@omophub/omophub-mcp 1.2.2 → 1.3.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +45 -4
- package/dist/client/api.d.ts +2 -2
- package/dist/client/api.d.ts.map +1 -1
- package/dist/client/api.js +1 -1
- package/dist/client/api.js.map +1 -1
- package/dist/client/resolve.d.ts +26 -0
- package/dist/client/resolve.d.ts.map +1 -0
- package/dist/client/resolve.js +55 -0
- package/dist/client/resolve.js.map +1 -0
- package/dist/client/types.d.ts +13 -8
- package/dist/client/types.d.ts.map +1 -1
- package/dist/formatters/index.d.ts.map +1 -1
- package/dist/formatters/index.js +21 -4
- package/dist/formatters/index.js.map +1 -1
- package/dist/index.d.ts.map +1 -1
- package/dist/index.js +12 -9
- package/dist/index.js.map +1 -1
- package/dist/resources/index.d.ts.map +1 -1
- package/dist/resources/index.js +7 -4
- package/dist/resources/index.js.map +1 -1
- package/dist/server.d.ts +2 -1
- package/dist/server.d.ts.map +1 -1
- package/dist/server.js +1 -3
- package/dist/server.js.map +1 -1
- package/dist/tools/concepts.d.ts.map +1 -1
- package/dist/tools/concepts.js +7 -4
- package/dist/tools/concepts.js.map +1 -1
- package/dist/tools/explore.d.ts.map +1 -1
- package/dist/tools/explore.js +6 -4
- package/dist/tools/explore.js.map +1 -1
- package/dist/tools/hierarchy.d.ts.map +1 -1
- package/dist/tools/hierarchy.js +4 -2
- package/dist/tools/hierarchy.js.map +1 -1
- package/dist/tools/mappings.d.ts.map +1 -1
- package/dist/tools/mappings.js +4 -2
- package/dist/tools/mappings.js.map +1 -1
- package/dist/tools/search.d.ts.map +1 -1
- package/dist/tools/search.js +4 -2
- package/dist/tools/search.js.map +1 -1
- package/dist/tools/semantic-search.d.ts.map +1 -1
- package/dist/tools/semantic-search.js +4 -2
- package/dist/tools/semantic-search.js.map +1 -1
- package/dist/tools/similar.d.ts.map +1 -1
- package/dist/tools/similar.js +4 -2
- package/dist/tools/similar.js.map +1 -1
- package/dist/tools/vocabularies.d.ts.map +1 -1
- package/dist/tools/vocabularies.js +36 -10
- package/dist/tools/vocabularies.js.map +1 -1
- package/dist/transports/http.d.ts +3 -2
- package/dist/transports/http.d.ts.map +1 -1
- package/dist/transports/http.js +126 -19
- package/dist/transports/http.js.map +1 -1
- package/dist/utils/auth.d.ts +1 -1
- package/dist/utils/auth.d.ts.map +1 -1
- package/dist/utils/auth.js +1 -6
- package/dist/utils/auth.js.map +1 -1
- package/package.json +2 -2
package/README.md
CHANGED
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@@ -2,7 +2,7 @@
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<p>
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<strong>Medical vocabularies for AI agents.</strong><br/>
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Search, map, and navigate
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Search, map, and navigate 10M+ OMOP concepts: SNOMED CT, ICD-10, RxNorm, LOINC, and more. Directly from Claude, Cursor, VS Code, or any MCP-compatible client.
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</p>
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<p>
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@@ -140,7 +140,48 @@ npx -y @omophub/omophub-mcp --transport=http --port=3100 --api-key=oh_your_key_h
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# Health check: http://localhost:3100/health
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```
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Connect MCP clients to
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Connect MCP clients to `/` or `/mcp`. Useful for centralized deployments where multiple AI agents share one server instance.
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</details>
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<details>
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<summary><strong>Hosted (mcp.omophub.com)</strong></summary>
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Connect directly to the OMOPHub-hosted MCP server - no installation required. Each client authenticates with their own API key via the `Authorization` header:
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**Claude Code:**
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```bash
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claude mcp add omophub --transport http \
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-H "Authorization: Bearer oh_your_key_here" \
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https://mcp.omophub.com
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```
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**VS Code** (`.vscode/mcp.json`):
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```json
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{
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"servers": {
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"omophub": {
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"type": "http",
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"url": "https://mcp.omophub.com",
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"headers": { "Authorization": "Bearer oh_your_key_here" }
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}
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}
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}
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```
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**Cursor / Windsurf:**
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```json
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{
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"mcpServers": {
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"omophub": {
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"url": "https://mcp.omophub.com",
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"headers": { "Authorization": "Bearer oh_your_key_here" }
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}
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}
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}
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```
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> **Note:** Claude Desktop's Custom Connectors UI only supports OAuth and cannot send custom headers. Use the [npx setup](#claude-desktop) instead.
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</details>
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<summary><strong>Docker</strong></summary>
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```bash
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# HTTP mode (default in Docker)
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# HTTP mode (default in Docker) - serves MCP on port 3100
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docker run -e OMOPHUB_API_KEY=oh_your_key_here -p 3100:3100 omophub/omophub-mcp
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# Stdio mode (for piping)
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@@ -256,7 +297,7 @@ In **HTTP mode**, the health endpoint is available at `/health` on the same port
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```bash
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npx @omophub/omophub-mcp --transport=http --port=3100 --api-key=oh_your_key
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curl http://localhost:3100/health
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# → {"status":"ok","version":"1.
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# → {"status":"ok","version":"1.3.1","uptime_seconds":42}
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```
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In **stdio mode**, use `--health-port` for a standalone health endpoint:
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package/dist/client/api.d.ts
CHANGED
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import type { ApiResponse } from './types.js';
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export declare class OmopHubClient {
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readonly baseUrl: string;
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private readonly apiKey;
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private readonly analyticsOptout;
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constructor(apiKey: string, baseUrl?: string);
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constructor(apiKey: string | undefined, baseUrl?: string);
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request<T>(path: string, params?: Record<string, string | number | boolean | undefined>, toolName?: string): Promise<ApiResponse<T>>;
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post<T>(path: string, body: Record<string, unknown>, toolName?: string): Promise<ApiResponse<T>>;
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}
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package/dist/client/api.d.ts.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"api.d.ts","sourceRoot":"","sources":["../../src/client/api.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AAkB9C,qBAAa,aAAa;IACxB,
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{"version":3,"file":"api.d.ts","sourceRoot":"","sources":["../../src/client/api.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AAkB9C,qBAAa,aAAa;IACxB,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAS;IAChC,OAAO,CAAC,QAAQ,CAAC,eAAe,CAAU;gBAE9B,MAAM,EAAE,MAAM,GAAG,SAAS,EAAE,OAAO,CAAC,EAAE,MAAM;IAUlD,OAAO,CAAC,CAAC,EACb,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,GAAG,OAAO,GAAG,SAAS,CAAC,EAC9D,QAAQ,CAAC,EAAE,MAAM,GAChB,OAAO,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC;IAqFpB,IAAI,CAAC,CAAC,EACV,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,QAAQ,CAAC,EAAE,MAAM,GAChB,OAAO,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC;CA0E3B"}
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package/dist/client/api.js
CHANGED
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@@ -19,7 +19,7 @@ export class OmopHubClient {
