK,CAAC,IAAI,CAAC,oFAAoF,CAAC,CAAC;IACjG,KAAK,CAAC,IAAI,CAAC,2DAA2D,CAAC,CAAC;IACxE,KAAK,CAAC,IAAI,CACR,UAAU,CACR,oFAAoF,EACpF,EAAE,CACH,CACF,CAAC;IACF,KAAK,CAAC,IAAI,CAAC,yCAAyC,CAAC,CAAC;IACtD,KAAK,CAAC,IAAI,CAAC,8DAA8D,CAAC,CAAC;IAC3E,KAAK,CAAC,IAAI,CAAC,4DAA4D,CAAC,CAAC;IACzE,KAAK,CAAC,IAAI,CAAC,qDAAqD,CAAC,CAAC;IAClE,KAAK,CAAC,IAAI,CAAC,+DAA+D,CAAC,CAAC;IAC5E,KAAK,CAAC,IAAI,CACR,UAAU,CACR,uFAAuF,EACvF,EAAE,CACH,CACF,CAAC;IAEF,OAAO,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAClD,CAAC;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAG,MAAM,CAAC,eAAe,EAAE;IACxD,WAAW,EAAE,gFAAgF;IAC7F,IAAI,EAAE,UAAU;IAEhB,QAAQ,EAAE,CAAC,IAAI,EAAE,EAAE;QACjB,MAAM,IAAI,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC;QAE7B,OAAO;YACL;gBACE,IAAI,EAAE,WAAoB;gBAC1B,OAAO,EAAE;oBACP,IAAI,EAAE,MAAe;oBACrB,IAAI,EAAE;wBACJ,mDAAmD;wBACnD,8EAA8E;wBAC9E,+FAA+F;wBAC/F,4FAA4F;qBAC7F,CAAC,IAAI,CAAC,GAAG,CAAC;iBACZ;aACF;YACD;gBACE,IAAI,EAAE,MAAe;gBACrB,OAAO,EAAE;oBACP,IAAI,EAAE,MAAe;oBACrB,IAAI,EAAE,IAAI;iBACX;aACF;SACF,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
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@@ -14,5 +14,5 @@ export declare const databaseInfoResource: import("@cyanheads/mcp-ts-core").Reso
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fullName: z.ZodOptional<z.ZodString>;
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description: z.ZodOptional<z.ZodString>;
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}, z.core.$strip>>>;
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-
}, z.core.$strip
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+
}, z.core.$strip>, undefined>;
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//# sourceMappingURL=database-info.resource.d.ts.map
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"database-info.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/database-info.resource.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoBrD,eAAO,MAAM,oBAAoB;;;;;;;;;;
|
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1
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+
{"version":3,"file":"database-info.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/database-info.resource.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoBrD,eAAO,MAAM,oBAAoB;;;;;;;;;;6BA+C/B,CAAC"}
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@@ -0,0 +1,38 @@
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1
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+
/**
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2
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+
* @fileoverview Shared `errors[]` contract entries for tool definitions.
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3
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*
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4
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* The NCBI service layer (queue, retry loop, deadline) throws three failure
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5
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* modes that any NCBI-consuming tool can surface. They're collected here so
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6
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* tool definitions can spread them into their own `errors[]` without
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* duplicating the contract — keeping the public failure surface consistent
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* and machine-readable across the whole server.
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*
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10
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* Service-layer throws stamp `data.reason` to match these entries (see
|
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11
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* `src/services/ncbi/request-queue.ts` and `src/services/ncbi/ncbi-service.ts`)
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12
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+
* so wire payloads carry the same `error.data.reason` clients see from
|
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13
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* `ctx.fail` in tool handlers.
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*
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* @module src/mcp-server/tools/definitions/_error-contracts
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*/
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import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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/**
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* Cross-tool error reasons shared by every tool that calls the NCBI service.
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+
* Spread these into a tool's `errors[]` alongside any tool-specific entries.
