@cyanheads/pubmed-mcp-server 2.7.0 → 2.7.2
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 +16 -4
- package/README.md +10 -2
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +6 -0
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts +6 -0
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js.map +1 -1
- package/dist/services/error-contracts.d.ts +6 -0
- package/dist/services/error-contracts.d.ts.map +1 -1
- package/dist/services/error-contracts.js +7 -0
- package/dist/services/error-contracts.js.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.js +38 -1
- package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
- package/dist/services/europe-pmc/types.d.ts +4 -0
- package/dist/services/europe-pmc/types.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.js +8 -6
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/package.json +12 -7
- package/server.json +3 -3
package/CLAUDE.md
CHANGED
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@@ -2,7 +2,7 @@
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**Server:** @cyanheads/pubmed-mcp-server
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**Version:** 2.6.12
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.3`
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**Engines:** Bun ≥1.3.2, Node ≥24.0.0
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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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@@ -262,7 +262,7 @@ Available skills:
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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, 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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| `release-and-publish` | Ship a release: verification gate, push commits+tags, publish to npm / MCP Registry / GHCR / `.mcpb` bundle on GitHub Releases |
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| `api-auth` | Auth modes, scopes, JWT/OAuth |
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| `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
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| `api-config` | AppConfig, parseConfig, env vars |
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| `bun run build` | Compile TypeScript |
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| `bun run rebuild` | Clean + build |
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| `bun run clean` | Remove build artifacts |
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| `bun run devcheck` | Lint + format + typecheck + security |
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| `bun run devcheck` | Lint + format + typecheck + security + packaging alignment |
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| `bun run audit:refresh` | Delete `bun.lock`, reinstall, and re-run `bun audit`. Use when `devcheck` flags a transitive advisory — `bun update` is sticky on transitive resolutions, so the advisory may be a stale-lockfile false positive. If it survives the refresh, it's real. |
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| `bun run tree` | Generate directory structure doc |
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| `bun run format` | Auto-fix formatting |
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| `bun run test` | Run tests |
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| `bun run lint:mcp` | Validate MCP definitions against spec |
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| `bun run lint:packaging` | Validate env var alignment between `manifest.json` and `server.json` (skipped cleanly when `manifest.json` is absent) |
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| `bun run list-skills` | List skills in `skills/` with name + description |
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| `bun run bundle` | Build and pack as `dist/pubmed-mcp-server.mcpb` for one-click Claude Desktop install |
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| `bun run start:stdio` | Production mode (stdio) |
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| `bun run start:http` | Production mode (HTTP) |
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---
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## Bundling
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`bun run bundle` produces `dist/pubmed-mcp-server.mcpb` for one-click install in Claude Desktop. MCPB is stdio-only — HTTP and Docker deployments are unaffected. The `release-and-publish` skill attaches the bundle to the GitHub Release at a stable `releases/latest/download/pubmed-mcp-server.mcpb` URL that powers the README install badge.
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**Adding an env var requires both files**: `server.json` stdio `environmentVariables[]` (registry discovery) and `manifest.json` `mcp_config.env` (bundle install UX, plus `user_config` if user-prompted). `bun run lint:packaging` (run by `devcheck`) verifies the env var names align.
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---
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## Publishing
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Run the `release-and-publish` skill after git wrapup — it runs the verification gate (`devcheck`, `rebuild`, `test`), pushes commits and tags, and publishes to npm, the MCP Registry, and
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Run the `release-and-publish` skill after git wrapup — it runs the verification gate (`devcheck`, `rebuild`, `test`), pushes commits and tags, and publishes to npm, the MCP Registry, GHCR, and attaches the `.mcpb` bundle to the GitHub Release, halting on the first failure. For reference, the underlying commands are:
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```bash
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bun publish --access public
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package/README.md
CHANGED
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@@ -7,9 +7,17 @@
