@omophub/omophub-mcp 1.3.1 → 1.5.0
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 +9 -1
- package/dist/client/resolve.js +1 -1
- package/dist/client/resolve.js.map +1 -1
- package/dist/server.d.ts.map +1 -1
- package/dist/server.js +3 -2
- package/dist/server.js.map +1 -1
- package/dist/tools/concepts.js +2 -2
- package/dist/tools/concepts.js.map +1 -1
- package/dist/tools/fhir.d.ts +4 -0
- package/dist/tools/fhir.d.ts.map +1 -0
- package/dist/tools/fhir.js +177 -0
- package/dist/tools/fhir.js.map +1 -0
- package/dist/tools/index.d.ts +1 -0
- package/dist/tools/index.d.ts.map +1 -1
- package/dist/tools/index.js +1 -0
- package/dist/tools/index.js.map +1 -1
- package/dist/transports/http.d.ts.map +1 -1
- package/dist/transports/http.js +4 -0
- package/dist/transports/http.js.map +1 -1
- package/package.json +1 -1
package/README.md
CHANGED
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@@ -221,6 +221,8 @@ docker run -i -e OMOPHUB_API_KEY=oh_your_key_here omophub/omophub-mcp --transpor
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| `semantic_search` | Search using natural language with neural embeddings (understands clinical meaning) |
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| `find_similar_concepts` | Find concepts similar to a reference concept, name, or description |
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| `explore_concept` | Get concept details, hierarchy, and cross-vocabulary mappings in one call |
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| `fhir_resolve` | Resolve a FHIR coded value (incl. administrative codes via the HL7 FHIR-to-OMOP IG ConceptMaps) to its OMOP standard concept and CDM target table |
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| `fhir_resolve_codeable_concept` | Resolve a FHIR CodeableConcept — best match by OHDSI vocabulary preference, honoring `userSelected` |
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### Resources
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@@ -258,6 +260,12 @@ docker run -i -e OMOPHUB_API_KEY=oh_your_key_here omophub/omophub-mcp --transpor
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**Explore a concept →** `explore_concept`
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> "Give me everything about SNOMED concept 201826"
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**FHIR-to-OMOP resolution →** `fhir_resolve`
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> "Resolve FHIR SNOMED code 44054006 to OMOP — what table does it go in?"
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**CodeableConcept →** `fhir_resolve_codeable_concept`
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> "This CodeableConcept has both SNOMED 44054006 and ICD-10 E11.9 — which should I use for OMOP?"
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+
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**Find similar →** `find_similar_concepts`
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> "What concepts are similar to 'Type 2 diabetes mellitus'?"
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@@ -297,7 +305,7 @@ 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":"1.5.0","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/resolve.js
CHANGED
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@@ -28,7 +28,7 @@ function pruneClientCache() {
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*/
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export function resolveClient(extra, defaultClient) {
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const headers = extra?.requestInfo?.headers;
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const rawHeader = headers?.
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const rawHeader = headers?.authorization ?? headers?.Authorization;
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if (!rawHeader)
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return defaultClient;
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const authHeader = Array.isArray(rawHeader) ? rawHeader[0] : rawHeader;
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@@ -1 +1 @@
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1
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-
{"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,
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{"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,aAAa,IAAI,OAAO,EAAE,aAAa,CAAC;IAEnE,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"}
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package/dist/server.d.ts.map
CHANGED
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@@ -1 +1 @@
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1
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{"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;
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{"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;AAiBrD,wBAAgB,YAAY,CAAC,MAAM,EAAE,aAAa,GAAG,SAAS,CA8B7D"}
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package/dist/server.js
CHANGED
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@@ -1,7 +1,7 @@
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import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
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import { registerPrompts } from './prompts/index.js';