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+
*/
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+
export declare const NCBI_SERVICE_ERRORS: readonly [{
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+
readonly reason: "queue_full";
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+
readonly code: JsonRpcErrorCode.RateLimited;
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readonly when: "Local NCBI request queue is at capacity.";
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readonly retryable: true;
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}, {
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readonly reason: "ncbi_unreachable";
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readonly code: JsonRpcErrorCode.ServiceUnavailable;
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readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
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readonly retryable: true;
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}, {
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readonly reason: "ncbi_deadline_exceeded";
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readonly code: JsonRpcErrorCode.Timeout;
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readonly when: "Total request deadline expired before NCBI returned a response.";
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readonly retryable: true;
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}];
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//# sourceMappingURL=_error-contracts.d.ts.map
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@@ -0,0 +1 @@
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1
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+
{"version":3,"file":"_error-contracts.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;GAGG;AACH,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;EAmBtB,CAAC"}
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@@ -0,0 +1,42 @@
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1
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+
/**
|
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2
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+
* @fileoverview Shared `errors[]` contract entries for tool definitions.
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3
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+
*
|
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4
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+
* The NCBI service layer (queue, retry loop, deadline) throws three failure
|
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5
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+
* modes that any NCBI-consuming tool can surface. They're collected here so
|
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6
|
+
* tool definitions can spread them into their own `errors[]` without
|
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7
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+
* duplicating the contract — keeping the public failure surface consistent
|
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8
|
+
* and machine-readable across the whole server.
|
|
9
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+
*
|
|
10
|
+
* Service-layer throws stamp `data.reason` to match these entries (see
|
|
11
|
+
* `src/services/ncbi/request-queue.ts` and `src/services/ncbi/ncbi-service.ts`)
|
|
12
|
+
* so wire payloads carry the same `error.data.reason` clients see from
|
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13
|
+
* `ctx.fail` in tool handlers.
|
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14
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+
*
|
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15
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+
* @module src/mcp-server/tools/definitions/_error-contracts
|
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16
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+
*/
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17
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+
import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
|
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18
|
+
/**
|
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19
|
+
* Cross-tool error reasons shared by every tool that calls the NCBI service.
|
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20
|
+
* Spread these into a tool's `errors[]` alongside any tool-specific entries.
|
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21
|
+
*/
|
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22
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+
export const NCBI_SERVICE_ERRORS = [
|
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23
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+
{
|
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|
+
reason: 'queue_full',
|
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25
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+
code: JsonRpcErrorCode.RateLimited,
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+
when: 'Local NCBI request queue is at capacity.',
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+
retryable: true,
|
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+
},
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+
{
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+
reason: 'ncbi_unreachable',
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+
code: JsonRpcErrorCode.ServiceUnavailable,
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+
when: 'NCBI E-utilities is unreachable after all retry attempts.',
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+