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apiKey;
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analyticsOptout;
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constructor(apiKey, baseUrl) {
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this.apiKey = apiKey;
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this.apiKey = apiKey ?? '';
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this.baseUrl = (baseUrl ||
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process.env.OMOPHUB_BASE_URL ||
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'https://api.omophub.com/v1').replace(/\/$/, '');
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package/dist/client/api.js.map
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{"version":3,"file":"api.js","sourceRoot":"","sources":["../../src/client/api.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAC;AACrD,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAC;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAC;AAGxC,MAAM,WAAW,GAAG,CAAC,CAAC;AAEtB,kFAAkF;AAClF,SAAS,eAAe,CAAC,MAAc,EAAE,UAAkB;IACzD,MAAM,OAAO,GAAG,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;IACrC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,OAAO,IAAI,CAAC;QAAE,OAAO,OAAO,GAAG,IAAI,CAAC;IAElE,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;IAChC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;QACxB,MAAM,OAAO,GAAG,IAAI,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;QAClC,OAAO,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,UAAU,CAAC;IAC5C,CAAC;IAED,OAAO,UAAU,CAAC;AACpB,CAAC;AAED,MAAM,OAAO,aAAa;
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+
{"version":3,"file":"api.js","sourceRoot":"","sources":["../../src/client/api.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAC;AACrD,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAC;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,eAAe,CAAC;AAGxC,MAAM,WAAW,GAAG,CAAC,CAAC;AAEtB,kFAAkF;AAClF,SAAS,eAAe,CAAC,MAAc,EAAE,UAAkB;IACzD,MAAM,OAAO,GAAG,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;IACrC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,OAAO,IAAI,CAAC;QAAE,OAAO,OAAO,GAAG,IAAI,CAAC;IAElE,MAAM,IAAI,GAAG,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;IAChC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC;QACxB,MAAM,OAAO,GAAG,IAAI,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;QAClC,OAAO,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,UAAU,CAAC;IAC5C,CAAC;IAED,OAAO,UAAU,CAAC;AACpB,CAAC;AAED,MAAM,OAAO,aAAa;IACf,OAAO,CAAS;IACR,MAAM,CAAS;IACf,eAAe,CAAU;IAE1C,YAAY,MAA0B,EAAE,OAAgB;QACtD,IAAI,CAAC,MAAM,GAAG,MAAM,IAAI,EAAE,CAAC;QAC3B,IAAI,CAAC,OAAO,GAAG,CACb,OAAO;YACP,OAAO,CAAC,GAAG,CAAC,gBAAgB;YAC5B,4BAA4B,CAC7B,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC;QACrB,IAAI,CAAC,eAAe,GAAG,OAAO,CAAC,GAAG,CAAC,wBAAwB,KAAK,MAAM,CAAC;IACzE,CAAC;IAED,KAAK,CAAC,OAAO,CACX,IAAY,EACZ,MAA8D,EAC9D,QAAiB;QAEjB,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,GAAG,IAAI,CAAC,OAAO,GAAG,IAAI,EAAE,CAAC,CAAC;QAE9C,IAAI,MAAM,EAAE,CAAC;YACX,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC;gBAClD,IAAI,KAAK,KAAK,SAAS,IAAI,KAAK,KAAK,EAAE,EAAE,CAAC;oBACxC,GAAG,CAAC,YAAY,CAAC,GAAG,CAAC,GAAG,EAAE,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC;gBAC3C,CAAC;YACH,CAAC;QACH,CAAC;QAED,MAAM,OAAO,GAA2B;YACtC,aAAa,EAAE,UAAU,IAAI,CAAC,MAAM,EAAE;YACtC,YAAY,EAAE,eAAe,OAAO,EAAE;YACtC,MAAM,EAAE,kBAAkB;SAC3B,CAAC;QAEF,IAAI,CAAC,IAAI,CAAC,eAAe,EAAE,CAAC;YAC1B,OAAO,CAAC,cAAc,CAAC,GAAG,MAAM,CAAC;YACjC,IAAI,QAAQ,EAAE,CAAC;gBACb,OAAO,CAAC,YAAY,CAAC,GAAG,QAAQ,CAAC;YACnC,CAAC;QACH,CAAC;QAED,IAAI,SAAS,GAAiB,IAAI,CAAC;QAEnC,KAAK,IAAI,OAAO,GAAG,CAAC,EAAE,OAAO,IAAI,WAAW,EAAE,OAAO,EAAE,EAAE,CAAC;YACxD,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YAEzB,IAAI,CAAC;gBACH,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,QAAQ,EAAE,EAAE;oBAC3C,OAAO;oBACP,MAAM,EAAE,WAAW,CAAC,OAAO,CAAC,MAAM,CAAC;iBACpC,CAAC,CAAC;gBACH,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,EAAE,GAAG,KAAK,CAAC;gBAEpC,MAAM,CAAC,KAAK,CAAC,aAAa,EAAE;oBAC1B,SAAS,EAAE,QAAQ;oBACnB,QAAQ,EAAE,IAAI;oBACd,WAAW,EAAE,QAAQ;oBACrB,MAAM,EAAE,QAAQ,CAAC,MAAM;iBACxB,CAAC,CAAC;gBAEH,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,IAAI,OAAO,GAAG,WAAW,EAAE,CAAC;oBACrD,MAAM,UAAU,GAAG,QAAQ,CAAC,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC;oBACvD,MAAM,UAAU,GAAG,IAAI,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC;oBACxC,MAAM,MAAM,GAAG,UAAU,CAAC,CAAC,CAAC,eAAe,CAAC,UAAU,EAAE,UAAU,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC;oBACjF,MAAM,CAAC,IAAI,CAAC,6BAA6B,MAAM,IAAI,EAAE;wBACnD,SAAS,EAAE,QAAQ;wBACnB,QAAQ,EAAE,IAAI;qBACf,CAAC,CAAC;oBACH,MAAM,IAAI,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC,CAAC;oBAC5D,SAAS;gBACX,CAAC;gBAED,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;oBACjB,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;oBACnC,IAAI,OAAe,CAAC;oBACpB,IAAI,CAAC;wBACH,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAuD,CAAC;wBACtF,OAAO,GAAG,MAAM,CAAC,KAAK,EAAE,OAAO,IAAI,MAAM,CAAC,OAAO,IAAI,IAAI,CAAC;oBAC5D,CAAC;oBAAC,MAAM,CAAC;wBACP,OAAO,GAAG,IAAI,IAAI,QAAQ,CAAC,UAAU,CAAC;oBACxC,CAAC;oBACD,MAAM,IAAI,eAAe,CAAC,QAAQ,CAAC,MAAM,EAAE,OAAO,EAAE,IAAI,CAAC,CAAC;gBAC5D,CAAC;gBAED,OAAO,CAAC,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAmB,CAAC;YACnD,CAAC;YAAC,OAAO,KAAK,EAAE,CAAC;gBACf,IAAI,KAAK,YAAY,eAAe;oBAAE,MAAM,KAAK,CAAC;gBAClD,SAAS,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC;gBAEtE,IAAI,OAAO,GAAG,WAAW,EAAE,CAAC;oBAC1B,MAAM,CAAC,IAAI,CAAC,qCAAqC,OAAO,GAAG,CAAC,GAAG,EAAE;wBAC/D,SAAS,EAAE,QAAQ;wBACnB,QAAQ,EAAE,IAAI;qBACf,CAAC,CAAC;oBACH,MAAM,IAAI,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,IAAI,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;gBAC5E,CAAC;YACH,CAAC;QACH,CAAC;QAED,MAAM,SAAS,IAAI,IAAI,KAAK,CAAC,8BAA8B,CAAC,CAAC;IAC/D,CAAC;IAED,KAAK,CAAC,IAAI,CACR,IAAY,EACZ,IAA6B,EAC7B,QAAiB;QAEjB,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,GAAG,IAAI,EAAE,CAAC;QAErC,MAAM,OAAO,GAA2B;YACtC,aAAa,EAAE,UAAU,IAAI,CAAC,MAAM,EAAE;YACtC,YAAY,EAAE,eAAe,OAAO,EAAE;YACtC,cAAc,EAAE,kBAAkB;YAClC,MAAM,EAAE,kBAAkB;SAC3B,CAAC;QAEF,IAAI,CAAC,IAAI,CAAC,eAAe,EAAE,CAAC;YAC1B,OAAO,CAAC,cAAc,CAAC,GAAG,MAAM,CAAC;YACjC,IAAI,QAAQ,EAAE,CAAC;gBACb,OAAO,CAAC,YAAY,CAAC,GAAG,QAAQ,CAAC;YACnC,CAAC;QACH,CAAC;QAED,MAAM,SAAS,GAAiB,IAAI,CAAC;QAErC,KAAK,IAAI,OAAO,GAAG,CAAC,EAAE,OAAO,IAAI,WAAW,EAAE,OAAO,EAAE,EAAE,CAAC;YACxD,MAAM,KAAK,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;YAEzB,IAAI,CAAC;gBACH,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE;oBAChC,MAAM,EAAE,MAAM;oBACd,OAAO;oBACP,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC;oBAC1B,MAAM,EAAE,WAAW,CAAC,OAAO,CAAC,MAAM,CAAC;iBACpC,CAAC,CAAC;gBAEH,MAAM,CAAC,KAAK,CAAC,kBAAkB,EAAE;oBAC/B,SAAS,EAAE,QAAQ;oBACnB,QAAQ,EAAE,IAAI;oBACd,WAAW,EAAE,IAAI,CAAC,GAAG,EAAE,GAAG,KAAK;oBAC/B,MAAM,EAAE,QAAQ,CAAC,MAAM;iBACxB,CAAC,CAAC;gBAEH,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,IAAI,OAAO,GAAG,WAAW,EAAE,CAAC;oBACrD,MAAM,UAAU,GAAG,QAAQ,CAAC,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC,CAAC;oBACvD,MAAM,UAAU,GAAG,IAAI,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC;oBACxC,MAAM,MAAM,GAAG,UAAU,CAAC,CAAC,CAAC,eAAe,CAAC,UAAU,EAAE,UAAU,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC;oBACjF,MAAM,CAAC,IAAI,CAAC,6BAA6B,MAAM,IAAI,EAAE;wBACnD,SAAS,EAAE,QAAQ;wBACnB,QAAQ,EAAE,IAAI;qBACf,CAAC,CAAC;oBACH,MAAM,IAAI,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,MAAM,CAAC,CAAC,CAAC;oBAC5D,SAAS;gBACX,CAAC;gBAED,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;oBACjB,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;oBACnC,IAAI,OAAe,CAAC;oBACpB,IAAI,CAAC;wBACH,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAG7B,CAAC;wBACF,OAAO,GAAG,MAAM,CAAC,KAAK,EAAE,OAAO,IAAI,MAAM,CAAC,OAAO,IAAI,IAAI,CAAC;oBAC5D,CAAC;oBAAC,MAAM,CAAC;wBACP,OAAO,GAAG,IAAI,IAAI,QAAQ,CAAC,UAAU,CAAC;oBACxC,CAAC;oBACD,MAAM,IAAI,eAAe,CAAC,QAAQ,CAAC,MAAM,EAAE,OAAO,EAAE,IAAI,CAAC,CAAC;gBAC5D,CAAC;gBAED,OAAO,CAAC,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAmB,CAAC;YACnD,CAAC;YAAC,OAAO,KAAK,EAAE,CAAC;gBACf,IAAI,KAAK,YAAY,eAAe;oBAAE,MAAM,KAAK,CAAC;gBAClD,wEAAwE;gBACxE,MAAM,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,KAAK,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC;YAClE,CAAC;QACH,CAAC;QAED,MAAM,SAAS,IAAI,IAAI,KAAK,CAAC,mCAAmC,CAAC,CAAC;IACpE,CAAC;CACF"}
|
|
@@ -0,0 +1,26 @@
|
|
|
1
|
+
/**
|
|
2
|
+
* Per-request client resolution for hosted MCP deployments.
|
|
3
|
+
*
|
|
4
|
+
* In self-hosted mode (stdio or HTTP with OMOPHUB_API_KEY env var),
|
|
5
|
+
* the default client is used for all requests.
|
|
6
|
+
*
|
|
7
|
+
* In hosted mode, each client sends their own API key via
|
|
8
|
+
* Authorization: Bearer header, and we create/cache a client per key.
|
|
9
|
+
*/
|
|
10
|
+
import { OmopHubClient } from './api.js';
|
|
11
|
+
/** Minimal type for the `extra` parameter passed to MCP tool handlers. */
|
|
12
|
+
interface ToolExtra {
|
|
13
|
+
requestInfo?: {
|
|
14
|
+
headers?: Record<string, string | string[] | undefined>;
|
|
15
|
+
};
|
|
16
|
+
}
|
|
17
|
+
/**
|
|
18
|
+
* Resolve the OmopHubClient for a request.
|
|
19
|
+
*
|
|
20
|
+
* Priority:
|
|
21
|
+
* 1. Authorization: Bearer header from the HTTP request (hosted mode)
|
|
22
|
+
* 2. Default client created at startup (self-hosted mode / stdio)
|
|
23
|
+
*/
|
|
24
|
+
export declare function resolveClient(extra: ToolExtra, defaultClient: OmopHubClient): OmopHubClient;
|
|
25
|
+
export {};
|
|
26
|
+
//# sourceMappingURL=resolve.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"resolve.d.ts","sourceRoot":"","sources":["../../src/client/resolve.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,aAAa,EAAE,MAAM,UAAU,CAAC;AAEzC,0EAA0E;AAC1E,UAAU,SAAS;IACjB,WAAW,CAAC,EAAE;QACZ,OAAO,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,SAAS,CAAC,CAAC;KACzD,CAAC;CACH;AAcD;;;;;;GAMG;AACH,wBAAgB,aAAa,CAAC,KAAK,EAAE,SAAS,EAAE,aAAa,EAAE,aAAa,GAAG,aAAa,CA4B3F"}
|
|
@@ -0,0 +1,55 @@
|
|
|
1
|
+
/**
|
|
2
|
+
* Per-request client resolution for hosted MCP deployments.