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<div align="center">
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[](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server)
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[](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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</div>
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<div align="center">
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[](https://github.com/cyanheads/pubmed-mcp-server/releases/latest/download/pubmed-mcp-server.mcpb) [](cursor://anysphere.cursor-deeplink/mcp/install?name=pubmed-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvcHVibWVkLW1jcC1zZXJ2ZXIiXX0=) [](vscode:mcp/install?%7B%22name%22%3A%22pubmed-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads%2Fpubmed-mcp-server%22%5D%7D)
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</div>
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@@ -180,5 +180,11 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
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readonly when: "Europe PMC returned a body that could not be parsed (invalid JSON or XML).";
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readonly recovery: "Retry the request; Europe PMC returned a malformed response that could not be parsed.";
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readonly retryable: true;
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}, {
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readonly reason: "europepmc_invalid_input";
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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readonly when: "Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).";
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readonly recovery: "Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.";
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readonly retryable: false;
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}]>;
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//# sourceMappingURL=fetch-fulltext.tool.d.ts.map
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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;;;;;;;;;;;;;;;;;;GAkBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoR/D,eAAO,MAAM,iBAAiB
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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;;;;;;;;;;;;;;;;;;GAkBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoR/D,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsc5B,CAAC"}
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readonly when: "Europe PMC returned a body that could not be parsed (invalid JSON or XML).";
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readonly recovery: "Retry the request; Europe PMC returned a malformed response that could not be parsed.";
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readonly retryable: true;
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}, {
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readonly reason: "europepmc_invalid_input";
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readonly code: JsonRpcErrorCode.ValidationError;
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readonly when: "Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).";
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readonly recovery: "Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.";
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readonly retryable: false;
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}, {
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readonly reason: "europepmc_disabled";
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readonly code: JsonRpcErrorCode.ConfigurationError;
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{"version":3,"file":"pubmed-europepmc-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmBjE,eAAO,MAAM,yBAAyB
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{"version":3,"file":"pubmed-europepmc-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmBjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA8NpC,CAAC"}
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sort: z
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.string()
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.optional()
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.describe('Optional EPMC sort
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.describe('Optional EPMC sort: `<field> asc|desc`. Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Fields outside the documented set are rejected by EPMC.'),
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}),
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output: z.object({
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query: z.string().describe('Effective query string echoed by Europe PMC'),
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{"version":3,"file":"pubmed-europepmc-search.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,wBAAwB,EAAE,MAAM,+BAA+B,CAAC;AACzE,OAAO,EAAE,mBAAmB,EAAE,MAAM,6CAA6C,CAAC;AAClF,OAAO,EACL,qBAAqB,EACrB,yBAAyB,GAE1B,MAAM,gCAAgC,CAAC;AACxC,OAAO,EACL,WAAW,EACX,oBAAoB,EACpB,cAAc,EACd,oBAAoB,GACrB,MAAM,gBAAgB,CAAC;AAExB,MAAM,UAAU,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC,CAAC;AAE/D,gFAAgF;AAEhF,MAAM,CAAC,MAAM,yBAAyB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACvE,WAAW,EACT,4YAA4Y;IAC9Y,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,EAAE,oBAAoB,EAAE,cAAc,CAAC,CAAC;IAChF,SAAS,EACP,2HAA2H;IAE7H,MAAM,EAAE;QACN,GAAG,wBAAwB;QAC3B;YACE,MAAM,EAAE,oBAAoB;YAC5B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;YACzC,IAAI,EAAE,6DAA6D;YACnE,QAAQ,EAAE,mFAAmF;SAC9F;KACO;IAEV,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,kPAAkP,CACnP;QACH,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CAAC,yCAAyC,CAAC;QACtD,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,OAAO,CAAC,GAAG,CAAC;aACZ,QAAQ,CACP,8HAA8H,CAC/H;QACH,OAAO,EAAE,CAAC;aACP,KAAK,CAAC,UAAU,CAAC;aACjB,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,EAAE;aACV,QAAQ,CACP,gDAAgD,yBAAyB,CAAC,IAAI,CAAC,IAAI,CAAC,mGAAmG,qBAAqB,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAC3N;QACH,UAAU,EAAE,CAAC;aACV,IAAI,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;aACtB,OAAO,CAAC,MAAM,CAAC;aACf,QAAQ,CACP,qGAAqG,CACtG;QACH,IAAI,EAAE,CAAC;aACJ,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,