retryable: true,
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+
},
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+
{
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+
reason: 'ncbi_deadline_exceeded',
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+
code: JsonRpcErrorCode.Timeout,
|
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38
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+
when: 'Total request deadline expired before NCBI returned a response.',
|
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39
|
+
retryable: true,
|
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+
},
|
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+
];
|
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+
//# sourceMappingURL=_error-contracts.js.map
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@@ -0,0 +1 @@
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1
|
+
{"version":3,"file":"_error-contracts.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;GAGG;AACH,MAAM,CAAC,MAAM,mBAAmB,GAAG;IACjC;QACE,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,gBAAgB,CAAC,WAAW;QAClC,IAAI,EAAE,0CAA0C;QAChD,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,kBAAkB;QAC1B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,2DAA2D;QACjE,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,wBAAwB;QAChC,IAAI,EAAE,gBAAgB,CAAC,OAAO;QAC9B,IAAI,EAAE,iEAAiE;QACvE,SAAS,EAAE,IAAI;KAChB;CACO,CAAC"}
|
|
@@ -21,5 +21,5 @@ export declare const convertIdsTool: import("@cyanheads/mcp-ts-core").ToolDefini
|
|
|
21
21
|
}, z.core.$strip>>;
|
|
22
22
|
totalConverted: z.ZodNumber;
|
|
23
23
|
totalSubmitted: z.ZodNumber;
|
|
24
|
-
}, z.core.$strip
|
|
24
|
+
}, z.core.$strip>, undefined>;
|
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25
25
|
//# sourceMappingURL=convert-ids.tool.d.ts.map
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|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"convert-ids.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAajD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;
|
|
1
|
+
{"version":3,"file":"convert-ids.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAajD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;6BAyGzB,CAAC"}
|
|
@@ -33,10 +33,19 @@ export const convertIdsTool = tool('pubmed_convert_ids', {
|
|
|
33
33
|
.array(z
|
|
34
34
|
.object({
|
|
35
35
|
requestedId: z.string().describe('The ID that was submitted'),
|
|
36
|
-
pmid: z.string().optional().describe('PubMed ID'),
|
|
37
|
-
pmcid: z
|
|
38
|
-
|
|
39
|
-
|
|
36
|
+
pmid: z.string().optional().describe('PubMed ID; absent if no mapping was found'),
|
|
37
|
+
pmcid: z
|
|
38
|
+
.string()
|
|
39
|
+
.optional()
|
|
40
|
+
.describe('PubMed Central ID; absent if the article has no PMC copy'),
|
|
41
|
+
doi: z
|
|
42
|
+
.string()
|
|
43
|
+
.optional()
|
|
44
|
+
.describe('Digital Object Identifier; absent if no DOI is on record'),
|
|
45
|
+
errmsg: z
|
|
46
|
+
.string()
|
|
47
|
+
.optional()
|
|
48
|
+
.describe('Error message if conversion failed. Presence of `errmsg` is the failure signal; absence means the conversion succeeded.'),
|
|
40
49
|
})
|
|
41
50
|
.describe('Per-ID conversion record'))
|
|
42
51
|
.describe('Conversion results, one per input ID'),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
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1
|
+
{"version":3,"file":"convert-ids.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,gBAAgB,CAAC;AAE9E;;;;GAIG;AACH,MAAM,gBAAgB,GAAG,gCAAgC,CAAC;AAC1D,MAAM,qBAAqB,GACzB,gIAAgI,CAAC;AAEnI,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EAAE,gQAAgQ;IAC7Q,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,eAAe,EAAE,cAAc,CAAC,CAAC;IACrD,SAAS,EACP,+GAA+G;IAEjH,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;aACxB,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CACP,sIAAsI,CACvI;QACH,MAAM,EAAE,CAAC;aACN,IAAI,CAAC,CAAC,OAAO,EAAE,MAAM,EAAE,KAAK,CAAC,CAAC;aAC9B,QAAQ,CACP,sFAAsF,CACvF;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;YAC7D,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;YACjF,KAAK,EAAE,CAAC;iBACL,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,0DAA0D,CAAC;YACvE,GAAG,EAAE,CAAC;iBACH,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,0DAA0D,CAAC;YACvE,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,yHAAyH,CAC1H;SACJ,CAAC;aACD,QAAQ,CAAC,0BAA0B,CAAC,CACxC;aACA,QAAQ,CAAC,sCAAsC,CAAC;QACnD,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QAC3E,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;KAC/D,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,8BAA8B,EAAE;YAC3C,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,MAAM;YACvB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QAEH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,KAAK,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;QAE9F,0EAA0E;QAC1E,MAAM,OAAO,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;YAC5B,MAAM,WAAW,GAAG,MAAM,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC;YAC9C,IAAI,MAA0B,CAAC;YAC/B,IAAI,CAAC,CAAC,MAAM,KAAK,SAAS,EAAE,CAAC;gBAC3B,MAAM,QAAQ,GAAG,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC;gBAClC,IAAI,gBAAgB,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC;oBACpC,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,gCAAgC,EAAE,EAAE,WAAW,EAAE,QAAQ,EAAE,CAAC,CAAC;oBAC3E,MAAM,GAAG,qBAAqB,CAAC;gBACjC,CAAC;qBAAM,CAAC;oBACN,MAAM,GAAG,QAAQ,CAAC;gBACpB,CAAC;YACH,CAAC;YACD,OAAO;gBACL,WAAW;gBACX,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,IAAI,EAAE,IAAI,EAAE,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrD,GAAG,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,IAAI,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;gBACxD,GAAG,CAAC,CAAC,CAAC,GAAG,KAAK,