|
|
3
|
+
*
|
|
4
|
+
* In self-hosted mode (stdio or HTTP with OMOPHUB_API_KEY env var),
|
|
5
|
+
* the default client is used for all requests.
|
|
6
|
+
*
|
|
7
|
+
* In hosted mode, each client sends their own API key via
|
|
8
|
+
* Authorization: Bearer header, and we create/cache a client per key.
|
|
9
|
+
*/
|
|
10
|
+
import { OmopHubClient } from './api.js';
|
|
11
|
+
// LRU-style cache of clients keyed by API key (max 100 entries)
|
|
12
|
+
const clientCache = new Map();
|
|
13
|
+
const MAX_CACHED_CLIENTS = 100;
|
|
14
|
+
function pruneClientCache() {
|
|
15
|
+
if (clientCache.size <= MAX_CACHED_CLIENTS)
|
|
16
|
+
return;
|
|
17
|
+
const entries = [...clientCache.entries()].sort((a, b) => a[1].lastUsed - b[1].lastUsed);
|
|
18
|
+
for (const [key] of entries.slice(0, entries.length - MAX_CACHED_CLIENTS)) {
|
|
19
|
+
clientCache.delete(key);
|
|
20
|
+
}
|
|
21
|
+
}
|
|
22
|
+
/**
|
|
23
|
+
* Resolve the OmopHubClient for a request.
|
|
24
|
+
*
|
|
25
|
+
* Priority:
|
|
26
|
+
* 1. Authorization: Bearer header from the HTTP request (hosted mode)
|
|
27
|
+
* 2. Default client created at startup (self-hosted mode / stdio)
|
|
28
|
+
*/
|
|
29
|
+
export function resolveClient(extra, defaultClient) {
|
|
30
|
+
const headers = extra?.requestInfo?.headers;
|
|
31
|
+
const rawHeader = headers?.['authorization'] ?? headers?.['Authorization'];
|
|
32
|
+
if (!rawHeader)
|
|
33
|
+
return defaultClient;
|
|
34
|
+
const authHeader = Array.isArray(rawHeader) ? rawHeader[0] : rawHeader;
|
|
35
|
+
if (!authHeader)
|
|
36
|
+
return defaultClient;
|
|
37
|
+
const match = /^Bearer\s+(.+)$/i.exec(authHeader);
|
|
38
|
+
if (!match)
|
|
39
|
+
return defaultClient;
|
|
40
|
+
const apiKey = match[1].trim();
|
|
41
|
+
if (!apiKey)
|
|
42
|
+
return defaultClient;
|
|
43
|
+
// Check cache
|
|
44
|
+
const cached = clientCache.get(apiKey);
|
|
45
|
+
if (cached) {
|
|
46
|
+
cached.lastUsed = Date.now();
|
|
47
|
+
return cached.client;
|
|
48
|
+
}
|
|
49
|
+
// Create new client for this key, inheriting baseUrl from the default client
|
|
50
|
+
const client = new OmopHubClient(apiKey, defaultClient.baseUrl);
|
|
51
|
+
clientCache.set(apiKey, { client, lastUsed: Date.now() });
|
|
52
|
+
pruneClientCache();
|
|
53
|
+
return client;
|
|
54
|
+
}
|
|
55
|
+
//# sourceMappingURL=resolve.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"resolve.js","sourceRoot":"","sources":["../../src/client/resolve.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,aAAa,EAAE,MAAM,UAAU,CAAC;AASzC,gEAAgE;AAChE,MAAM,WAAW,GAAG,IAAI,GAAG,EAAuD,CAAC;AACnF,MAAM,kBAAkB,GAAG,GAAG,CAAC;AAE/B,SAAS,gBAAgB;IACvB,IAAI,WAAW,CAAC,IAAI,IAAI,kBAAkB;QAAE,OAAO;IACnD,MAAM,OAAO,GAAG,CAAC,GAAG,WAAW,CAAC,OAAO,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC;IACzF,KAAK,MAAM,CAAC,GAAG,CAAC,IAAI,OAAO,CAAC,KAAK,CAAC,CAAC,EAAE,OAAO,CAAC,MAAM,GAAG,kBAAkB,CAAC,EAAE,CAAC;QAC1E,WAAW,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;IAC1B,CAAC;AACH,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,aAAa,CAAC,KAAgB,EAAE,aAA4B;IAC1E,MAAM,OAAO,GAAG,KAAK,EAAE,WAAW,EAAE,OAAO,CAAC;IAC5C,MAAM,SAAS,GAAG,OAAO,EAAE,CAAC,eAAe,CAAC,IAAI,OAAO,EAAE,CAAC,eAAe,CAAC,CAAC;IAE3E,IAAI,CAAC,SAAS;QAAE,OAAO,aAAa,CAAC;IAErC,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC;IACvE,IAAI,CAAC,UAAU;QAAE,OAAO,aAAa,CAAC;IAEtC,MAAM,KAAK,GAAG,kBAAkB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;IAClD,IAAI,CAAC,KAAK;QAAE,OAAO,aAAa,CAAC;IAEjC,MAAM,MAAM,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;IAC/B,IAAI,CAAC,MAAM;QAAE,OAAO,aAAa,CAAC;IAElC,cAAc;IACd,MAAM,MAAM,GAAG,WAAW,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IACvC,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,CAAC,QAAQ,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;QAC7B,OAAO,MAAM,CAAC,MAAM,CAAC;IACvB,CAAC;IAED,6EAA6E;IAC7E,MAAM,MAAM,GAAG,IAAI,aAAa,CAAC,MAAM,EAAE,aAAa,CAAC,OAAO,CAAC,CAAC;IAChE,WAAW,CAAC,GAAG,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,IAAI,CAAC,GAAG,EAAE,EAAE,CAAC,CAAC;IAC1D,gBAAgB,EAAE,CAAC;IAEnB,OAAO,MAAM,CAAC;AAChB,CAAC"}
|
package/dist/client/types.d.ts
CHANGED
|
@@ -32,15 +32,20 @@ export interface SearchResult extends Concept {
|
|
|
32
32
|
score?: number;
|
|
33
33
|
}
|
|
34
34
|
export interface Mapping {
|
|
35
|
-
concept_id
|
|
36
|
-
concept_name
|
|
37
|
-
vocabulary_id
|
|
38
|
-
concept_code
|
|
39
|
-
domain_id
|
|
40
|
-
standard_concept
|
|
41
|
-
concept_class_id
|
|
42
|
-
relationship_id
|
|
35
|
+
concept_id?: number;
|
|
36
|
+
concept_name?: string;
|
|
37
|
+
vocabulary_id?: string;
|
|
38
|
+
concept_code?: string;
|
|
39
|
+
domain_id?: string;
|
|
40
|
+
standard_concept?: string | null;
|
|
41
|
+
concept_class_id?: string;
|
|
42
|
+
relationship_id?: string;
|
|
43
43
|
relationship_name?: string;
|
|
44
|
+
target_concept_id?: number;
|
|
45
|
+
target_concept_name?: string;
|
|
46
|
+
source_concept_id?: number;
|
|
47
|
+
source_concept_name?: string;
|
|
48
|
+
confidence?: number;
|
|
44
49
|
}
|
|
45
50
|
export interface HierarchyNode extends Concept {
|
|
46
51
|
level?: number;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../src/client/types.ts"],"names":[],"mappings":"AAAA,MAAM,WAAW,cAAc;IAC7B,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,OAAO,CAAC;IAClB,YAAY,EAAE,OAAO,CAAC;CACvB;AAED,MAAM,WAAW,WAAW,CAAC,CAAC;IAC5B,OAAO,EAAE,OAAO,CAAC;IACjB,IAAI,EAAE,CAAC,CAAC;IACR,IAAI,CAAC,EAAE;QACL,UAAU,CAAC,EAAE,cAAc,CAAC;QAC5B,iBAAiB,CAAC,EAAE,MAAM,CAAC;QAC3B,OAAO,CAAC,EAAE,MAAM,CAAC;KAClB,CAAC;CACH;AAED,MAAM,WAAW,OAAO;IACtB,UAAU,EAAE,MAAM,CAAC;IACnB,YAAY,EAAE,MAAM,CAAC;IACrB,SAAS,EAAE,MAAM,CAAC;IAClB,aAAa,EAAE,MAAM,CAAC;IACtB,gBAAgB,EAAE,MAAM,CAAC;IACzB,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAC;IAChC,YAAY,EAAE,MAAM,CAAC;IACrB,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC/B,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;CACrB;AAED,MAAM,WAAW,YAAa,SAAQ,OAAO;IAC3C,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,OAAO;
|
|
1
|
+
{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../src/client/types.ts"],"names":[],"mappings":"AAAA,MAAM,WAAW,cAAc;IAC7B,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,MAAM,CAAC;IAClB,WAAW,EAAE,MAAM,CAAC;IACpB,WAAW,EAAE,MAAM,CAAC;IACpB,QAAQ,EAAE,OAAO,CAAC;IAClB,YAAY,EAAE,OAAO,CAAC;CACvB;AAED,MAAM,WAAW,WAAW,CAAC,CAAC;IAC5B,OAAO,EAAE,OAAO,CAAC;IACjB,IAAI,EAAE,CAAC,CAAC;IACR,IAAI,CAAC,EAAE;QACL,UAAU,CAAC,EAAE,cAAc,CAAC;QAC5B,iBAAiB,CAAC,EAAE,MAAM,CAAC;QAC3B,OAAO,CAAC,EAAE,MAAM,CAAC;KAClB,CAAC;CACH;AAED,MAAM,WAAW,OAAO;IACtB,UAAU,EAAE,MAAM,CAAC;IACnB,YAAY,EAAE,MAAM,CAAC;IACrB,SAAS,EAAE,MAAM,CAAC;IAClB,aAAa,EAAE,MAAM,CAAC;IACtB,gBAAgB,EAAE,MAAM,CAAC;IACzB,gBAAgB,EAAE,MAAM,GAAG,IAAI,CAAC;IAChC,YAAY,EAAE,MAAM,CAAC;IACrB,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,cAAc,CAAC,EAAE,MAAM,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IAC/B,QAAQ,CAAC,EAAE,MAAM,EAAE,CAAC;CACrB;AAED,MAAM,WAAW,YAAa,SAAQ,OAAO;IAC3C,KAAK,CAAC,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,OAAO;IAEtB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,gBAAgB,CAAC,EAAE,MAAM,GAAG,IAAI,CAAC;IACjC,gBAAgB,CAAC,EAAE,MAAM,CAAC;IAC1B,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAE3B,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B,mBAAmB,CAAC,EAAE,MAAM,CAAC;IAC7B,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B,mBAAmB,CAAC,EAAE,MAAM,CAAC;IAC7B,