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import { registerResources } from './resources/index.js';
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import { registerConceptTools, registerExploreTools, registerHierarchyTools, registerMappingTools, registerSearchTools, registerSemanticSearchTools, registerSimilarTools, registerVocabularyTools, } from './tools/index.js';
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import { registerConceptTools, registerExploreTools, registerFhirTools, registerHierarchyTools, registerMappingTools, registerSearchTools, registerSemanticSearchTools, registerSimilarTools, registerVocabularyTools, } from './tools/index.js';
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import { logger } from './utils/logger.js';
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import { VERSION } from './version.js';
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export function createServer(client) {
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registerMappingTools(server, client);
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registerHierarchyTools(server, client);
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registerVocabularyTools(server, client);
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registerFhirTools(server, client);
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// Register resources and prompts
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registerResources(server, client);
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registerPrompts(server);
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logger.info('OMOPHub MCP server initialized', {
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-
tools:
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tools: 11,
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resources: 2,
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prompts: 2,
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});
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package/dist/server.js.map
CHANGED
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@@ -1 +1 @@
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{"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;
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{"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,iBAAiB,EACjB,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;IACxC,iBAAiB,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAElC,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,EAAE;QACT,SAAS,EAAE,CAAC;QACZ,OAAO,EAAE,CAAC;KACX,CAAC,CAAC;IAEH,OAAO,MAAM,CAAC;AAChB,CAAC"}
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package/dist/tools/concepts.js
CHANGED
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@@ -41,11 +41,11 @@ export function registerConceptTools(server, client) {
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};
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}
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});
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server.tool('get_concept_by_code', "Look up an OMOP concept using a vocabulary-specific code and vocabulary ID. Both parameters are required to avoid ambiguity
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server.tool('get_concept_by_code', "Look up an OMOP concept using a vocabulary-specific code and vocabulary ID. Both parameters are required to avoid ambiguity - the same code can exist in multiple vocabularies (e.g., 'E11' exists in both ICD10CM and ICD10). If multiple concepts share the same code within a vocabulary, all matches are returned - prefer the one with standard_concept='S'.", {
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vocabulary_id: z
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.string()
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.max(50)
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.describe("The vocabulary system. Examples: 'ICD10CM', 'SNOMED', 'RxNorm', 'LOINC', '
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.describe("The vocabulary system. Examples: 'ICD10CM', 'SNOMED', 'RxNorm', 'LOINC', 'HCPCS', 'NDC'"),
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concept_code: z
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.string()
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-
{"version":3,"file":"concepts.js","sourceRoot":"","sources":["../../src/tools/concepts.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AAErD,OAAO,EAAE,aAAa,EAAE,MAAM,wBAAwB,CAAC;AACvD,OAAO,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AACjD,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AAEvD,MAAM,UAAU,oBAAoB,CAAC,MAAiB,EAAE,MAAqB;IAC3E,MAAM,CAAC,IAAI,CACT,aAAa,EACb,8PAA8P,EAC9P;QACE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,0CAA0C,CAAC;KAC5E,EACD,KAAK,EAAE,EAAE,UAAU,EAAE,EAAE,KAAK,EAAE,EAAE;QAC9B,IAAI,CAAC;YACH,MAAM,EAAE,GAAG,aAAa,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;YACxC,MAAM,QAAQ,GAAG,WAAW,UAAU,EAAE,CAAC;YACzC,MAAM,MAAM,GAAG,YAAY,CAAC,GAAG,CAAC,QAAQ,CAAqC,CAAC;YAE9E,IAAI,MAAM,EAAE,CAAC;gBACX,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,aAAa,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;gBAClD,OAAO;oBACL,OAAO,EAAE;wBACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE;wBAC/B,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,EAAE;qBACtC;iBACF,CAAC;YACJ,CAAC;YAED,MAAM,QAAQ,GAAG,MAAM,EAAE,CAAC,OAAO,CAC/B,aAAa,UAAU,EAAE,EACzB,SAAS,EACT,aAAa,CACd,CAAC;YAEF,YAAY,CAAC,GAAG,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;YACrC,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC;YAEpD,OAAO;gBACL,OAAO,EAAE;oBACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE;oBAC/B,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,EAAE;iBACtC;aACF,CAAC;QACJ,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,iBAAiB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAC;YAC/D,OAAO;gBACL,OAAO,EAAE;oBACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE;oBAC/B,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,EAAE;iBACtC;gBACD,OAAO,EAAE,IAAI;aACd,CAAC;QACJ,CAAC;IACH,CAAC,CACF,CAAC;IAEF,MAAM,CAAC,IAAI,CACT,qBAAqB,EACrB,mWAAmW,EACnW;QACE,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CACP,