SAAS,IAAI,EAAE,GAAG,EAAE,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAClD,GAAG,CAAC,MAAM,KAAK,SAAS,IAAI,EAAE,MAAM,EAAE,CAAC;aACxC,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,cAAc,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,MAAM,CAAC;QAC/D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,8BAA8B,EAAE;YAC3C,cAAc;YACd,cAAc,EAAE,KAAK,CAAC,GAAG,CAAC,MAAM;SACjC,CAAC,CAAC;QAEH,OAAO,EAAE,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,KAAK,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC;IACvE,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,0BAA0B;YAC1B,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;YAClE,EAAE;YACF,+CAA+C;YAC/C,4BAA4B;SAC7B,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CACR,KAAK,CAAC,CAAC,WAAW,MAAM,CAAC,CAAC,IAAI,IAAI,GAAG,MAAM,CAAC,CAAC,KAAK,IAAI,GAAG,MAAM,CAAC,CAAC,GAAG,IAAI,GAAG,MAAM,CAAC,CAAC,MAAM,IAAI,GAAG,IAAI,CACrG,CAAC;QACJ,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"}
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@@ -4,6 +4,7 @@
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* @module src/mcp-server/tools/definitions/fetch-articles.tool
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*/
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import { z } from '@cyanheads/mcp-ts-core';
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import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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export declare const fetchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
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pmids: z.ZodArray<z.ZodString>;
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includeMesh: z.ZodDefault<z.ZodBoolean>;
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@@ -68,5 +69,24 @@ export declare const fetchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDef
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}, z.core.$strip>>;
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totalReturned: z.ZodNumber;
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unavailablePmids: z.ZodOptional<z.ZodArray<z.ZodString>>;
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}, z.core.$strip
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}, z.core.$strip>, readonly [{
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readonly reason: "queue_full";
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readonly code: JsonRpcErrorCode.RateLimited;
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readonly when: "Local NCBI request queue is at capacity.";
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readonly retryable: true;
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}, {
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readonly reason: "ncbi_unreachable";
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readonly code: JsonRpcErrorCode.ServiceUnavailable;
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readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
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readonly retryable: true;
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}, {
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readonly reason: "ncbi_deadline_exceeded";
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readonly code: JsonRpcErrorCode.Timeout;
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readonly when: "Total request deadline expired before NCBI returned a response.";
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readonly retryable: true;
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}, {
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readonly reason: "invalid_efetch_response";
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readonly code: JsonRpcErrorCode.SerializationError;
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readonly when: "NCBI EFetch returned a payload missing the PubmedArticleSet wrapper.";
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}]>;
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//# sourceMappingURL=fetch-articles.tool.d.ts.map
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@@ -1 +1 @@
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1
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{"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;
|
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1
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+
{"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAwK5B,CAAC"}
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@@ -4,10 +4,12 @@
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4
4
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* @module src/mcp-server/tools/definitions/fetch-articles.tool
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5
5
|
*/
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6
6
|
import { tool, z } from '@cyanheads/mcp-ts-core';
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7
|
+
import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
|
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7
8
|
import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
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8
9
|
import { parseFullArticle } from '../../../services/ncbi/parsing/article-parser.js';
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10
|
import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
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10
11
|
import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTICLE, } from './_concepts.js';
|
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12
|
+
import { NCBI_SERVICE_ERRORS } from './_error-contracts.js';