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{"version":3,"file":"pubmed-europepmc-search.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,wBAAwB,EAAE,MAAM,+BAA+B,CAAC;AACzE,OAAO,EAAE,mBAAmB,EAAE,MAAM,6CAA6C,CAAC;AAClF,OAAO,EACL,qBAAqB,EACrB,yBAAyB,GAE1B,MAAM,gCAAgC,CAAC;AACxC,OAAO,EACL,WAAW,EACX,oBAAoB,EACpB,cAAc,EACd,oBAAoB,GACrB,MAAM,gBAAgB,CAAC;AAExB,MAAM,UAAU,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC,CAAC;AAE/D,gFAAgF;AAEhF,MAAM,CAAC,MAAM,yBAAyB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACvE,WAAW,EACT,4YAA4Y;IAC9Y,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,EAAE,oBAAoB,EAAE,cAAc,CAAC,CAAC;IAChF,SAAS,EACP,2HAA2H;IAE7H,MAAM,EAAE;QACN,GAAG,wBAAwB;QAC3B;YACE,MAAM,EAAE,oBAAoB;YAC5B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;YACzC,IAAI,EAAE,6DAA6D;YACnE,QAAQ,EAAE,mFAAmF;SAC9F;KACO;IAEV,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,kPAAkP,CACnP;QACH,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CAAC,yCAAyC,CAAC;QACtD,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,OAAO,CAAC,GAAG,CAAC;aACZ,QAAQ,CACP,8HAA8H,CAC/H;QACH,OAAO,EAAE,CAAC;aACP,KAAK,CAAC,UAAU,CAAC;aACjB,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,EAAE;aACV,QAAQ,CACP,gDAAgD,yBAAyB,CAAC,IAAI,CAAC,IAAI,CAAC,mGAAmG,qBAAqB,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAC3N;QACH,UAAU,EAAE,CAAC;aACV,IAAI,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;aACtB,OAAO,CAAC,MAAM,CAAC;aACf,QAAQ,CACP,qGAAqG,CACtG;QACH,IAAI,EAAE,CAAC;aACJ,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,6VAA6V,CAC9V;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;QACzE,IAAI,EAAE,CAAC;aACJ,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,MAAM,EAAE,UAAU,CAAC,QAAQ,CACzB,gHAAgH,CACjH;YACD,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,QAAQ,CAAC,+DAA+D,CAAC;YAC5E,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;YAClE,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACxD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;YAC3D,oBAAoB,EAAE,CAAC;iBACpB,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,yCAAyC,CAAC;YACtD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;YACnE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,4BAA4B,CAAC;YACnE,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;YACvD,YAAY,EAAE,CAAC;iBACZ,OAAO,EAAE;iBACT,QAAQ,EAAE;iBACV,QAAQ,CAAC,gDAAgD,CAAC;YAC7D,cAAc,EAAE,CAAC;iBACd,OAAO,EAAE;iBACT,QAAQ,EAAE;iBACV,QAAQ,CACP,iMAAiM,CAClM;YACH,eAAe,EAAE,CAAC;iBACf,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,qFAAqF,CACtF;YACH,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;YACrF,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;SACvD,CAAC;aACD,QAAQ,CAAC,iDAAiD,CAAC,CAC/D;aACA,QAAQ,CAAC,8DAA8D,CAAC;QAC3E,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;QACxE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yDAAyD,CAAC;QAC1F,cAAc,EAAE,CAAC;aACd,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,kFAAkF,CAAC;QAC/F,cAAc,EAAE,CAAC;aACd,KAAK,CAAC,UAAU,CAAC;aACjB,QAAQ,CAAC,2DAA2D,CAAC;QACxE,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QAChF,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,6DAA6D,CAAC;KAC3E,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,mCAAmC,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QAC1E,MAAM,IAAI,GAAG,mBAAmB,EAAE,CAAC;QACnC,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,MAAM,GAAG,CAAC,IAAI,CACZ,oBAAoB,EACpB,mFAAmF,EACnF,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,oBAAoB,CAAC,EAAE,CAC7C,CAAC;QACJ,CAAC;QAED,MAAM,OAAO,GAAG,CAAC,KAAK,CAAC,OAAO,IAAI,yBAAyB,CAA+B,CAAC;QAC3F,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC;YAC/B,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,QAAQ,EAAE,KAAK,CAAC,QAAQ;YACxB,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,OAAO;YACP,GAAG,CAAC,KAAK,CAAC,IAAI,IAAI,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE,CAAC;YACvC,GAAG,CAAC,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC;SAC1C,CAAC,CAAC;QAEH,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACnC,MAAM,EAAE,CAAC,CAAC,MAA+C;YACzD,MAAM,EAAE,CAAC,CAAC,EAAE;YACZ,GAAG,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC;YAClC,GAAG,CAAC,CAAC,CAAC,YAAY,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,YAAY,EAAE,CAAC;YAClD,GAAG,CAAC,CAAC,CAAC,YAAY,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,YAAY,EAAE,CAAC;YAClD,GAAG,CAAC,CAAC,CAAC,OAAO,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC;YACxC,GAAG,CAAC,CAAC,CAAC,oBAAoB,IAAI,EAAE,oBAAoB,EAAE,CAAC,CAAC,oBAAoB,EAAE,CAAC;YAC/E,GAAG,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;YAC/B,GAAG,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC;YAClC,GAAG,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|
|
@@ -78,6 +78,12 @@ export declare const EUROPEPMC_SERVICE_ERRORS: readonly [{
|
|
|
78
78
|
readonly when: "Europe PMC returned a body that could not be parsed (invalid JSON or XML).";
|
|
79
79
|
readonly recovery: "Retry the request; Europe PMC returned a malformed response that could not be parsed.";
|
|
80
80
|
readonly retryable: true;
|
|
81
|
+
}, {
|
|
82
|
+
readonly reason: "europepmc_invalid_input";
|
|
83
|
+
readonly code: JsonRpcErrorCode.ValidationError;
|
|
84
|
+
readonly when: "Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).";
|
|
85
|
+
readonly recovery: "Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.";
|
|
86
|
+
readonly retryable: false;
|
|
81
87
|
}];
|
|
82
88
|
/**
|
|
83
89
|
* Reason identifier union for type-safe authoring on the service layer.