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+
{"version":3,"file":"concepts.js","sourceRoot":"","sources":["../../src/tools/concepts.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AAErD,OAAO,EAAE,aAAa,EAAE,MAAM,wBAAwB,CAAC;AACvD,OAAO,EAAE,YAAY,EAAE,MAAM,mBAAmB,CAAC;AACjD,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AAEvD,MAAM,UAAU,oBAAoB,CAAC,MAAiB,EAAE,MAAqB;IAC3E,MAAM,CAAC,IAAI,CACT,aAAa,EACb,8PAA8P,EAC9P;QACE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,0CAA0C,CAAC;KAC5E,EACD,KAAK,EAAE,EAAE,UAAU,EAAE,EAAE,KAAK,EAAE,EAAE;QAC9B,IAAI,CAAC;YACH,MAAM,EAAE,GAAG,aAAa,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;YACxC,MAAM,QAAQ,GAAG,WAAW,UAAU,EAAE,CAAC;YACzC,MAAM,MAAM,GAAG,YAAY,CAAC,GAAG,CAAC,QAAQ,CAAqC,CAAC;YAE9E,IAAI,MAAM,EAAE,CAAC;gBACX,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,aAAa,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;gBAClD,OAAO;oBACL,OAAO,EAAE;wBACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE;wBAC/B,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,EAAE;qBACtC;iBACF,CAAC;YACJ,CAAC;YAED,MAAM,QAAQ,GAAG,MAAM,EAAE,CAAC,OAAO,CAC/B,aAAa,UAAU,EAAE,EACzB,SAAS,EACT,aAAa,CACd,CAAC;YAEF,YAAY,CAAC,GAAG,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;YACrC,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC;YAEpD,OAAO;gBACL,OAAO,EAAE;oBACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE;oBAC/B,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,EAAE;iBACtC;aACF,CAAC;QACJ,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,iBAAiB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAC;YAC/D,OAAO;gBACL,OAAO,EAAE;oBACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE;oBAC/B,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,EAAE;iBACtC;gBACD,OAAO,EAAE,IAAI;aACd,CAAC;QACJ,CAAC;IACH,CAAC,CACF,CAAC;IAEF,MAAM,CAAC,IAAI,CACT,qBAAqB,EACrB,mWAAmW,EACnW;QACE,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CACP,yFAAyF,CAC1F;QACH,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CACP,+FAA+F,CAChG;KACJ,EACD,KAAK,EAAE,EAAE,aAAa,EAAE,YAAY,EAAE,EAAE,KAAK,EAAE,EAAE;QAC/C,IAAI,CAAC;YACH,MAAM,EAAE,GAAG,aAAa,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;YACxC,MAAM,QAAQ,GAAG,QAAQ,aAAa,IAAI,YAAY,EAAE,CAAC;YACzD,MAAM,MAAM,GAAG,YAAY,CAAC,GAAG,CAAC,QAAQ,CAAiD,CAAC;YAE1F,IAAI,MAAM,EAAE,CAAC;gBACX,MAAM,QAAQ,GAAG,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;gBAC1E,MAAM,SAAS,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAAC;gBACxD,OAAO;oBACL,OAAO,EAAE;wBACP,GAAG,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;wBAClE,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,EAAE;qBAC1D;iBACF,CAAC;YACJ,CAAC;YAED,mEAAmE;YACnE,MAAM,QAAQ,GAAG,MAAM,EAAE,CAAC,OAAO,CAC/B,qBAAqB,kBAAkB,CAAC,aAAa,CAAC,IAAI,kBAAkB,CAAC,YAAY,CAAC,EAAE,EAC5F,SAAS,EACT,qBAAqB,CACtB,CAAC;YAEF,YAAY,CAAC,GAAG,CAAC,QAAQ,EAAE,QAAQ,CAAC,CAAC;YAErC,MAAM,QAAQ,GAAG,KAAK,CAAC,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC;YAChF,MAAM,SAAS,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAAC;YAExD,OAAO;gBACL,OAAO,EAAE;oBACP,GAAG,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;oBAClE,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,EAAE;iBAC1D;aACF,CAAC;QACJ,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,iBAAiB,CAAC,KAAK,EAAE,qBAAqB,CAAC,CAAC;YACvE,OAAO;gBACL,OAAO,EAAE;oBACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE;oBAC/B,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,EAAE;iBACtC;gBACD,OAAO,EAAE,IAAI;aACd,CAAC;QACJ,CAAC;IACH,CAAC,CACF,CAAC;AACJ,CAAC"}
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@@ -0,0 +1 @@
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1
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+
{"version":3,"file":"fhir.d.ts","sourceRoot":"","sources":["../../src/tools/fhir.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAEzE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AAyEtD,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,aAAa,GAAG,IAAI,CAwJhF"}
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@@ -0,0 +1,177 @@
|
|
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1
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+
import { z } from 'zod';
|
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2
|
+
import { resolveClient } from '../client/resolve.js';
|
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3
|
+
import { formatErrorForMcp } from '../utils/errors.js';
|
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4
|
+
function formatResolution(res) {
|
|
5
|
+
// concept_id 0 is the OMOP "no matching concept" sentinel — surface it as
|
|
6
|
+
// unmapped rather than presenting it as a successful resolution.