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB;AAED,MAAM,WAAW,aAAc,SAAQ,OAAO;IAC5C,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,wBAAwB,CAAC,EAAE,MAAM,CAAC;IAClC,wBAAwB,CAAC,EAAE,MAAM,CAAC;CACnC;AAED,MAAM,WAAW,iBAAiB;IAChC,OAAO,EAAE,OAAO,CAAC;IACjB,SAAS,CAAC,EAAE,aAAa,EAAE,CAAC;IAC5B,WAAW,CAAC,EAAE,aAAa,EAAE,CAAC;IAC9B,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,iBAAiB,CAAC,EAAE,MAAM,CAAC;CAC5B;AAED,yFAAyF;AACzF,MAAM,WAAW,oBAAoB;IACnC,UAAU,EAAE,MAAM,CAAC;IACnB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,SAAS,CAAC,EAAE,aAAa,EAAE,CAAC;IAC5B,WAAW,CAAC,EAAE,aAAa,EAAE,CAAC;IAC9B,eAAe,CAAC,EAAE,MAAM,CAAC;IACzB,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B,iBAAiB,CAAC,EAAE;QAClB,eAAe,CAAC,EAAE,MAAM,CAAC;QACzB,iBAAiB,CAAC,EAAE,MAAM,CAAC;KAC5B,CAAC;CACH;AAED,MAAM,WAAW,UAAU;IACzB,aAAa,EAAE,MAAM,CAAC;IACtB,eAAe,EAAE,MAAM,CAAC;IACxB,oBAAoB,CAAC,EAAE,MAAM,CAAC;IAC9B,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAC5B,qBAAqB,CAAC,EAAE,MAAM,CAAC;IAC/B,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,sBAAsB,CAAC,EAAE,MAAM,CAAC;IAChC,eAAe,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC1C;AAED,MAAM,WAAW,gBAAgB;IAC/B,cAAc,EAAE,OAAO,CAAC;IACxB,QAAQ,EAAE,OAAO,EAAE,CAAC;IACpB,cAAc,EAAE,MAAM,CAAC;CACxB"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/formatters/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,WAAW,EACX,OAAO,EAEP,iBAAiB,EAEjB,gBAAgB,EAChB,YAAY,EACZ,UAAU,EACX,MAAM,oBAAoB,CAAC;AAa5B,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,WAAW,CAAC,YAAY,EAAE,CAAC,EACrC,KAAK,EAAE,MAAM,GACZ;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAyChC;AAED,wBAAgB,aAAa,CAAC,OAAO,EAAE,OAAO,GAAG;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAgC9E;
|
|
1
|
+
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/formatters/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EACV,WAAW,EACX,OAAO,EAEP,iBAAiB,EAEjB,gBAAgB,EAChB,YAAY,EACZ,UAAU,EACX,MAAM,oBAAoB,CAAC;AAa5B,wBAAgB,iBAAiB,CAC/B,QAAQ,EAAE,WAAW,CAAC,YAAY,EAAE,CAAC,EACrC,KAAK,EAAE,MAAM,GACZ;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAyChC;AAED,wBAAgB,aAAa,CAAC,OAAO,EAAE,OAAO,GAAG;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAgC9E;AAqBD,wBAAgB,cAAc,CAC5B,QAAQ,EAAE,WAAW,CAAC,gBAAgB,CAAC,EACvC,SAAS,EAAE,MAAM,GAChB;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CA6ChC;AAED,wBAAgB,eAAe,CAC7B,QAAQ,EAAE,WAAW,CAAC,iBAAiB,CAAC,EACxC,SAAS,EAAE,IAAI,GAAG,MAAM,GAAG,MAAM,GAChC;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAsDhC;AAED,wBAAgB,oBAAoB,CAClC,QAAQ,EAAE,WAAW,CAAC,UAAU,EAAE,CAAC,EACnC,MAAM,CAAC,EAAE,MAAM,GACd;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAwChC;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,GAAG;IAAE,IAAI,EAAE,MAAM,CAAC;IAAC,IAAI,EAAE,MAAM,CAAA;CAAE,CAKzE"}
|
package/dist/formatters/index.js
CHANGED
|
@@ -76,6 +76,17 @@ export function formatConcept(concept) {
|
|
|
76
76
|
json: JSON.stringify(concept),
|
|
77
77
|
};
|
|
78
78
|
}
|
|
79
|
+
/** Normalize a mapping to flat target fields regardless of API shape */
|
|
80
|
+
function normalizeMapping(m) {
|
|
81
|
+
return {
|
|
82
|
+
concept_id: m.concept_id ?? m.target_concept_id,
|
|
83
|
+
concept_name: m.concept_name ?? m.target_concept_name ?? 'Unknown',
|
|
84
|
+
vocabulary_id: m.vocabulary_id ?? '',
|
|
85
|
+
concept_code: m.concept_code ?? '',
|
|
86
|
+
relationship_id: m.relationship_id ?? 'Maps to',
|
|
87
|
+
standard_concept: m.standard_concept,
|
|
88
|
+
};
|
|
89
|
+
}
|
|
79
90
|
export function formatMappings(response, conceptId) {
|
|
80
91
|
const data = response.data;
|
|
81
92
|
const mappings = data.mappings;
|
|
@@ -92,7 +103,13 @@ export function formatMappings(response, conceptId) {
|
|
|
92
103
|
}
|
|
93
104
|
const source = data.source_concept;
|
|
94
105
|
const header = `Mappings for **${source?.concept_name || `Concept ${conceptId}`}** (${source?.vocabulary_id || 'unknown'} → targets):`;
|
|
95
|
-
const
|
|
106
|
+
const normalized = mappings.map(normalizeMapping);
|
|
107
|
+
const lines = normalized.map((m, i) => {
|
|
108
|
+
const idPart = m.concept_id ? ` (ID: ${m.concept_id})` : '';
|
|
109
|
+
const vocabPart = m.vocabulary_id ? ` ${m.vocabulary_id} |` : '';
|
|
110
|
+
const codePart = m.concept_code ? ` Code: ${m.concept_code} |` : '';
|
|
111
|
+
return `${i + 1}. **${m.concept_name}**${idPart}\n ${vocabPart}${codePart} Relationship: ${m.relationship_id}`;
|
|
112
|
+
});
|
|
96
113
|
return {
|
|
97
114
|
text: `${header}\n\n${lines.join('\n\n')}`,
|
|
98
115
|
json: JSON.stringify({
|
|
@@ -100,11 +117,11 @@ export function formatMappings(response, conceptId) {
|
|
|
100
117
|
source_concept_name: source?.concept_name,
|
|
101
118
|
mapped: true,
|
|
102
119
|
total_mappings: data.total_mappings ?? mappings.length,
|
|
103
|
-
mappings:
|
|
120
|
+
mappings: normalized.map((m) => ({
|
|
104
121
|
concept_id: m.concept_id,
|
|
105
122
|
concept_name: m.concept_name,
|
|
106
|
-
vocabulary_id: m.vocabulary_id,
|
|
107
|
-
concept_code: m.concept_code,
|
|
123
|
+
vocabulary_id: m.vocabulary_id || undefined,
|
|
124
|
+
concept_code: m.concept_code || undefined,
|
|
108
125
|
relationship_id: m.relationship_id,
|
|
109
126
|
standard_concept: m.standard_concept,
|
|
110
127
|
})),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/formatters/index.ts"],"names":[],"mappings":"AAWA,SAAS,WAAW,CAAC,CAAyB,EAAE,KAAc;IAC5D,MAAM,MAAM,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,KAAK,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;IAC3D,MAAM,GAAG,GACP,CAAC,CAAC,gBAAgB,KAAK,GAAG;QACxB,CAAC,CAAC,aAAa;QACf,CAAC,CAAC,CAAC,CAAC,gBAAgB,KAAK,GAAG;YAC1B,CAAC,CAAC,mBAAmB;YACrB,CAAC,CAAC,EAAE,CAAC;IACX,OAAO,GAAG,MAAM,KAAK,CAAC,CAAC,YAAY,WAAW,CAAC,CAAC,UAAU,SAAS,CAAC,CAAC,aAAa,MAAM,CAAC,CAAC,SAAS,YAAY,CAAC,CAAC,YAAY,GAAG,GAAG,EAAE,CAAC;AACxI,CAAC;AAED,MAAM,UAAU,iBAAiB,CAC/B,QAAqC,EACrC,KAAa;IAEb,MAAM,OAAO,GAAG,QAAQ,CAAC,IAAI,CAAC;IAC9B,MAAM,UAAU,GAAG,QAAQ,CAAC,IAAI,EAAE,UAAU,CAAC;IAC7C,MAAM,KAAK,GAAG,UAAU,EAAE,WAAW,IAAI,OAAO,CAAC,MAAM,CAAC;IACxD,MAAM,IAAI,GAAG,UAAU,EAAE,IAAI,IAAI,CAAC,CAAC;IACnC,MAAM,UAAU,GAAG,UAAU,EAAE,WAAW,IAAI,CAAC,CAAC;IAEhD,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACzB,OAAO;YACL,IAAI,EAAE,0BAA0B,KAAK,8DAA8D;YACnG,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,KAAK,EAAE,CAAC;SACnF,CAAC;IACJ,CAAC;IAED,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,WAAW,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;IACvD,MAAM,MAAM,GAAG,SAAS,KAAK,WAAW,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,SAAS,KAAK,mBAAmB,IAAI,OAAO,UAAU,IAAI,CAAC;IAEzH,IAAI,IAAI,GAAG,GAAG,MAAM,OAAO,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC;IAEhD,IAAI,UAAU,EAAE,QAAQ,EAAE,CAAC;QACzB,IAAI,IAAI,kBAAkB,IAAI,GAAG,CAAC,uBAAuB,CAAC;IAC5D,CAAC;IAED,OAAO;QACL,IAAI;QACJ,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;YACnB,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBAC3B,UAAU,EAAE,CAAC,CAAC,UAAU;gBACxB,YAAY,EAAE,CAAC,CAAC,YAAY;gBAC5B,aAAa,EAAE,CAAC,CAAC,aAAa;gBAC9B,SAAS,EAAE,CAAC,CAAC,SAAS;gBACtB,YAAY,EAAE,CAAC,CAAC,YAAY;gBAC5B,gBAAgB,EAAE,CAAC,CAAC,gBAAgB;gBACpC,gBAAgB,EAAE,CAAC,CAAC,gBAAgB;aACrC,CAAC,CAAC;YACH,KAAK;YACL,IAAI;YACJ,WAAW,EAAE,UAAU;YACvB,KAAK;SACN,CAAC;KACH,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,OAAgB;IAC5C,MAAM,GAAG,GACP,OAAO,CAAC,gBAAgB,KAAK,GAAG;QAC9B,CAAC,CAAC,UAAU;QACZ,CAAC,CAAC,OAAO,CAAC,gBAAgB,KAAK,GAAG;YAChC,CAAC,CAAC,gBAAgB;YAClB,CAAC,CAAC,cAAc