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"error-contracts.d.ts","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqCtB,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,wBAAwB;;;;;;EAS3B,CAAC;AAEX;;;GAGG;AACH,eAAO,MAAM,wBAAwB
|
|
1
|
+
{"version":3,"file":"error-contracts.d.ts","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqCtB,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,wBAAwB;;;;;;EAS3B,CAAC;AAEX;;;GAGG;AACH,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;EAyB3B,CAAC;AAEX;;;;GAIG;AACH,MAAM,MAAM,kBAAkB,GAC1B,CAAC,OAAO,mBAAmB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GAC9C,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,CAAC;AAQxD;;;;;;;;;;;;GAYG;AACH,wBAAgB,WAAW,CAAC,MAAM,EAAE,kBAAkB,GAAG;IAAE,QAAQ,EAAE;QAAE,IAAI,EAAE,MAAM,CAAA;KAAE,CAAA;CAAE,CAMtF"}
|
|
@@ -89,6 +89,13 @@ export const EUROPEPMC_SERVICE_ERRORS = [
|
|
|
89
89
|
recovery: 'Retry the request; Europe PMC returned a malformed response that could not be parsed.',
|
|
90
90
|
retryable: true,
|
|
91
91
|
},
|
|
92
|
+
{
|
|
93
|
+
reason: 'europepmc_invalid_input',
|
|
94
|
+
code: JsonRpcErrorCode.ValidationError,
|
|
95
|
+
when: 'Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).',
|
|
96
|
+
recovery: 'Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.',
|
|
97
|
+
retryable: false,
|
|
98
|
+
},
|
|
92
99
|
];
|
|
93
100
|
const REASON_TO_RECOVERY = new Map([...NCBI_SERVICE_ERRORS, ...UNPAYWALL_SERVICE_ERRORS, ...EUROPEPMC_SERVICE_ERRORS].map((entry) => [entry.reason, entry.recovery]));
|
|
94
101
|
/**
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"error-contracts.js","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,MAAM,CAAC,MAAM,mBAAmB,GAAG;IACjC;QACE,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,gBAAgB,CAAC,WAAW;QAClC,IAAI,EAAE,0CAA0C;QAChD,QAAQ,EAAE,qEAAqE;QAC/E,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,kBAAkB;QAC1B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,2DAA2D;QACjE,QAAQ,EAAE,4EAA4E;QACtF,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,wBAAwB;QAChC,IAAI,EAAE,gBAAgB,CAAC,OAAO;QAC9B,IAAI,EAAE,iEAAiE;QACvE,QAAQ,EAAE,+DAA+D;QACzE,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,mEAAmE;QACzE,QAAQ,EAAE,iFAAiF;QAC3F,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,yBAAyB;QACjC,IAAI,EAAE,gBAAgB,CAAC,QAAQ;QAC/B,IAAI,EAAE,uEAAuE;QAC7E,QAAQ,EACN,gGAAgG;QAClG,SAAS,EAAE,KAAK;KACjB;CACO,CAAC;AAEX;;;;GAIG;AACH,MAAM,CAAC,MAAM,wBAAwB,GAAG;IACtC;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,qEAAqE;QAC3E,QAAQ,EACN,gGAAgG;QAClG,SAAS,EAAE,IAAI;KAChB;CACO,CAAC;AAEX;;;GAGG;AACH,MAAM,CAAC,MAAM,wBAAwB,GAAG;IACtC;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,sDAAsD;QAC5D,QAAQ,EACN,iGAAiG;QACnG,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,4BAA4B;QACpC,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,4EAA4E;QAClF,QAAQ,EACN,uFAAuF;QACzF,SAAS,EAAE,IAAI;KAChB;CACO,CAAC;AAYX,MAAM,kBAAkB,GAAG,IAAI,GAAG,CAChC,CAAC,GAAG,mBAAmB,EAAE,GAAG,wBAAwB,EAAE,GAAG,wBAAwB,CAAC,CAAC,GAAG,CACpF,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,QAAQ,CAAC,CAC1C,CACF,CAAC;AAEF;;;;;;;;;;;;GAYG;AACH,MAAM,UAAU,WAAW,CAAC,MAA0B;IACpD,MAAM,IAAI,GAAG,kBAAkB,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IAC5C,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,wDAAwD,MAAM,GAAG,CAAC,CAAC;IACrF,CAAC;IACD,OAAO,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,EAAE,CAAC;AAChC,CAAC"}
|
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1
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+