|
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7
|
+
const header = res.standard_concept.concept_id === 0
|
|
8
|
+
? 'Unmapped: no OMOP standard concept (concept_id 0) for this input'
|
|
9
|
+
: `Resolved: ${res.standard_concept.concept_name} (ID: ${res.standard_concept.concept_id})`;
|
|
10
|
+
const lines = [
|
|
11
|
+
header,
|
|
12
|
+
`Vocabulary: ${res.vocabulary_id ?? 'N/A'} | Type: ${res.mapping_type}`,
|
|
13
|
+
`Target table: ${res.target_table ?? 'unknown'} | Alignment: ${res.domain_resource_alignment}`,
|
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14
|
+
];
|
|
15
|
+
if (res.similarity_score !== undefined) {
|
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16
|
+
lines.push(`Similarity: ${res.similarity_score.toFixed(2)}`);
|
|
17
|
+
}
|
|
18
|
+
if (res.mapping_quality) {
|
|
19
|
+
lines.push(`Quality: ${res.mapping_quality}`);
|
|
20
|
+
}
|
|
21
|
+
if (res.value_as_concept) {
|
|
22
|
+
lines.push(`Value concept: ${res.value_as_concept.concept_name} (${res.value_as_concept.concept_id}) → ${res.value_target_field ?? 'value_as_concept_id'}`);
|
|
23
|
+
}
|
|
24
|
+
if (res.concept_map_id) {
|
|
25
|
+
lines.push(`Via IG ConceptMap: ${res.concept_map_id}`);
|
|
26
|
+
}
|
|
27
|
+
if (res.mapping_note) {
|
|
28
|
+
lines.push(`Note: ${res.mapping_note}`);
|
|
29
|
+
}
|
|
30
|
+
if (res.recommendations && res.recommendations.length > 0) {
|
|
31
|
+
lines.push(`Recommendations (${res.recommendations.length}):`);
|
|
32
|
+
for (const rec of res.recommendations.slice(0, 5)) {
|
|
33
|
+
lines.push(` - ${rec.concept_name} (${rec.concept_id}) via ${rec.relationship_id}`);
|
|
34
|
+
}
|
|
35
|
+
}
|
|
36
|
+
return lines.join('\n');
|
|
37
|
+
}
|
|
38
|
+
export function registerFhirTools(server, client) {
|
|
39
|
+
server.tool('fhir_resolve', "Resolve a FHIR coded value (system URI + code) to its OMOP standard concept and CDM target table. Supports text-only input via semantic search fallback and optional Phoebe recommendations. Examples: system='http://snomed.info/sct' code='44054006' for Type 2 diabetes, or display='heart attack' for text-only resolution.", {
|
|
40
|
+
system: z
|
|
41
|
+
.string()
|
|
42
|
+
.optional()
|
|
43
|
+
.describe('FHIR code system URI (e.g. http://snomed.info/sct, http://loinc.org)'),
|
|
44
|
+
code: z.string().optional().describe('Code value from the FHIR Coding'),
|
|
45
|
+
display: z
|
|
46
|
+
.string()
|
|
47
|
+
.optional()
|
|
48
|
+
.describe('Display text for semantic search fallback when code is unavailable'),
|
|
49
|
+
vocabulary_id: z
|
|
50
|
+
.string()
|
|
51
|
+
.optional()
|
|
52
|
+
.describe('Direct OMOP vocabulary_id (e.g. SNOMED, ICD10CM), bypasses URI resolution'),
|
|
53
|
+
resource_type: z
|
|
54
|
+
.string()
|
|
55
|
+
.optional()
|
|
56
|
+
.describe('FHIR resource type (Condition, Observation, MedicationRequest, Procedure, etc.)'),
|
|
57
|
+
include_recommendations: z
|
|
58
|
+
.boolean()
|
|
59
|
+
.optional()
|
|
60
|
+
.default(false)
|
|
61
|
+
.describe('Include Phoebe-recommended related concepts'),
|
|
62
|
+
include_quality: z
|
|
63
|
+
.boolean()
|
|
64
|
+
.optional()
|
|
65
|
+
.default(false)
|
|
66
|
+
.describe('Include mapping quality signal (high/medium/low/manual_review)'),
|
|
67
|
+
on_unmapped: z
|
|
68
|
+
.enum(['error', 'sentinel'])
|
|
69
|
+
.optional()
|
|
70
|
+
.describe("Behavior when nothing resolves: 'error' (default, 404) or 'sentinel' (return a concept_id 0 record)"),
|
|
71
|
+
}, async (params, extra) => {
|
|
72
|
+
try {
|
|
73
|
+
const rc = resolveClient(extra, client);
|
|
74
|
+
const body = {};
|
|
75
|
+
if (params.system)
|
|
76
|
+