,CAAC;IAEvB,MAAM,KAAK,GAAG;QACZ,KAAK,OAAO,CAAC,YAAY,IAAI;QAC7B,EAAE;QACF,mBAAmB;QACnB,mBAAmB;QACnB,kBAAkB,OAAO,CAAC,UAAU,IAAI;QACxC,kBAAkB,OAAO,CAAC,aAAa,IAAI;QAC3C,cAAc,OAAO,CAAC,SAAS,IAAI;QACnC,qBAAqB,OAAO,CAAC,gBAAgB,IAAI;QACjD,oBAAoB,OAAO,CAAC,YAAY,IAAI;QAC5C,uBAAuB,GAAG,IAAI;KAC/B,CAAC;IAEF,IAAI,OAAO,CAAC,gBAAgB;QAAE,KAAK,CAAC,IAAI,CAAC,kBAAkB,OAAO,CAAC,gBAAgB,IAAI,CAAC,CAAC;IACzF,IAAI,OAAO,CAAC,cAAc;QAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,OAAO,CAAC,cAAc,IAAI,CAAC,CAAC;IACnF,IAAI,OAAO,CAAC,cAAc;QAAE,KAAK,CAAC,IAAI,CAAC,sBAAsB,OAAO,CAAC,cAAc,IAAI,CAAC,CAAC;IACzF,IAAI,OAAO,CAAC,QAAQ,IAAI,OAAO,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACpD,KAAK,CAAC,IAAI,CAAC,gBAAgB,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC9D,CAAC;IAED,OAAO;QACL,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC;QACtB,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC;KAC9B,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,cAAc,CAC5B,QAAuC,EACvC,SAAiB;IAEjB,MAAM,IAAI,GAAG,QAAQ,CAAC,IAAI,CAAC;IAC3B,MAAM,QAAQ,GAAG,IAAI,CAAC,QAAQ,CAAC;IAE/B,IAAI,CAAC,QAAQ,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvC,OAAO;YACL,IAAI,EAAE,iCAAiC,SAAS,KAAK,IAAI,CAAC,cAAc,EAAE,YAAY,IAAI,SAAS,IAAI;YACvG,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;gBACnB,iBAAiB,EAAE,SAAS;gBAC5B,mBAAmB,EAAE,IAAI,CAAC,cAAc,EAAE,YAAY;gBACtD,MAAM,EAAE,KAAK;gBACb,QAAQ,EAAE,EAAE;aACb,CAAC;SACH,CAAC;IACJ,CAAC;IAED,MAAM,MAAM,GAAG,IAAI,CAAC,cAAc,CAAC;IACnC,MAAM,MAAM,GAAG,kBAAkB,MAAM,EAAE,YAAY,IAAI,WAAW,SAAS,EAAE,OAAO,MAAM,EAAE,aAAa,IAAI,SAAS,cAAc,CAAC;IAEvI,MAAM,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/formatters/index.ts"],"names":[],"mappings":"AAWA,SAAS,WAAW,CAAC,CAAyB,EAAE,KAAc;IAC5D,MAAM,MAAM,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,GAAG,KAAK,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;IAC3D,MAAM,GAAG,GACP,CAAC,CAAC,gBAAgB,KAAK,GAAG;QACxB,CAAC,CAAC,aAAa;QACf,CAAC,CAAC,CAAC,CAAC,gBAAgB,KAAK,GAAG;YAC1B,CAAC,CAAC,mBAAmB;YACrB,CAAC,CAAC,EAAE,CAAC;IACX,OAAO,GAAG,MAAM,KAAK,CAAC,CAAC,YAAY,WAAW,CAAC,CAAC,UAAU,SAAS,CAAC,CAAC,aAAa,MAAM,CAAC,CAAC,SAAS,YAAY,CAAC,CAAC,YAAY,GAAG,GAAG,EAAE,CAAC;AACxI,CAAC;AAED,MAAM,UAAU,iBAAiB,CAC/B,QAAqC,EACrC,KAAa;IAEb,MAAM,OAAO,GAAG,QAAQ,CAAC,IAAI,CAAC;IAC9B,MAAM,UAAU,GAAG,QAAQ,CAAC,IAAI,EAAE,UAAU,CAAC;IAC7C,MAAM,KAAK,GAAG,UAAU,EAAE,WAAW,IAAI,OAAO,CAAC,MAAM,CAAC;IACxD,MAAM,IAAI,GAAG,UAAU,EAAE,IAAI,IAAI,CAAC,CAAC;IACnC,MAAM,UAAU,GAAG,UAAU,EAAE,WAAW,IAAI,CAAC,CAAC;IAEhD,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACzB,OAAO;YACL,IAAI,EAAE,0BAA0B,KAAK,8DAA8D;YACnG,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,OAAO,EAAE,EAAE,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE,UAAU,EAAE,KAAK,EAAE,CAAC;SACnF,CAAC;IACJ,CAAC;IAED,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,WAAW,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;IACvD,MAAM,MAAM,GAAG,SAAS,KAAK,WAAW,KAAK,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,SAAS,KAAK,mBAAmB,IAAI,OAAO,UAAU,IAAI,CAAC;IAEzH,IAAI,IAAI,GAAG,GAAG,MAAM,OAAO,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE,CAAC;IAEhD,IAAI,UAAU,EAAE,QAAQ,EAAE,CAAC;QACzB,IAAI,IAAI,kBAAkB,IAAI,GAAG,CAAC,uBAAuB,CAAC;IAC5D,CAAC;IAED,OAAO;QACL,IAAI;QACJ,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;YACnB,OAAO,EAAE,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBAC3B,UAAU,EAAE,CAAC,CAAC,UAAU;gBACxB,YAAY,EAAE,CAAC,CAAC,YAAY;gBAC5B,aAAa,EAAE,CAAC,CAAC,aAAa;gBAC9B,SAAS,EAAE,CAAC,CAAC,SAAS;gBACtB,YAAY,EAAE,CAAC,CAAC,YAAY;gBAC5B,gBAAgB,EAAE,CAAC,CAAC,gBAAgB;gBACpC,gBAAgB,EAAE,CAAC,CAAC,gBAAgB;aACrC,CAAC,CAAC;YACH,KAAK;YACL,IAAI;YACJ,WAAW,EAAE,UAAU;YACvB,KAAK;SACN,CAAC;KACH,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,OAAgB;IAC5C,MAAM,GAAG,GACP,OAAO,CAAC,gBAAgB,KAAK,GAAG;QAC9B,CAAC,CAAC,UAAU;QACZ,CAAC,CAAC,OAAO,CAAC,gBAAgB,KAAK,GAAG;YAChC,CAAC,CAAC,gBAAgB;YAClB,CAAC,CAAC,cAAc,CAAC;IAEvB,MAAM,KAAK,GAAG;QACZ,KAAK,OAAO,CAAC,YAAY,IAAI;QAC7B,EAAE;QACF,mBAAmB;QACnB,mBAAmB;QACnB,kBAAkB,OAAO,CAAC,UAAU,IAAI;QACxC,kBAAkB,OAAO,CAAC,aAAa,IAAI;QAC3C,cAAc,OAAO,CAAC,SAAS,IAAI;QACnC,qBAAqB,OAAO,CAAC,gBAAgB,IAAI;QACjD,oBAAoB,OAAO,CAAC,YAAY,IAAI;QAC5C,uBAAuB,GAAG,IAAI;KAC/B,CAAC;IAEF,IAAI,OAAO,CAAC,gBAAgB;QAAE,KAAK,CAAC,IAAI,CAAC,kBAAkB,OAAO,CAAC,gBAAgB,IAAI,CAAC,CAAC;IACzF,IAAI,OAAO,CAAC,cAAc;QAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,OAAO,CAAC,cAAc,IAAI,CAAC,CAAC;IACnF,IAAI,OAAO,CAAC,cAAc;QAAE,KAAK,CAAC,IAAI,CAAC,sBAAsB,OAAO,CAAC,cAAc,IAAI,CAAC,CAAC;IACzF,IAAI,OAAO,CAAC,QAAQ,IAAI,OAAO,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACpD,KAAK,CAAC,IAAI,CAAC,gBAAgB,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;IAC9D,CAAC;IAED,OAAO;QACL,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC;QACtB,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC;KAC9B,CAAC;AACJ,CAAC;AAED,wEAAwE;AACxE,SAAS,gBAAgB,CAAC,CAAU;IAQlC,OAAO;QACL,UAAU,EAAE,CAAC,CAAC,UAAU,IAAI,CAAC,CAAC,iBAAiB;QAC/C,YAAY,EAAE,CAAC,CAAC,YAAY,IAAI,CAAC,CAAC,mBAAmB,IAAI,SAAS;QAClE,aAAa,EAAE,CAAC,CAAC,aAAa,IAAI,EAAE;QACpC,YAAY,EAAE,CAAC,CAAC,YAAY,IAAI,EAAE;QAClC,eAAe,EAAE,CAAC,CAAC,eAAe,IAAI,SAAS;QAC/C,gBAAgB,EAAE,CAAC,CAAC,gBAAgB;KACrC,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,cAAc,CAC5B,QAAuC,EACvC,SAAiB;IAEjB,MAAM,IAAI,GAAG,QAAQ,CAAC,IAAI,CAAC;IAC3B,MAAM,QAAQ,GAAG,IAAI,CAAC,QAAQ,CAAC;IAE/B,IAAI,CAAC,QAAQ,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QACvC,OAAO;YACL,IAAI,EAAE,iCAAiC,SAAS,KAAK,IAAI,CAAC,cAAc,EAAE,YAAY,IAAI,SAAS,IAAI;YACvG,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;gBACnB,iBAAiB,EAAE,SAAS;gBAC5B,mBAAmB,EAAE,IAAI,CAAC,cAAc,EAAE,YAAY;gBACtD,MAAM,EAAE,KAAK;gBACb,QAAQ,EAAE,EAAE;aACb,CAAC;SACH,CAAC;IACJ,CAAC;IAED,MAAM,MAAM,GAAG,IAAI,CAAC,cAAc,CAAC;IACnC,MAAM,MAAM,GAAG,kBAAkB,MAAM,EAAE,YAAY,IAAI,WAAW,SAAS,EAAE,OAAO,MAAM,EAAE,aAAa,IAAI,SAAS,cAAc,CAAC;IAEvI,MAAM,UAAU,GAAG,QAAQ,CAAC,GAAG,CAAC,gBAAgB,CAAC,CAAC;IAElD,MAAM,KAAK,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;QACpC,MAAM,MAAM,GAAG,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC;QAC5D,MAAM,SAAS,GAAG,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,aAAa,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;QACjE,MAAM,QAAQ,GAAG,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,YAAY,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC;QACpE,OAAO,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,YAAY,KAAK,MAAM,OAAO,SAAS,GAAG,QAAQ,kBAAkB,CAAC,CAAC,eAAe,EAAE,CAAC;IAClH,CAAC,CAAC,CAAC;IAEH,OAAO;QACL,IAAI,EAAE,GAAG,MAAM,OAAO,KAAK,CAAC,IAAI,CAAC,MAAM,CAAC,EAAE;QAC1C,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC;YACnB,iBAAiB,EAAE,SAAS;YAC5B,mBAAmB,EAAE,MAAM,EAAE,YAAY;YACzC,MAAM,EAAE,IAAI;YACZ,cAAc,EAAE,IAAI,CAAC,cAAc,IAAI,QAAQ,CAAC,MAAM;YACtD,QAAQ,EAAE,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBAC/B,UAAU,EAAE,CAAC,CAAC,UAAU;gBACxB,YAAY,EAAE,CAAC,CAAC,YAAY;gBAC5B,aAAa,EAAE,CAAC,CAAC,aAAa,IAAI,SAAS;gBAC3C,YAAY,EAAE,CAAC,CAAC,YAAY,IAAI,SAAS;gBACzC,eAAe,EAAE,CAAC,CAAC,eAAe;gBAClC,gBAAgB,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|
package/dist/index.d.ts.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";
|
|
1
|
+
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AAYA,MAAM,MAAM,aAAa,GAAG,OAAO,GAAG,MAAM,CAAC;AAI7C,wBAAgB,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,GAAG;IACzC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,SAAS,CAAC,EAAE,aAAa,CAAC;IAC1B,IAAI,CAAC,EAAE,MAAM,CAAC;CACf,CAiCA;AAED,wBAAgB,iBAAiB,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAYtE;AAED,wBAAgB,gBAAgB,CAAC,YAAY,CAAC,EAAE,aAAa,GAAG,aAAa,CAS5E;AAED,wBAAgB,WAAW,CAAC,OAAO,CAAC,EAAE,MAAM,GAAG,MAAM,CAYpD;AAED,wBAAsB,IAAI,IAAI,OAAO,CAAC,IAAI,CAAC,CAqC1C"}