{"version":3,"file":"error-contracts.js","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,MAAM,CAAC,MAAM,mBAAmB,GAAG;IACjC;QACE,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,gBAAgB,CAAC,WAAW;QAClC,IAAI,EAAE,0CAA0C;QAChD,QAAQ,EAAE,qEAAqE;QAC/E,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,kBAAkB;QAC1B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,2DAA2D;QACjE,QAAQ,EAAE,4EAA4E;QACtF,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,wBAAwB;QAChC,IAAI,EAAE,gBAAgB,CAAC,OAAO;QAC9B,IAAI,EAAE,iEAAiE;QACvE,QAAQ,EAAE,+DAA+D;QACzE,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,mEAAmE;QACzE,QAAQ,EAAE,iFAAiF;QAC3F,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,yBAAyB;QACjC,IAAI,EAAE,gBAAgB,CAAC,QAAQ;QAC/B,IAAI,EAAE,uEAAuE;QAC7E,QAAQ,EACN,gGAAgG;QAClG,SAAS,EAAE,KAAK;KACjB;CACO,CAAC;AAEX;;;;GAIG;AACH,MAAM,CAAC,MAAM,wBAAwB,GAAG;IACtC;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,qEAAqE;QAC3E,QAAQ,EACN,gGAAgG;QAClG,SAAS,EAAE,IAAI;KAChB;CACO,CAAC;AAEX;;;GAGG;AACH,MAAM,CAAC,MAAM,wBAAwB,GAAG;IACtC;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,sDAAsD;QAC5D,QAAQ,EACN,iGAAiG;QACnG,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,4BAA4B;QACpC,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,4EAA4E;QAClF,QAAQ,EACN,uFAAuF;QACzF,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,yBAAyB;QACjC,IAAI,EAAE,gBAAgB,CAAC,eAAe;QACtC,IAAI,EAAE,+FAA+F;QACrG,QAAQ,EACN,8GAA8G;QAChH,SAAS,EAAE,KAAK;KACjB;CACO,CAAC;AAYX,MAAM,kBAAkB,GAAG,IAAI,GAAG,CAChC,CAAC,GAAG,mBAAmB,EAAE,GAAG,wBAAwB,EAAE,GAAG,wBAAwB,CAAC,CAAC,GAAG,CACpF,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,QAAQ,CAAC,CAC1C,CACF,CAAC;AAEF;;;;;;;;;;;;GAYG;AACH,MAAM,UAAU,WAAW,CAAC,MAA0B;IACpD,MAAM,IAAI,GAAG,kBAAkB,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IAC5C,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,wDAAwD,MAAM,GAAG,CAAC,CAAC;IACrF,CAAC;IACD,OAAO,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,EAAE,CAAC;AAChC,CAAC"}
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@@ -1 +1 @@
|
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1
|
-
{"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;
|
|
1
|
+
{"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAeH,OAAO,KAAK,EAAE,QAAQ,EAAgB,MAAM,4CAA4C,CAAC;AAEzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,iBAAiB,CAAC;AACrD,OAAO,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAC;AAC3D,OAAO,KAAK,EACV,uBAAuB,EAEvB,qBAAqB,EAErB,qBAAqB,EACrB,eAAe,EAChB,MAAM,YAAY,CAAC;AA2BpB;;;;;;;GAOG;AACH,qBAAa,gBAAgB;IAIzB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAL7B,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAY;gBAG1B,MAAM,EAAE,kBAAkB,EAC1B,KAAK,EAAE,qBAAqB,EAC5B,UAAU,EAAE,MAAM;IAmBrC;;;OAGG;IACG,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,qBAAqB,CAAC;IAkF3E;;;;;;;OAOG;IACG,WAAW,CACf,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,eAAe,EACvB,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,uBAAuB,CAAC;IAkBnC;;;;;;;;OAQG;IACH,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,QAAQ,GAAG,SAAS;IAgCnD;;;;OAIG;YACW,SAAS;CAsDxB;AAMD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAuB3C;AAED,6EAA6E;AAC7E,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}
|
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@@ -11,8 +11,9 @@
|
|
|
11
11
|
*
|
|
12
12
|
* @module src/services/europe-pmc/europe-pmc-service
|
|
13
13
|
*/
|
|
14
|
-
import { internalError, JsonRpcErrorCode, McpError, serializationError, } from '@cyanheads/mcp-ts-core/errors';
|
|
14
|
+
import { internalError, JsonRpcErrorCode, McpError, serializationError, validationError, } from '@cyanheads/mcp-ts-core/errors';
|
|
15
15
|
import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
|
|
16
|
+
// biome-ignore lint/suspicious/noDeprecatedImports: staying on in-tree XMLValidator — see ncbi/response-handler.ts
|
|
16
17
|
import { XMLParser, XMLValidator } from 'fast-xml-parser';
|
|
17
18
|
import { getServerConfig } from '../../config/server-config.js';
|
|
18
19
|
import { recoveryFor } from '../../services/error-contracts.js';
|
|
@@ -93,6 +94,42 @@ export class EuropePmcService {
|
|
|
93
94
|
...recoveryFor('europepmc_invalid_response'),
|
|
94
95
|
}, { cause: error });
|
|
95
96
|
}
|
|
97
|
+
/**
|
|
98
|
+
* EPMC surfaces structured input errors (e.g. empty query) via `errMsg`
|
|
99
|
+
* with HTTP 200. Route to ValidationError (non-retryable) so the caller
|
|
100
|
+
* fixes the input instead of looping on the same request.