body.system = params.system;
|
|
77
|
+
if (params.code)
|
|
78
|
+
body.code = params.code;
|
|
79
|
+
if (params.display)
|
|
80
|
+
body.display = params.display;
|
|
81
|
+
if (params.vocabulary_id)
|
|
82
|
+
body.vocabulary_id = params.vocabulary_id;
|
|
83
|
+
if (params.resource_type)
|
|
84
|
+
body.resource_type = params.resource_type;
|
|
85
|
+
if (params.include_recommendations)
|
|
86
|
+
body.include_recommendations = true;
|
|
87
|
+
if (params.include_quality)
|
|
88
|
+
body.include_quality = true;
|
|
89
|
+
if (params.on_unmapped)
|
|
90
|
+
body.on_unmapped = params.on_unmapped;
|
|
91
|
+
const response = await rc.post('/fhir/resolve', body, 'fhir_resolve');
|
|
92
|
+
const res = response.data?.resolution;
|
|
93
|
+
const text = res ? formatResolution(res) : 'Resolution failed — no data returned';
|
|
94
|
+
return {
|
|
95
|
+
content: [
|
|
96
|
+
{ type: 'text', text },
|
|
97
|
+
{ type: 'text', text: JSON.stringify(response, null, 2) },
|
|
98
|
+
],
|
|
99
|
+
};
|
|
100
|
+
}
|
|
101
|
+
catch (error) {
|
|
102
|
+
const { text, json } = formatErrorForMcp(error, 'fhir_resolve');
|
|
103
|
+
return {
|
|
104
|
+
content: [
|
|
105
|
+
{ type: 'text', text },
|
|
106
|
+
{ type: 'text', text: json },
|
|
107
|
+
],
|
|
108
|
+
isError: true,
|
|
109
|
+
};
|
|
110
|
+
}
|
|
111
|
+
});
|
|
112
|
+
server.tool('fhir_resolve_codeable_concept', 'Resolve a FHIR CodeableConcept with multiple codings. Picks the best match per OHDSI vocabulary preference (SNOMED > RxNorm > LOINC > CVX > ICD-10). Falls back to the text field via semantic search if no coding resolves.', {
|
|
113
|
+
coding: z
|
|
114
|
+
.array(z.object({
|
|
115
|
+
system: z.string().trim().min(1).describe('FHIR code system URI'),
|
|
116
|
+
code: z.string().trim().min(1).describe('Code value'),
|
|
117
|
+
display: z.string().optional().describe('Display text'),
|
|
118
|
+
user_selected: z
|
|
119
|
+
.boolean()
|
|
120
|
+
.optional()
|
|
121
|
+
.describe('FHIR Coding.userSelected — wins over vocabulary preference when set'),
|
|
122
|
+
}))
|
|
123
|
+
.min(1)
|
|
124
|
+
.max(20)
|
|
125
|
+
.describe('Array of FHIR Coding entries from the CodeableConcept'),
|
|
126
|
+
text: z
|
|
127
|
+
.string()
|
|
128
|
+
.optional()
|
|
129
|
+
.describe('CodeableConcept.text — semantic fallback if no coding resolves'),
|
|
130
|
+
resource_type: z.string().optional().describe('FHIR resource type'),
|
|
131
|
+
include_recommendations: z.boolean().optional().default(false),
|
|
132
|
+
include_quality: z.boolean().optional().default(false),
|
|
133
|
+
on_unmapped: z
|
|
134
|
+
.enum(['error', 'sentinel'])
|
|
135
|
+
.optional()
|
|
136
|
+
.describe("Behavior when nothing resolves: 'error' (default, 404) or 'sentinel' (concept_id 0 record)"),
|
|
137
|
+
}, async (params, extra) => {
|
|
138
|
+
try {
|
|
139
|
+
const rc = resolveClient(extra, client);
|
|
140
|
+
const body = { coding: params.coding };
|
|
141
|
+
if (params.text)
|
|
142
|
+
body.text = params.text;
|
|
143
|
+
if (params.resource_type)
|
|
144
|
+
body.resource_type = params.resource_type;
|
|
145
|
+
if (params.include_recommendations)
|
|
146
|
+
body.include_recommendations = true;
|
|
147
|
+
if (params.include_quality)
|
|
148
|
+
body.include_quality = true;
|
|
149
|
+
if (params.on_unmapped)
|
|
150
|
+
body.on_unmapped = params.on_unmapped;
|
|
151
|
+
const response = await rc.post('/fhir/resolve/codeable-concept', body, 'fhir_resolve_codeable_concept');
|
|
152
|
+
const best = response.data?.best_match?.resolution;
|
|
153
|
+
const altCount = response.data?.alternatives?.length ?? 0;
|
|
154
|
+
const text = best
|
|