|
package/dist/index.js
CHANGED
|
@@ -2,6 +2,7 @@
|
|
|
2
2
|
import { realpathSync } from 'node:fs';
|
|
3
3
|
import url from 'node:url';
|
|
4
4
|
import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
|
|
5
|
+
import { OmopHubClient } from './client/api.js';
|
|
5
6
|
import { startHealthServer } from './health.js';
|
|
6
7
|
import { createServer } from './server.js';
|
|
7
8
|
import { startHttpTransport } from './transports/http.js';
|
|
@@ -73,22 +74,24 @@ export function resolvePort(cliPort) {
|
|
|
73
74
|
}
|
|
74
75
|
export async function main() {
|
|
75
76
|
const args = parseArgs(process.argv);
|
|
76
|
-
|
|
77
|
-
|
|
78
|
-
|
|
79
|
-
|
|
80
|
-
|
|
81
|
-
logger.error(error instanceof Error ? error.message : String(error));
|
|
77
|
+
const apiKey = resolveApiKey(args.apiKey);
|
|
78
|
+
const transportType = resolveTransport(args.transport);
|
|
79
|
+
if (!apiKey && transportType === 'stdio') {
|
|
80
|
+
logger.error('OMOPHub API key required for stdio mode. Set OMOPHUB_API_KEY or pass --api-key=KEY.\n' +
|
|
81
|
+
'Get your free API key at: https://dashboard.omophub.com/api-keys');
|
|
82
82
|
process.exit(1);
|
|
83
83
|
}
|
|
84
|
-
|
|
85
|
-
|
|
84
|
+
if (!apiKey) {
|
|
85
|
+
logger.info('No default API key — hosted mode: all requests must include Authorization: Bearer header');
|
|
86
|
+
}
|
|
87
|
+
const defaultClient = new OmopHubClient(apiKey, args.baseUrl);
|
|
86
88
|
if (transportType === 'http') {
|
|
87
89
|
const port = resolvePort(args.port);
|
|
88
90
|
logger.info('Starting OMOPHub MCP server (http transport)');
|
|
89
|
-
await startHttpTransport(
|
|
91
|
+
await startHttpTransport(createServer, defaultClient, port);
|
|
90
92
|
}
|
|
91
93
|
else {
|
|
94
|
+
const server = createServer(defaultClient);
|
|
92
95
|
const transport = new StdioServerTransport();
|
|
93
96
|
logger.info('Starting OMOPHub MCP server (stdio transport)');
|
|
94
97
|
await server.connect(transport);
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AAEA,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AACvC,OAAO,GAAG,MAAM,UAAU,CAAC;AAC3B,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC3C,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAC;AAC1D,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAI3C,MAAM,iBAAiB,GAAG,IAAI,CAAC;AAE/B,MAAM,UAAU,SAAS,CAAC,IAAc;IAOtC,MAAM,MAAM,GAMR,EAAE,CAAC;IAEP,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;QAChC,IAAI,GAAG,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,CAAC;YACjC,MAAM,CAAC,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC;QACjD,CAAC;aAAM,IAAI,GAAG,CAAC,UAAU,CAAC,aAAa,CAAC,EAAE,CAAC;YACzC,MAAM,CAAC,OAAO,GAAG,GAAG,CAAC,KAAK,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC;QACnD,CAAC;aAAM,IAAI,GAAG,CAAC,UAAU,CAAC,gBAAgB,CAAC,EAAE,CAAC;YAC5C,MAAM,IAAI,GAAG,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;YAC9D,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,IAAI,GAAG,CAAC,IAAI,IAAI,GAAG,KAAK,EAAE,CAAC;gBACpD,MAAM,CAAC,UAAU,GAAG,IAAI,CAAC;YAC3B,CAAC;QACH,CAAC;aAAM,IAAI,GAAG,CAAC,UAAU,CAAC,cAAc,CAAC,EAAE,CAAC;YAC1C,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,cAAc,CAAC,MAAM,CAAC,CAAC;YAC/C,IAAI,KAAK,KAAK,OAAO,IAAI,KAAK,KAAK,MAAM,EAAE,CAAC;gBAC1C,MAAM,CAAC,SAAS,GAAG,KAAK,CAAC;YAC3B,CAAC;QACH,CAAC;aAAM,IAAI,GAAG,CAAC,UAAU,CAAC,SAAS,CAAC,EAAE,CAAC;YACrC,MAAM,IAAI,GAAG,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;YACvD,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,IAAI,GAAG,CAAC,IAAI,IAAI,GAAG,KAAK,EAAE,CAAC;gBACpD,MAAM,CAAC,IAAI,GAAG,IAAI,CAAC;YACrB,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,OAAgB;IAChD,IAAI,OAAO,KAAK,SAAS;QAAE,OAAO,OAAO,CAAC;IAE1C,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,WAAW,CAAC;IACxC,IAAI,OAAO,EAAE,CAAC;QACZ,MAAM,IAAI,GAAG,QAAQ,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;QACnC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,IAAI,GAAG,CAAC,IAAI,IAAI,GAAG,KAAK,EAAE,CAAC;YACpD,OAAO,IAAI,CAAC;QACd,CAAC;IACH,CAAC;IAED,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,YAA4B;IAC3D,IAAI,YAAY;QAAE,OAAO,YAAY,CAAC;IAEtC,MAAM,YAAY,GAAG,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC;IAC/C,IAAI,YAAY,KAAK,MAAM,IAAI,YAAY,KAAK,OAAO,EAAE,CAAC;QACxD,OAAO,YAAY,CAAC;IACtB,CAAC;IAED,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,OAAgB;IAC1C,IAAI,OAAO,KAAK,SAAS;QAAE,OAAO,OAAO,CAAC;IAE1C,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC;IACrC,IAAI,OAAO,EAAE,CAAC;QACZ,MAAM,IAAI,GAAG,QAAQ,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;QACnC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,IAAI,GAAG,CAAC,IAAI,IAAI,GAAG,KAAK,EAAE,CAAC;YACpD,OAAO,IAAI,CAAC;QACd,CAAC;IACH,CAAC;IAED,OAAO,iBAAiB,CAAC;AAC3B,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,IAAI;IACxB,MAAM,IAAI,GAAG,SAAS,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;IAErC,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AAEA,OAAO,EAAE,YAAY,EAAE,MAAM,SAAS,CAAC;AACvC,OAAO,GAAG,MAAM,UAAU,CAAC;AAC3B,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAChD,OAAO,EAAE,YAAY,EAAE,MAAM,aAAa,CAAC;AAC3C,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAC;AAC1D,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAI3C,MAAM,iBAAiB,GAAG,IAAI,CAAC;AAE/B,MAAM,UAAU,SAAS,CAAC,IAAc;IAOtC,MAAM,MAAM,GAMR,EAAE,CAAC;IAEP,KAAK,MAAM,GAAG,IAAI,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;QAChC,IAAI,GAAG,CAAC,UAAU,CAAC,YAAY,CAAC,EAAE,CAAC;YACjC,MAAM,CAAC,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC;QACjD,CAAC;aAAM,IAAI,GAAG,CAAC,UAAU,CAAC,aAAa,CAAC,EAAE,CAAC;YACzC,MAAM,CAAC,OAAO,GAAG,GAAG,CAAC,KAAK,CAAC,aAAa,CAAC,MAAM,CAAC,CAAC;QACnD,CAAC;aAAM,IAAI,GAAG,CAAC,UAAU,CAAC,gBAAgB,CAAC,EAAE,CAAC;YAC5C,MAAM,IAAI,GAAG,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;YAC9D,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,IAAI,GAAG,CAAC,IAAI,IAAI,GAAG,KAAK,EAAE,CAAC;gBACpD,MAAM,CAAC,UAAU,GAAG,IAAI,CAAC;YAC3B,CAAC;QACH,CAAC;aAAM,IAAI,GAAG,CAAC,UAAU,CAAC,cAAc,CAAC,EAAE,CAAC;YAC1C,MAAM,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,cAAc,CAAC,MAAM,CAAC,CAAC;YAC/C,IAAI,KAAK,KAAK,OAAO,IAAI,KAAK,KAAK,MAAM,EAAE,CAAC;gBAC1C,MAAM,CAAC,SAAS,GAAG,KAAK,CAAC;YAC3B,CAAC;QACH,CAAC;aAAM,IAAI,GAAG,CAAC,UAAU,CAAC,SAAS,CAAC,EAAE,CAAC;YACrC,MAAM,IAAI,GAAG,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC,CAAC;YACvD,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,IAAI,GAAG,CAAC,IAAI,IAAI,GAAG,KAAK,EAAE,CAAC;gBACpD,MAAM,CAAC,IAAI,GAAG,IAAI,CAAC;YACrB,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,OAAgB;IAChD,IAAI,OAAO,KAAK,SAAS;QAAE,OAAO,OAAO,CAAC;IAE1C,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,WAAW,CAAC;IACxC,IAAI,OAAO,EAAE,CAAC;QACZ,MAAM,IAAI,GAAG,QAAQ,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;QACnC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,IAAI,GAAG,CAAC,IAAI,IAAI,GAAG,KAAK,EAAE,CAAC;YACpD,OAAO,IAAI,CAAC;QACd,CAAC;IACH,CAAC;IAED,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,YAA4B;IAC3D,IAAI,YAAY;QAAE,OAAO,YAAY,CAAC;IAEtC,MAAM,YAAY,GAAG,OAAO,CAAC,GAAG,CAAC,aAAa,CAAC;IAC/C,IAAI,YAAY,KAAK,MAAM,IAAI,YAAY,KAAK,OAAO,EAAE,CAAC;QACxD,OAAO,YAAY,CAAC;IACtB,CAAC;IAED,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