|
|
101
|
+
*/
|
|
102
|
+
const errMsg = typeof parsed.errMsg === 'string' ? parsed.errMsg : undefined;
|
|
103
|
+
if (errMsg) {
|
|
104
|
+
throw validationError(`Europe PMC rejected the request: ${errMsg}`, {
|
|
105
|
+
reason: 'europepmc_invalid_input',
|
|
106
|
+
epmcErrCode: parsed.errCode,
|
|
107
|
+
epmcErrMsg: errMsg,
|
|
108
|
+
recovery: { hint: `Europe PMC reported: "${errMsg}". Fix the input and retry.` },
|
|
109
|
+
});
|
|
110
|
+
}
|
|
111
|
+
/**
|
|
112
|
+
* EPMC silently returns a `{ version }`-only envelope (no `hitCount`, no
|
|
113
|
+
* `request` echo, no `resultList`) when it rejects a parameter — most
|
|
114
|
+
* commonly an undocumented `sort` field. Without this guard the response
|
|
115
|
+
* normalizes to a fake 0-hit success and the caller never learns the sort
|
|
116
|
+
* was rejected. Route to ValidationError (non-retryable) since retrying
|
|
117
|
+
* the same input will be rejected again.
|
|
118
|
+
*/
|
|
119
|
+
if (parsed.hitCount === undefined &&
|
|
120
|
+
parsed.request === undefined &&
|
|
121
|
+
parsed.resultList === undefined) {
|
|
122
|
+
const rejectionHint = params.sort
|
|
123
|
+
? `Europe PMC silently rejected the request. Most likely cause: invalid sort field "${params.sort}". Use a documented sort like \`P_PDATE_D desc\`, \`CITED desc\`, \`AUTH_FIRST asc\`, or \`PUB_YEAR desc\`, or omit \`sort\` for relevance ranking.`
|
|
124
|
+
: 'Europe PMC silently rejected the request (empty envelope, no hitCount). Verify query syntax, sort field, and cursorMark.';
|
|
125
|
+
throw validationError(rejectionHint, {
|
|
126
|
+
reason: 'europepmc_invalid_input',
|
|
127
|
+
...(params.sort && { sort: params.sort }),
|
|
128
|
+
...(params.cursorMark && params.cursorMark !== '*' && { cursorMark: params.cursorMark }),
|
|
129
|
+
responseSnippet: text.substring(0, 200),
|
|
130
|
+
recovery: { hint: rejectionHint },
|
|
131
|
+
});
|
|
132
|
+
}
|
|
96
133
|
const hits = ensureArray(parsed.resultList?.result);
|
|
97
134
|
const echoed = parsed.request?.queryString ?? params.query;
|
|
98
135
|
// EPMC echoes back the input cursor mark on the final page, so absence of
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"europe-pmc-service.js","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EACL,aAAa,EACb,gBAAgB,EAChB,QAAQ,EACR,kBAAkB,
|
|
1
|
+
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|
|
@@ -68,6 +68,10 @@ export interface EuropePmcResultList {
|
|
|
68
68
|
* effective query so callers can preview what EPMC actually searched.