155
|
+
? `Best match: ${best.standard_concept.concept_name} (${best.source_concept.vocabulary_id})\n` +
|
|
156
|
+
`Target table: ${best.target_table ?? 'unknown'} | Alternatives: ${altCount}`
|
|
157
|
+
: 'No resolution found — all codings failed to resolve';
|
|
158
|
+
return {
|
|
159
|
+
content: [
|
|
160
|
+
{ type: 'text', text },
|
|
161
|
+
{ type: 'text', text: JSON.stringify(response, null, 2) },
|
|
162
|
+
],
|
|
163
|
+
};
|
|
164
|
+
}
|
|
165
|
+
catch (error) {
|
|
166
|
+
const { text, json } = formatErrorForMcp(error, 'fhir_resolve_codeable_concept');
|
|
167
|
+
return {
|
|
168
|
+
content: [
|
|
169
|
+
{ type: 'text', text },
|
|
170
|
+
{ type: 'text', text: json },
|
|
171
|
+
],
|
|
172
|
+
isError: true,
|
|
173
|
+
};
|
|
174
|
+
}
|
|
175
|
+
});
|
|
176
|
+
}
|
|
177
|
+
//# sourceMappingURL=fhir.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"fhir.js","sourceRoot":"","sources":["../../src/tools/fhir.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,OAAO,EAAE,aAAa,EAAE,MAAM,sBAAsB,CAAC;AACrD,OAAO,EAAE,iBAAiB,EAAE,MAAM,oBAAoB,CAAC;AAiCvD,SAAS,gBAAgB,CAAC,GAAmB;IAC3C,0EAA0E;IAC1E,iEAAiE;IACjE,MAAM,MAAM,GACV,GAAG,CAAC,gBAAgB,CAAC,UAAU,KAAK,CAAC;QACnC,CAAC,CAAC,kEAAkE;QACpE,CAAC,CAAC,aAAa,GAAG,CAAC,gBAAgB,CAAC,YAAY,SAAS,GAAG,CAAC,gBAAgB,CAAC,UAAU,GAAG,CAAC;IAChG,MAAM,KAAK,GAAG;QACZ,MAAM;QACN,eAAe,GAAG,CAAC,aAAa,IAAI,KAAK,YAAY,GAAG,CAAC,YAAY,EAAE;QACvE,iBAAiB,GAAG,CAAC,YAAY,IAAI,SAAS,iBAAiB,GAAG,CAAC,yBAAyB,EAAE;KAC/F,CAAC;IACF,IAAI,GAAG,CAAC,gBAAgB,KAAK,SAAS,EAAE,CAAC;QACvC,KAAK,CAAC,IAAI,CAAC,eAAe,GAAG,CAAC,gBAAgB,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;IAC/D,CAAC;IACD,IAAI,GAAG,CAAC,eAAe,EAAE,CAAC;QACxB,KAAK,CAAC,IAAI,CAAC,YAAY,GAAG,CAAC,eAAe,EAAE,CAAC,CAAC;IAChD,CAAC;IACD,IAAI,GAAG,CAAC,gBAAgB,EAAE,CAAC;QACzB,KAAK,CAAC,IAAI,CACR,kBAAkB,GAAG,CAAC,gBAAgB,CAAC,YAAY,KAAK,GAAG,CAAC,gBAAgB,CAAC,UAAU,OAAO,GAAG,CAAC,kBAAkB,IAAI,qBAAqB,EAAE,CAChJ,CAAC;IACJ,CAAC;IACD,IAAI,GAAG,CAAC,cAAc,EAAE,CAAC;QACvB,KAAK,CAAC,IAAI,CAAC,sBAAsB,GAAG,CAAC,cAAc,EAAE,CAAC,CAAC;IACzD,CAAC;IACD,IAAI,GAAG,CAAC,YAAY,EAAE,CAAC;QACrB,KAAK,CAAC,IAAI,CAAC,SAAS,GAAG,CAAC,YAAY,EAAE,CAAC,CAAC;IAC1C,CAAC;IACD,IAAI,GAAG,CAAC,eAAe,IAAI,GAAG,CAAC,eAAe,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC1D,KAAK,CAAC,IAAI,CAAC,oBAAoB,GAAG,CAAC,eAAe,CAAC,MAAM,IAAI,CAAC,CAAC;QAC/D,KAAK,MAAM,GAAG,IAAI,GAAG,CAAC,eAAe,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC;YAClD,KAAK,CAAC,IAAI,CAAC,OAAO,GAAG,CAAC,YAAY,KAAK,GAAG,CAAC,UAAU,SAAS,GAAG,CAAC,eAAe,EAAE,CAAC,CAAC;QACvF,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAC1B,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,MAAiB,EAAE,MAAqB;IACxE,MAAM,CAAC,IAAI,CACT,cAAc,EACd,iUAAiU,EACjU;QACE,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,sEAAsE,CAAC;QACnF,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QACvE,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,oEAAoE,CAAC;QACjF,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,2EAA2E,CAAC;QACxF,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,iFAAiF,CAClF;QACH,uBAAuB,EAAE,CAAC;aACvB,OAAO,EAAE;aACT,QAAQ,EAAE;aACV,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CAAC,6CAA6C,CAAC;QAC1D,eAAe,EAAE,CAAC;aACf,OAAO,EAAE;aACT,QAAQ,EAAE;aACV,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CAAC,gEAAgE,CAAC;QAC7E,WAAW,EAAE,CAAC;aACX,IAAI,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC;aAC3B,QAAQ,EAAE;aACV,QAAQ,CACP,qGAAqG,CACtG;KACJ,EACD,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,EAAE;QACtB,IAAI,CAAC;YACH,MAAM,EAAE,GAAG,aAAa,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;YACxC,MAAM,IAAI,GAA4B,EAAE,CAAC;YACzC,IAAI,MAAM,CAAC,MAAM;gBAAE,IAAI,CAAC,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC;YAC/C,IAAI,MAAM,CAAC,IAAI;gBAAE,IAAI,CAAC,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC;YACzC,IAAI,MAAM,CAAC,OAAO;gBAAE,IAAI,CAAC,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC;YAClD,IAAI,MAAM,CAAC,aAAa;gBAAE,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,aAAa,CAAC;YACpE,IAAI,MAAM,CAAC,aAAa;gBAAE,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,aAAa,CAAC;YACpE,IAAI,MAAM,CAAC,uBAAuB;gBAAE,IAAI,CAAC,uBAAuB,GAAG,IAAI,CAAC;YACxE,IAAI,MAAM,CAAC,eAAe;gBAAE,IAAI,CAAC,eAAe,GAAG,IAAI,CAAC;YACxD,IAAI,MAAM,CAAC,WAAW;gBAAE,IAAI,CAAC,WAAW,GAAG,MAAM,CAAC,WAAW,CAAC;YAE9D,MAAM,QAAQ,GAAG,MAAM,EAAE,CAAC,IAAI,CAAsB,eAAe,EAAE,IAAI,EAAE,cAAc,CAAC,CAAC;YAE3F,MAAM,GAAG,GAAG,QAAQ,CAAC,IAAI,EAAE,UAAU,CAAC;YACtC,MAAM,IAAI,GAAG,GAAG,CAAC,CAAC,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,sCAAsC,CAAC;YAElF,OAAO;gBACL,OAAO,EAAE;oBACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE;oBAC/B,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE,IAAI,EAAE,CAAC,CAAC,EAAE;iBACnE;aACF,CAAC;QACJ,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,iBAAiB,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC;YAChE,OAAO;gBACL,OAAO,EAAE;oBACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE;oBAC/B,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,EAAE;iBACtC;gBACD,OAAO,EAAE,IAAI;aACd,CAAC;QACJ,CAAC;IACH,CAAC,CACF,CAAC;IAEF,MAAM,CAAC,IAAI,CACT,+BAA+B,EAC/B,8NAA8N,EAC9N;QACE,MAAM,EAAE,CAAC;aACN,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,sBAAsB,CAAC;YACjE,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,YAAY,CAAC;YACrD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,cAAc,CAAC;YACvD,aAAa,EAAE,CAAC;iBACb,OAAO,EAAE;iBACT,QAAQ,EAAE;iBACV,QAAQ,CAAC,qEAAqE,CAAC;SACnF,CAAC,CACH;aACA,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CAAC,uDAAuD,CAAC;QACpE,IAAI,EAAE,CAAC;aACJ,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,gEAAgE,CAAC;QAC7E,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QACnE,uBAAuB,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC;QAC9D,eAAe,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC;QACtD,WAAW,EAAE,CAAC;aACX,IAAI,CAAC,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC;aAC3B,QAAQ,EAAE;aACV,QAAQ,CACP,4FAA4F,CAC7F;KACJ,EACD,KAAK,EAAE,MAAM,EAAE,KAAK,EAAE,EAAE;QACtB,IAAI,CAAC;YACH,MAAM,EAAE,GAAG,aAAa,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC;YACxC,MAAM,IAAI,GAA4B,EAAE,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC;YAChE,IAAI,MAAM,CAAC,IAAI;gBAAE,IAAI,CAAC,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC;YACzC,IAAI,MAAM,CAAC,aAAa;gBAAE,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,aAAa,CAAC;YACpE,IAAI,MAAM,CAAC,uBAAuB;gBAAE,IAAI,CAAC,uBAAuB,GAAG,IAAI,CAAC;YACxE,IAAI,MAAM,CAAC,eAAe;gBAAE,IAAI,CAAC,eAAe,GAAG,IAAI,CAAC;YACxD,IAAI,MAAM,CAAC,WAAW;gBAAE,IAAI,CAAC,WAAW,GAAG,MAAM,CAAC,WAAW,CAAC;YAE9D,MAAM,QAAQ,GAAG,MAAM,EAAE,CAAC,IAAI,CAC5B,gCAAgC,EAChC,IAAI,EACJ,+BAA+B,CAChC,CAAC;YAEF,MAAM,IAAI,GAAG,QAAQ,CAAC,IAAI,EAAE,UAAU,EAAE,UAAU,CAAC;YACnD,MAAM,QAAQ,GAAG,QAAQ,CAAC,IAAI,EAAE,YAAY,EAAE,MAAM,IAAI,CAAC,CAAC;YAC1D,MAAM,IAAI,GAAG,IAAI;gBACf,CAAC,CAAC,eAAe,IAAI,CAAC,gBAAgB,CAAC,YAAY,KAAK,IAAI,CAAC,cAAc,CAAC,aAAa,KAAK;oBAC5F,iBAAiB,IAAI,CAAC,YAAY,IAAI,SAAS,oBAAoB,QAAQ,EAAE;gBAC/E,CAAC,CAAC,qDAAqD,CAAC;YAE1D,OAAO;gBACL,OAAO,EAAE;oBACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE;oBAC/B,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,QAAQ,EAAE,IAAI,EAAE,CAAC,CAAC,EAAE;iBACnE;aACF,CAAC;QACJ,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,iBAAiB,CAAC,KAAK,EAAE,+BAA+B,CAAC,CAAC;YACjF,OAAO;gBACL,OAAO,EAAE;oBACP,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE;oBAC/B,EAAE,IAAI,EAAE,MAAe,EAAE,IAAI,EAAE,IAAI,EAAE;iBACtC;gBACD,OAAO,EAAE,IAAI;aACd,CAAC;QACJ,CAAC;IACH,CAAC,CACF,CAAC;AACJ,CAAC"}