,OAAgB;IAC1C,IAAI,OAAO,KAAK,SAAS;QAAE,OAAO,OAAO,CAAC;IAE1C,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAC;IACrC,IAAI,OAAO,EAAE,CAAC;QACZ,MAAM,IAAI,GAAG,QAAQ,CAAC,OAAO,EAAE,EAAE,CAAC,CAAC;QACnC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,IAAI,GAAG,CAAC,IAAI,IAAI,GAAG,KAAK,EAAE,CAAC;YACpD,OAAO,IAAI,CAAC;QACd,CAAC;IACH,CAAC;IAED,OAAO,iBAAiB,CAAC;AAC3B,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,IAAI;IACxB,MAAM,IAAI,GAAG,SAAS,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC;IAErC,MAAM,MAAM,GAAG,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;IAC1C,MAAM,aAAa,GAAG,gBAAgB,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;IAEvD,IAAI,CAAC,MAAM,IAAI,aAAa,KAAK,OAAO,EAAE,CAAC;QACzC,MAAM,CAAC,KAAK,CACV,uFAAuF;YACrF,kEAAkE,CACrE,CAAC;QACF,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC;IAED,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,MAAM,CAAC,IAAI,CACT,0FAA0F,CAC3F,CAAC;IACJ,CAAC;IAED,MAAM,aAAa,GAAG,IAAI,aAAa,CAAC,MAAM,EAAE,IAAI,CAAC,OAAO,CAAC,CAAC;IAE9D,IAAI,aAAa,KAAK,MAAM,EAAE,CAAC;QAC7B,MAAM,IAAI,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACpC,MAAM,CAAC,IAAI,CAAC,8CAA8C,CAAC,CAAC;QAC5D,MAAM,kBAAkB,CAAC,YAAY,EAAE,aAAa,EAAE,IAAI,CAAC,CAAC;IAC9D,CAAC;SAAM,CAAC;QACN,MAAM,MAAM,GAAG,YAAY,CAAC,aAAa,CAAC,CAAC;QAC3C,MAAM,SAAS,GAAG,IAAI,oBAAoB,EAAE,CAAC;QAC7C,MAAM,CAAC,IAAI,CAAC,+CAA+C,CAAC,CAAC;QAC7D,MAAM,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;QAEhC,MAAM,UAAU,GAAG,iBAAiB,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;QACtD,IAAI,UAAU,KAAK,SAAS,EAAE,CAAC;YAC7B,iBAAiB,CAAC,UAAU,CAAC,CAAC;QAChC,CAAC;IACH,CAAC;AACH,CAAC;AAED,SAAS,aAAa;IACpB,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC;QAAE,OAAO,KAAK,CAAC;IACnC,IAAI,CAAC;QACH,OAAO,MAAM,CAAC,IAAI,CAAC,GAAG,KAAK,GAAG,CAAC,aAAa,CAAC,YAAY,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC;IACnF,CAAC;IAAC,MAAM,CAAC;QACP,OAAO,KAAK,CAAC;IACf,CAAC;AACH,CAAC;AAED,MAAM,WAAW,GAAG,aAAa,EAAE,CAAC;AAEpC,IAAI,WAAW,EAAE,CAAC;IAChB,IAAI,EAAE,CAAC,KAAK,CAAC,CAAC,KAAc,EAAE,EAAE;QAC9B,MAAM,CAAC,KAAK,CAAC,aAAa,EAAE,EAAE,KAAK,EAAE,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QACtD,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAClB,CAAC,CAAC,CAAC;AACL,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/resources/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAEzE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;
|
|
1
|
+
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/resources/index.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAEzE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AA4CtD,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,aAAa,GAAG,IAAI,CAsEhF"}
|
package/dist/resources/index.js
CHANGED
|
@@ -1,4 +1,5 @@
|
|
|
1
1
|
import { ResourceTemplate } from '@modelcontextprotocol/sdk/server/mcp.js';
|
|
2
|
+
import { resolveClient } from '../client/resolve.js';
|
|
2
3
|
import { vocabularyCache } from '../utils/cache.js';
|
|
3
4
|
const PAGE_SIZE = 100;
|
|
4
5
|
const CACHE_KEY = 'vocabularies:all';
|
|
@@ -26,8 +27,9 @@ async function getCachedVocabularies(client, toolName) {
|
|
|
26
27
|
}
|
|
27
28
|
export function registerResources(server, client) {
|
|
28
29
|
// Static resource: vocabulary catalog
|
|
29
|
-
server.resource('vocabulary-list', 'omophub://vocabularies', async (uri) => {
|
|
30
|
-
const
|
|
30
|
+
server.resource('vocabulary-list', 'omophub://vocabularies', async (uri, extra) => {
|
|
31
|
+
const rc = resolveClient(extra, client);
|
|
32
|
+
const vocabs = await getCachedVocabularies(rc, 'resource:vocabulary-list');
|
|
31
33
|
const text = vocabs
|
|
32
34
|
.map((v) => `${v.vocabulary_id}: ${v.vocabulary_name}${v.concept_count != null ? ` (${v.concept_count.toLocaleString()} concepts)` : ''}`)
|
|
33
35
|
.join('\n');
|
|
@@ -45,9 +47,10 @@ export function registerResources(server, client) {
|
|
|
45
47
|
const vocabularyTemplate = new ResourceTemplate('omophub://vocabularies/{vocabulary_id}', {
|
|
46
48
|
list: undefined,
|
|
47
49
|
});
|
|
48
|
-
server.resource('vocabulary-details', vocabularyTemplate, async (uri, variables) => {
|
|
50
|
+
server.resource('vocabulary-details', vocabularyTemplate, async (uri, variables, extra) => {
|
|
51
|
+
const rc = resolveClient(extra, client);
|
|
49
52
|
const vocabularyId = String(variables.vocabulary_id);
|
|
50
|
-
const vocabs = await getCachedVocabularies(
|
|
53
|
+
const vocabs = await getCachedVocabularies(rc, 'resource:vocabulary-details');
|
|
51
54
|
const vocab = vocabs.find((v) => v.vocabulary_id.toLowerCase() === vocabularyId.toLowerCase());
|
|
52
55
|
if (!vocab) {
|
|
53
56
|
return {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/resources/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,gBAAgB,EAAE,MAAM,yCAAyC,CAAC;
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/resources/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,gBAAgB,EAAE,MAAM,yCAAyC,CAAC;AAE3E,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AAErD,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AAEpD,MAAM,SAAS,GAAG,GAAG,CAAC;AACtB,MAAM,SAAS,GAAG,kBAAkB,CAAC;AAErC,KAAK,UAAU,oBAAoB,CACjC,MAAqB,EACrB,QAAgB;IAEhB,MAAM,GAAG,GAAiB,EAAE,CAAC;IAC7B,IAAI,IAAI,GAAG,CAAC,CAAC;IAEb,uEAAuE;IACvE,OAAO,IAAI,EAAE,CAAC;QACZ,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,OAAO,CAC9B,eAAe,EACf,EAAE,aAAa,EAAE,IAAI,EAAE,SAAS,EAAE,SAAS,EAAE,IAAI,EAAE,EACnD,QAAQ,CACT,CAAC;QACF,MAAM,KAAK,GAAG,GAAG,CAAC,IAAI,CAAC,YAAY,CAAC;QACpC,GAAG,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,CAAC;QAEnB,IAAI,KAAK,CAAC,MAAM,GAAG,SAAS,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,UAAU,EAAE,QAAQ;YAAE,MAAM;QACvE,IAAI,EAAE,CAAC;IACT,CAAC;IAED,OAAO,GAAG,CAAC;AACb,CAAC;AAED,KAAK,UAAU,qBAAqB,CAClC,MAAqB,EACrB,QAAgB;IAEhB,MAAM,MAAM,GAAG,eAAe,CAAC,GAAG,CAAC,SAAS,CAAuC,CAAC;IACpF,IAAI,MAAM;QAAE,OAAO,MAAM,CAAC,IAAI,CAAC;IAE/B,MAAM,MAAM,GAAG,MAAM,oBAAoB,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;IAC5D,eAAe,CAAC,GAAG,CAAC,SAAS,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC;IACjD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,MAAiB,EAAE,MAAqB;IACxE,sCAAsC;IACtC,MAAM,CAAC,QAAQ,CAAC,iBAAiB,EAAE,wBAAwB,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE;QAChF,MAAM,EAAE,GAAG,aAAa,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;QACxC,MAAM,MAAM,GAAG,MAAM,qBAAqB,CAAC,EAAE,EAAE,0BAA0B,CAAC,CAAC;QAC3E,MAAM,IAAI,GAAG,MAAM;aAChB,GAAG,CACF,CAAC,CAAC,EAAE,EAAE,CACJ,GAAG,CAAC,CAAC,aAAa,KAAK,CAAC,CAAC,eAAe,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,aAAa,CAAC,cAAc,EAAE,YAAY,CAAC,CAAC,CAAC,EAAE,EAAE,CAChI;aACA,IAAI,CAAC,IAAI,CAAC,CAAC;QAEd,OAAO;YACL,QAAQ,EAAE;gBACR;oBACE,GAAG,EAAE,GAAG,CAAC,IAAI;oBACb,QAAQ,EAAE,YAAY;oBACtB,IAAI,EAAE,4BAA4B,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,OAAO,IAAI,EAAE;iBAC9D;aACF;SACF,CAAC;IACJ,CAAC,CAAC,CAAC;IAEH,mDAAmD;IACnD,MAAM,kBAAkB,GAAG,IAAI,gBAAgB,CAAC,wCAAwC,EAAE;QACxF,IAAI,EAAE,SAAS;KAChB,CAAC,CAAC;IAEH,MAAM,CAAC,QAAQ,CAAC,oBAAoB,EAAE,kBAAkB,EAAE,KAAK,EAAE,GAAG,EAAE,SAAS,EAAE,KAAK,EAAE,EAAE;QACxF,MAAM,EAAE,GAAG,aAAa,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;QACxC,MAAM,YAAY,GAAG,MAAM,CAAC,SAAS,CAAC,aAAa,CAAC,CAAC;QACrD,MAAM,MAAM,GAAG,MAAM,qBAAqB,CAAC,EAAE,EAAE,6BAA6B,CAAC,CAAC;QAE9E,MAAM,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,WAAW,EAAE,KAAK,YAAY,CAAC,WAAW,EAAE,CAAC,CAAC;QAE/F,IAAI,CAAC,KAAK,EAAE,CAAC;YACX,OAAO;gBACL,QAAQ,EAAE;oBACR;wBACE,GAAG,EAAE,GAAG,CAAC,IAAI;wBACb,QAAQ,EAAE,YAAY;wBACtB,IAAI,EAAE,eAAe,YAAY,cAAc;qBAChD;iBACF;aACF,CAAC;QACJ,CAAC;QAED,MAAM,KAAK,GAAG;YACZ,eAAe,KAAK,CAAC,aAAa,EAAE;YACpC,SAAS,KAAK,CAAC,eAAe,EAAE;YAChC,KAAK,CAAC,kBAAkB,CAAC,CAAC,CAAC,YAAY,KAAK,CAAC,kBAAkB,EAAE,CAAC,CAAC,CAAC,IAAI;YACxE,KAAK,CAAC,oBAAoB,CAAC,CAAC,CAAC,cAAc,KAAK,CAAC,oBAAoB,EAAE,CAAC,CAAC,CAAC,IAAI;YAC9E,KAAK,CAAC,aAAa,IAAI,IAAI;gBACzB,CAAC,CAAC,mBAAmB,KAAK,CAAC,aAAa,CAAC,cAAc,EAAE,EAAE;gBAC3D,CAAC,CAAC,IAAI;YACR,KAAK,CAAC,sBAAsB,IAAI,IAAI;gBAClC,CAAC,CAAC,sBAAsB,KAAK,CAAC,sBAAsB,CAAC,cAAc,EAAE,EAAE;gBACvE,CAAC,CAAC,IAAI;SACT,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;QAElB,OAAO;YACL,QAAQ,EAAE;gBACR;oBACE,GAAG,EAAE,GAAG,CAAC,IAAI;oBACb,QAAQ,EAAE,YAAY;oBACtB,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC;iBACvB;aACF;SACF,CAAC;IACJ,CAAC,CAAC,CAAC;AACL,CAAC"}