|
|
69
69
|
*/
|
|
70
70
|
export interface EuropePmcSearchResponse {
|
|
71
|
+
/** Structured error code on input rejection (e.g. empty query). */
|
|
72
|
+
errCode?: number | string;
|
|
73
|
+
/** Structured error message on input rejection (e.g. empty query). */
|
|
74
|
+
errMsg?: string;
|
|
71
75
|
/** Total matching records across all pages. */
|
|
72
76
|
hitCount?: number;
|
|
73
77
|
/** Cursor token for the next page; absent on the final page. */
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/types.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,qDAAqD;AACrD,eAAO,MAAM,kBAAkB,qDAAqD,CAAC;AAErF;;;;;GAKG;AACH,MAAM,MAAM,eAAe,GAAG,KAAK,GAAG,KAAK,GAAG,KAAK,GAAG,KAAK,GAAG,KAAK,GAAG,KAAK,GAAG,KAAK,GAAG,KAAK,GAAG,KAAK,CAAC;AAEpG,2DAA2D;AAC3D,eAAO,MAAM,yBAAyB,gCAAiC,CAAC;AACxE,eAAO,MAAM,qBAAqB,8CAA+C,CAAC;AAElF;;;;;GAKG;AACH,MAAM,WAAW,kBAAkB;IACjC,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,mBAAmB,CAAC,EAAE,OAAO,CAAC;IAC9B,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,oDAAoD;IACpD,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,wDAAwD;IACxD,oBAAoB,CAAC,EAAE,MAAM,CAAC;IAC9B,OAAO,CAAC,EAAE,GAAG,GAAG,GAAG,CAAC;IACpB,MAAM,CAAC,EAAE,GAAG,GAAG,GAAG,CAAC;IACnB,oFAAoF;IACpF,iBAAiB,CAAC,EAAE,GAAG,GAAG,GAAG,CAAC;IAC9B,6EAA6E;IAC7E,EAAE,EAAE,MAAM,CAAC;IACX,MAAM,CAAC,EAAE,GAAG,GAAG,GAAG,CAAC;IACnB,KAAK,CAAC,EAAE,GAAG,GAAG,GAAG,CAAC;IAClB,YAAY,CAAC,EAAE,GAAG,GAAG,GAAG,CAAC;IACzB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,6DAA6D;IAC7D,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,MAAM,EAAE,eAAe,CAAC;IACxB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC;CAC1B;AAED,+DAA+D;AAC/D,MAAM,WAAW,mBAAmB;IAClC,MAAM,CAAC,EAAE,kBAAkB,EAAE,GAAG,kBAAkB,CAAC;CACpD;AAED;;;;GAIG;AACH,MAAM,WAAW,uBAAuB;IACtC,mEAAmE;IACnE,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAAC;IAC1B,sEAAsE;IACtE,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,+CAA+C;IAC/C,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,gEAAgE;IAChE,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,mEAAmE;IACnE,OAAO,CAAC,EAAE;QACR,WAAW,CAAC,EAAE,MAAM,CAAC;QACrB,UAAU,CAAC,EAAE,MAAM,CAAC;QACpB,UAAU,CAAC,EAAE,MAAM,CAAC;QACpB,QAAQ,CAAC,EAAE,MAAM,CAAC;QAClB,IAAI,CAAC,EAAE,MAAM,CAAC;QACd,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC;KAC1B,CAAC;IACF,UAAU,CAAC,EAAE,mBAAmB,CAAC;IACjC,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC;CAC1B;AAED,8DAA8D;AAC9D,MAAM,WAAW,qBAAqB;IACpC,4EAA4E;IAC5E,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,MAAM,CAAC;IACjB,IAAI,EAAE,kBAAkB,EAAE,CAAC;IAC3B,uEAAuE;IACvE,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,KAAK,EAAE,MAAM,CAAC;CACf;AAED,uDAAuD;AACvD,MAAM,WAAW,qBAAqB;IACpC,yEAAyE;IACzE,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,+BAA+B;IAC/B,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,KAAK,EAAE,MAAM,CAAC;IACd,2EAA2E;IAC3E,UAAU,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,QAAQ,CAAC;IACxC,MAAM,CAAC,EAAE,WAAW,CAAC;IACrB,oDAAoD;IACpD,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,4EAA4E;IAC5E,OAAO,CAAC,EAAE,SAAS,eAAe,EAAE,CAAC;CACtC;AAED,uCAAuC;AACvC,MAAM,MAAM,uBAAuB,GAC/B;IAAE,IAAI,EAAE,OAAO,CAAC;IAAC,GAAG,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,eAAe,CAAA;CAAE,GACvE;IAAE,IAAI,EAAE,eAAe,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,CAAC"}
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;
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1
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+
{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAiBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAiMrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;;IAsBjD;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA4BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;CA0NL"}
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@@ -7,13 +7,15 @@
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7
7
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import { notFound, serializationError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
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8
8
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import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
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9
9
|
/**
|
|
10
|
-
* fast-xml-parser
|
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11
|
-
*
|
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12
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-
*
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13
|
-
* 5.8.0
|
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14
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-
* `
|
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15
|
-
*
|
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10
|
+
* fast-xml-parser 5.8.0 marks the in-tree `XMLValidator` as `@deprecated` in
|
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11
|
+
* favor of the new sibling package `fast-xml-validator`. The export still
|
|
12
|
+
* works; we stay on it until the sibling has real adoption (was 17 days old
|
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13
|
+
* with 1 star at 5.8.0 release). Both call sites strip `<!DOCTYPE ...>`
|
|
14
|
+
* before `XMLValidator.validate`, so the tightened DOCTYPE entity validation
|
|
15
|
+
* 5.8.0 adds via `xml-naming` cannot reach us. Revisit when the sibling
|
|
16
|
+
* matures.
|
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16
17
|
*/
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18
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+
// biome-ignore lint/suspicious/noDeprecatedImports: staying on in-tree XMLValidator — see block comment above
|
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17
19
|
import { XMLParser as FastXmlParser, XMLValidator } from 'fast-xml-parser';
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18
20
|
import { recoveryFor } from '../../services/error-contracts.js';
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19
21
|
/**
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@@ -1 +1 @@
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1
|
-
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package/package.json
CHANGED
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@@ -1,6 +1,6 @@
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|
1
1
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{
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|
2
2
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"name": "@cyanheads/pubmed-mcp-server",
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|
3
|
-
"version": "2.7.