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11
13
|
import { pmidStringSchema } from './_schemas.js';
|
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12
14
|
const AuthorSchema = z
|
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13
15
|
.object({
|
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@@ -97,6 +99,14 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
|
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97
99
|
annotations: { readOnlyHint: true, openWorldHint: true },
|
|
98
100
|
_meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID]),
|
|
99
101
|
sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/fetch-articles.tool.ts',
|
|
102
|
+
errors: [
|
|
103
|
+
...NCBI_SERVICE_ERRORS,
|
|
104
|
+
{
|
|
105
|
+
reason: 'invalid_efetch_response',
|
|
106
|
+
code: JsonRpcErrorCode.SerializationError,
|
|
107
|
+
when: 'NCBI EFetch returned a payload missing the PubmedArticleSet wrapper.',
|
|
108
|
+
},
|
|
109
|
+
],
|
|
100
110
|
input: z.object({
|
|
101
111
|
pmids: z.array(pmidStringSchema).min(1).max(200).describe('PubMed IDs to fetch'),
|
|
102
112
|
includeMesh: z.boolean().default(true).describe('Include MeSH terms'),
|
|
@@ -114,7 +124,7 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
|
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|
114
124
|
ctx.log.info('Executing pubmed_fetch', { pmidCount: input.pmids.length });
|
|
115
125
|
const xmlData = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 100, signal: ctx.signal });
|
|
116
126
|
if (!xmlData || !('PubmedArticleSet' in xmlData)) {
|
|
117
|
-
throw
|
|
127
|
+
throw ctx.fail('invalid_efetch_response', 'Invalid EFetch response from NCBI: missing PubmedArticleSet', { requestedPmids: input.pmids.length });
|
|
118
128
|
}
|
|
119
129
|
const rawArticles = xmlData.PubmedArticleSet?.PubmedArticle;
|
|
120
130
|
const xmlArticles = rawArticles ? ensureArray(rawArticles) : [];
|
|
@@ -1 +1 @@
|
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|
1
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-
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1
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+
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@@ -7,6 +7,7 @@
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* @module src/mcp-server/tools/definitions/fetch-fulltext.tool
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*/
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import { z } from '@cyanheads/mcp-ts-core';
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import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
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pmcids: z.ZodOptional<z.ZodArray<z.ZodString>>;
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pmids: z.ZodOptional<z.ZodArray<z.ZodString>>;
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@@ -90,5 +91,24 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
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detail: z.ZodOptional<z.ZodString>;
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}, z.core.$strip>>>;
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unavailablePmcIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
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-
}, z.core.$strip
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}, z.core.$strip>, readonly [{
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readonly reason: "queue_full";
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readonly code: JsonRpcErrorCode.RateLimited;
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readonly when: "Local NCBI request queue is at capacity.";
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readonly retryable: true;
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}, {
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readonly reason: "ncbi_unreachable";
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readonly code: JsonRpcErrorCode.ServiceUnavailable;
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readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
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readonly retryable: true;
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}, {
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readonly reason: "ncbi_deadline_exceeded";
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readonly code: JsonRpcErrorCode.Timeout;
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readonly when: "Total request deadline expired before NCBI returned a response.";
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readonly retryable: true;
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}, {
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readonly reason: "invalid_pmc_efetch_response";
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readonly code: JsonRpcErrorCode.SerializationError;
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readonly when: "PMC EFetch returned a payload missing the pmc-articleset wrapper.";
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}]>;
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//# sourceMappingURL=fetch-fulltext.tool.d.ts.map
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;
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1
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+
{"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiLjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAkP5B,CAAC"}
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@@ -7,6 +7,7 @@
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* @module src/mcp-server/tools/definitions/fetch-fulltext.tool
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*/
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9