|
package/dist/server.d.ts
CHANGED
|
@@ -1,3 +1,4 @@
|
|
|
1
1
|
import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
|
|
2
|
-
|
|
2
|
+
import type { OmopHubClient } from './client/api.js';
|
|
3
|
+
export declare function createServer(client: OmopHubClient): McpServer;
|
|
3
4
|
//# sourceMappingURL=server.d.ts.map
|
package/dist/server.d.ts.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;
|
|
1
|
+
{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AACpE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAgBrD,wBAAgB,YAAY,CAAC,MAAM,EAAE,aAAa,GAAG,SAAS,CA6B7D"}
|
package/dist/server.js
CHANGED
|
@@ -1,17 +1,15 @@
|
|
|
1
1
|
import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
|
|
2
|
-
import { OmopHubClient } from './client/api.js';
|
|
3
2
|
import { registerPrompts } from './prompts/index.js';
|
|
4
3
|
import { registerResources } from './resources/index.js';
|
|
5
4
|
import { registerConceptTools, registerExploreTools, registerHierarchyTools, registerMappingTools, registerSearchTools, registerSemanticSearchTools, registerSimilarTools, registerVocabularyTools, } from './tools/index.js';
|
|
6
5
|
import { logger } from './utils/logger.js';
|
|
7
6
|
import { VERSION } from './version.js';
|
|
8
|
-
export function createServer(
|
|
7
|
+
export function createServer(client) {
|
|
9
8
|
const server = new McpServer({
|
|
10
9
|
name: 'omophub',
|
|
11
10
|
version: VERSION,
|
|
12
11
|
description: 'Access OHDSI standardized medical vocabularies — search concepts, navigate hierarchies, and map between clinical coding systems like SNOMED CT, ICD-10, RxNorm, and LOINC.',
|
|
13
12
|
});
|
|
14
|
-
const client = new OmopHubClient(apiKey, baseUrl);
|
|
15
13
|
// Register tools
|
|
16
14
|
registerSearchTools(server, client);
|
|
17
15
|
registerSemanticSearchTools(server, client);
|
package/dist/server.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"server.js","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;
|
|
1
|
+
{"version":3,"file":"server.js","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAEpE,OAAO,EAAE,eAAe,EAAE,MAAM,oBAAoB,CAAC;AACrD,OAAO,EAAE,iBAAiB,EAAE,MAAM,sBAAsB,CAAC;AACzD,OAAO,EACL,oBAAoB,EACpB,oBAAoB,EACpB,sBAAsB,EACtB,oBAAoB,EACpB,mBAAmB,EACnB,2BAA2B,EAC3B,oBAAoB,EACpB,uBAAuB,GACxB,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EAAE,MAAM,EAAE,MAAM,mBAAmB,CAAC;AAC3C,OAAO,EAAE,OAAO,EAAE,MAAM,cAAc,CAAC;AAEvC,MAAM,UAAU,YAAY,CAAC,MAAqB;IAChD,MAAM,MAAM,GAAG,IAAI,SAAS,CAAC;QAC3B,IAAI,EAAE,SAAS;QACf,OAAO,EAAE,OAAO;QAChB,WAAW,EACT,4KAA4K;KAC/K,CAAC,CAAC;IAEH,iBAAiB;IACjB,mBAAmB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACpC,2BAA2B,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC5C,oBAAoB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACrC,oBAAoB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACrC,oBAAoB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACrC,oBAAoB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACrC,sBAAsB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACvC,uBAAuB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAExC,iCAAiC;IACjC,iBAAiB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAClC,eAAe,CAAC,MAAM,CAAC,CAAC;IAExB,MAAM,CAAC,IAAI,CAAC,gCAAgC,EAAE;QAC5C,KAAK,EAAE,CAAC;QACR,SAAS,EAAE,CAAC;QACZ,OAAO,EAAE,CAAC;KACX,CAAC,CAAC;IAEH,OAAO,MAAM,CAAC;AAChB,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"concepts.d.ts","sourceRoot":"","sources":["../../src/tools/concepts.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAEzE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;
|
|
1
|
+
{"version":3,"file":"concepts.d.ts","sourceRoot":"","sources":["../../src/tools/concepts.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAEzE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AAOtD,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,aAAa,GAAG,IAAI,CAmHnF"}
|
package/dist/tools/concepts.js
CHANGED
|
@@ -1,12 +1,14 @@
|
|
|
1
1
|
import { z } from 'zod';
|
|
2
|
+
import { resolveClient } from '../client/resolve.js';
|
|
2
3
|
import { formatConcept } from '../formatters/index.js';
|
|
3
4
|
import { conceptCache } from '../utils/cache.js';
|
|
4
5
|
import { formatErrorForMcp } from '../utils/errors.js';
|
|
5
6
|
export function registerConceptTools(server, client) {
|
|
6
7
|
server.tool('get_concept', 'Get detailed information about a specific OMOP concept by its numeric concept_id. Returns the concept name, vocabulary, domain, concept class, standard status, valid dates, and synonyms. Use this when you already have a concept_id and need its details.', {
|
|
7
8
|
concept_id: z.number().describe('The OMOP concept_id (numeric identifier)'),
|
|
8
|
-
}, async ({ concept_id }) => {
|
|
9
|
+
}, async ({ concept_id }, extra) => {
|
|
9
10
|
try {
|
|
11
|
+
const rc = resolveClient(extra, client);
|
|
10
12
|
const cacheKey = `concept:${concept_id}`;
|
|
11
13
|
const cached = conceptCache.get(cacheKey);
|
|
12
14
|
if (cached) {
|
|
@@ -18,7 +20,7 @@ export function registerConceptTools(server, client) {
|
|
|
18
20
|
],
|
|
19
21
|
};
|
|
20
22
|
}
|
|
21
|
-
const response = await
|
|
23
|
+
const response = await rc.request(`/concepts/${concept_id}`, undefined, 'get_concept');
|
|
22
24
|
conceptCache.set(cacheKey, response);
|
|
23
25
|
const { text, json } = formatConcept(response.data);
|
|
24
26
|
return {
|
|
@@ -48,8 +50,9 @@ export function registerConceptTools(server, client) {
|
|
|
48
50
|
.string()
|
|
49
51
|
.max(50)
|
|
50
52
|
.describe("The vocabulary-specific code. Examples: 'E11.9' (ICD-10), '44054006' (SNOMED), '4850' (LOINC)"),
|
|
51
|
-
}, async ({ vocabulary_id, concept_code }) => {
|
|
53
|
+
}, async ({ vocabulary_id, concept_code }, extra) => {
|
|
52
54
|
try {
|
|
55
|
+
const rc = resolveClient(extra, client);
|
|
53
56
|
const cacheKey = `code:${vocabulary_id}:${concept_code}`;
|
|
54
57
|
const cached = conceptCache.get(cacheKey);
|
|
55
58
|
if (cached) {
|
|
@@ -63,7 +66,7 @@ export function registerConceptTools(server, client) {
|
|
|
63
66
|
};
|
|
64
67
|
}
|
|
65
68
|
// Actual API uses /concepts/by-code/{vocabulary_id}/{concept_code}
|
|
66
|
-
const response = await
|
|
69
|
+
const response = await rc.request(`/concepts/by-code/${encodeURIComponent(vocabulary_id)}/${encodeURIComponent(concept_code)}`, undefined, 'get_concept_by_code');
|
|
67
70
|
conceptCache.set(cacheKey, response);
|
|
68
71
|
const concepts = Array.isArray(response.data) ? response.data : [response.data];
|
|
69
72
|
const formatted = concepts.map((c) => formatConcept(c));
|