|
|
3
|
+
"version": "2.7.2",
|
|
4
4
|
"mcpName": "io.github.cyanheads/pubmed-mcp-server",
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|
5
5
|
"description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
|
|
6
6
|
"type": "module",
|
|
@@ -18,7 +18,11 @@
|
|
|
18
18
|
"tree": "bun run scripts/tree.ts",
|
|
19
19
|
"format": "biome check --write --unsafe",
|
|
20
20
|
"test": "bunx vitest run",
|
|
21
|
+
"audit:refresh": "rm -f bun.lock && bun install && bun audit",
|
|
22
|
+
"list-skills": "bun run scripts/list-skills.ts",
|
|
21
23
|
"lint:mcp": "bun run scripts/lint-mcp.ts",
|
|
24
|
+
"lint:packaging": "bun run scripts/lint-packaging.ts",
|
|
25
|
+
"bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/pubmed-mcp-server.mcpb",
|
|
22
26
|
"changelog:build": "bun run scripts/build-changelog.ts",
|
|
23
27
|
"changelog:check": "bun run scripts/build-changelog.ts --check",
|
|
24
28
|
"publish-mcp": "mcp-publisher login github -token \"$(security find-generic-password -a \"$USER\" -s mcp-publisher-github-pat -w)\" && mcp-publisher publish",
|
|
@@ -72,24 +76,25 @@
|
|
|
72
76
|
"access": "public"
|
|
73
77
|
},
|
|
74
78
|
"dependencies": {
|
|
75
|
-
"@cyanheads/mcp-ts-core": "^0.9.
|
|
79
|
+
"@cyanheads/mcp-ts-core": "^0.9.3",
|
|
76
80
|
"defuddle": "^0.18.1",
|
|
77
|
-
"fast-xml-parser": "
|
|
81
|
+
"fast-xml-parser": "^5.8.0",
|
|
78
82
|
"linkedom": "^0.18.12",
|
|
79
83
|
"pino-pretty": "^13.1.3",
|
|
80
84
|
"sanitize-html": "^2.17.4",
|
|
81
|
-
"unpdf": "^1.6.2"
|
|
85
|
+
"unpdf": "^1.6.2",
|
|
86
|
+
"zod": "^4.4.3"
|
|
82
87
|
},
|
|
83
88
|
"devDependencies": {
|
|
84
89
|
"@biomejs/biome": "^2.4.15",
|
|
85
|
-
"@types/node": "^25.9.
|
|
90
|
+
"@types/node": "^25.9.1",
|
|
86
91
|
"@types/sanitize-html": "^2.16.1",
|
|
87
|
-
"@vitest/coverage-istanbul": "^4.1.
|
|
92
|
+
"@vitest/coverage-istanbul": "^4.1.7",
|
|
88
93
|
"depcheck": "^1.4.7",
|
|
89
94
|
"fast-check": "^4.8.0",
|
|
90
95
|
"ignore": "^7.0.5",
|
|
91
96
|
"tsc-alias": "^1.8.17",
|
|
92
97
|
"typescript": "^6.0.3",
|
|
93
|
-
"vitest": "^4.1.
|
|
98
|
+
"vitest": "^4.1.7"
|
|
94
99
|
}
|
|
95
100
|
}
|
package/server.json
CHANGED
|
@@ -6,7 +6,7 @@
|
|
|
6
6
|
"url": "https://github.com/cyanheads/pubmed-mcp-server",
|
|
7
7
|
"source": "github"
|
|
8
8
|
},
|
|
9
|
-
"version": "2.7.
|
|
9
|
+
"version": "2.7.2",
|
|
10
10
|
"remotes": [
|
|
11
11
|
{
|
|
12
12
|
"type": "streamable-http",
|
|
@@ -19,7 +19,7 @@
|
|
|
19
19
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
20
20
|
"identifier": "@cyanheads/pubmed-mcp-server",
|
|
21
21
|
"runtimeHint": "bun",
|
|
22
|
-
"version": "2.7.
|
|
22
|
+
"version": "2.7.2",
|
|
23
23
|
"packageArguments": [
|
|
24
24
|
{
|
|
25
25
|
"type": "positional",
|
|
@@ -66,7 +66,7 @@
|
|
|
66
66
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
67
67
|
"identifier": "@cyanheads/pubmed-mcp-server",
|
|
68
68
|
"runtimeHint": "bun",
|
|
69
|
-
"version": "2.7.
|
|
69
|
+
"version": "2.7.2",
|
|
70
70
|
"packageArguments": [
|
|
71
71
|
{
|
|
72
72
|
"type": "positional",
|