9
|
import { tool, z } from '@cyanheads/mcp-ts-core';
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10
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+
import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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10
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|
import { htmlExtractor, pdfParser } from '@cyanheads/mcp-ts-core/utils';
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11
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import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
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12
13
|
import { extractDoi, extractPmid } from '../../../services/ncbi/parsing/article-parser.js';
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@@ -15,6 +16,7 @@ import { findAll, findOne } from '../../../services/ncbi/parsing/pmc-xml-helpers
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15
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|
import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
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import { getUnpaywallService } from '../../../services/unpaywall/unpaywall-service.js';
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17
18
|
import { conceptMeta, EDAM_DATA_RETRIEVAL, SCHEMA_SCHOLARLY_ARTICLE } from './_concepts.js';
|
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19
|
+
import { NCBI_SERVICE_ERRORS } from './_error-contracts.js';
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18
20
|
import { pmidStringSchema } from './_schemas.js';
|
|
19
21
|
function normalizePmcId(id) {
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20
22
|
return id.replace(/^PMC/i, '');
|
|
@@ -144,10 +146,18 @@ const UnavailableSchema = z
|
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|
144
146
|
.describe('One PMID that could not be returned with an explanation of why');
|
|
145
147
|
// ─── Tool Definition ─────────────────────────────────────────────────────────
|
|
146
148
|
export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
|
|
147
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-
description: 'Fetch full-text articles. Primary source is PubMed Central (structured JATS with sections and references). When a PMID has no PMC copy, transparently falls back to Unpaywall (open-access copies hosted by publishers or institutional repositories) and returns best-effort HTML-as-Markdown or PDF-as-text. Set UNPAYWALL_EMAIL to enable the fallback.
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149
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+
description: 'Fetch full-text articles. Primary source is PubMed Central (structured JATS with sections and references). When a PMID has no PMC copy, transparently falls back to Unpaywall (open-access copies hosted by publishers or institutional repositories) and returns best-effort HTML-as-Markdown or PDF-as-text. Set UNPAYWALL_EMAIL to enable the fallback. Provide exactly one of `pmcids` (PMC IDs directly) or `pmids` (PubMed IDs, auto-resolved via the PMC ID Converter) — not both, not neither.',
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148
150
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annotations: { readOnlyHint: true, openWorldHint: true },
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149
151
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_meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL]),
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150
152
|
sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/fetch-fulltext.tool.ts',
|
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153
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+
errors: [
|
|
154
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+
...NCBI_SERVICE_ERRORS,
|
|
155
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+
{
|
|
156
|
+
reason: 'invalid_pmc_efetch_response',
|
|
157
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+
code: JsonRpcErrorCode.SerializationError,
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158
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+
when: 'PMC EFetch returned a payload missing the pmc-articleset wrapper.',
|
|
159
|
+
},
|
|
160
|
+
],
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151
161
|
input: z
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|
152
162
|
.object({
|
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153
163
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pmcids: z
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@@ -191,7 +201,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
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191
201
|
unavailablePmcIds: z
|
|
192
202
|
.array(z.string())
|
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193
203
|
.optional()
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194
|
-
.describe('PMC IDs requested directly
|
|
204
|
+
.describe('PMC IDs that returned no data, whether requested directly via `pmcids` or resolved from `pmids` via the PMC ID Converter'),
|
|
195
205
|
}),
|
|
196
206
|
async handler(input, ctx) {
|
|
197
207
|
ctx.log.info('Executing pubmed_fetch_fulltext', {
|
|
@@ -238,7 +248,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
|
|
|
238
248
|
});
|
|
239
249
|
const articleSet = findOne(xmlData, 'pmc-articleset');
|
|
240
250
|
if (!articleSet)
|
|
241
|
-
throw
|
|
251
|
+
throw ctx.fail('invalid_pmc_efetch_response', 'Invalid PMC EFetch response: missing pmc-articleset', { requestedPmcIdCount: pmcIds.length });
|
|
242
252
|
let parsed = findAll(articleSet, 'article').map(parsePmcArticle);
|
|
243
253
|
if (input.sections?.length) {
|
|
244
254
|
const sectionFilter = input.sections;
|