|
package/dist/tools/index.d.ts
CHANGED
|
@@ -1,5 +1,6 @@
|
|
|
1
1
|
export { registerConceptTools } from './concepts.js';
|
|
2
2
|
export { registerExploreTools } from './explore.js';
|
|
3
|
+
export { registerFhirTools } from './fhir.js';
|
|
3
4
|
export { registerHierarchyTools } from './hierarchy.js';
|
|
4
5
|
export { registerMappingTools } from './mappings.js';
|
|
5
6
|
export { registerSearchTools } from './search.js';
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/tools/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACrD,OAAO,EAAE,oBAAoB,EAAE,MAAM,cAAc,CAAC;AACpD,OAAO,EAAE,sBAAsB,EAAE,MAAM,gBAAgB,CAAC;AACxD,OAAO,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACrD,OAAO,EAAE,mBAAmB,EAAE,MAAM,aAAa,CAAC;AAClD,OAAO,EAAE,2BAA2B,EAAE,MAAM,sBAAsB,CAAC;AACnE,OAAO,EAAE,oBAAoB,EAAE,MAAM,cAAc,CAAC;AACpD,OAAO,EAAE,uBAAuB,EAAE,MAAM,mBAAmB,CAAC"}
|
|
1
|
+
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/tools/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACrD,OAAO,EAAE,oBAAoB,EAAE,MAAM,cAAc,CAAC;AACpD,OAAO,EAAE,iBAAiB,EAAE,MAAM,WAAW,CAAC;AAC9C,OAAO,EAAE,sBAAsB,EAAE,MAAM,gBAAgB,CAAC;AACxD,OAAO,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACrD,OAAO,EAAE,mBAAmB,EAAE,MAAM,aAAa,CAAC;AAClD,OAAO,EAAE,2BAA2B,EAAE,MAAM,sBAAsB,CAAC;AACnE,OAAO,EAAE,oBAAoB,EAAE,MAAM,cAAc,CAAC;AACpD,OAAO,EAAE,uBAAuB,EAAE,MAAM,mBAAmB,CAAC"}
|
package/dist/tools/index.js
CHANGED
|
@@ -1,5 +1,6 @@
|
|
|
1
1
|
export { registerConceptTools } from './concepts.js';
|
|
2
2
|
export { registerExploreTools } from './explore.js';
|
|
3
|
+
export { registerFhirTools } from './fhir.js';
|
|
3
4
|
export { registerHierarchyTools } from './hierarchy.js';
|
|
4
5
|
export { registerMappingTools } from './mappings.js';
|
|
5
6
|
export { registerSearchTools } from './search.js';
|
package/dist/tools/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/tools/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACrD,OAAO,EAAE,oBAAoB,EAAE,MAAM,cAAc,CAAC;AACpD,OAAO,EAAE,sBAAsB,EAAE,MAAM,gBAAgB,CAAC;AACxD,OAAO,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACrD,OAAO,EAAE,mBAAmB,EAAE,MAAM,aAAa,CAAC;AAClD,OAAO,EAAE,2BAA2B,EAAE,MAAM,sBAAsB,CAAC;AACnE,OAAO,EAAE,oBAAoB,EAAE,MAAM,cAAc,CAAC;AACpD,OAAO,EAAE,uBAAuB,EAAE,MAAM,mBAAmB,CAAC"}
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/tools/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACrD,OAAO,EAAE,oBAAoB,EAAE,MAAM,cAAc,CAAC;AACpD,OAAO,EAAE,iBAAiB,EAAE,MAAM,WAAW,CAAC;AAC9C,OAAO,EAAE,sBAAsB,EAAE,MAAM,gBAAgB,CAAC;AACxD,OAAO,EAAE,oBAAoB,EAAE,MAAM,eAAe,CAAC;AACrD,OAAO,EAAE,mBAAmB,EAAE,MAAM,aAAa,CAAC;AAClD,OAAO,EAAE,2BAA2B,EAAE,MAAM,sBAAsB,CAAC;AACnE,OAAO,EAAE,oBAAoB,EAAE,MAAM,cAAc,CAAC;AACpD,OAAO,EAAE,uBAAuB,EAAE,MAAM,mBAAmB,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"http.d.ts","sourceRoot":"","sources":["../../src/transports/http.ts"],"names":[],"mappings":"AACA,OAAO,EAAsC,KAAK,MAAM,EAAuB,MAAM,WAAW,CAAC;AACjG,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAGzE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AA4BtD;;;GAGG;AACH,wBAAsB,kBAAkB,CACtC,aAAa,EAAE,CAAC,MAAM,EAAE,aAAa,KAAK,SAAS,EACnD,aAAa,EAAE,aAAa,EAC5B,IAAI,EAAE,MAAM,GACX,OAAO,CAAC,MAAM,CAAC,
|
|
1
|
+
{"version":3,"file":"http.d.ts","sourceRoot":"","sources":["../../src/transports/http.ts"],"names":[],"mappings":"AACA,OAAO,EAAsC,KAAK,MAAM,EAAuB,MAAM,WAAW,CAAC;AACjG,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAGzE,OAAO,KAAK,EAAE,aAAa,EAAE,MAAM,kBAAkB,CAAC;AA4BtD;;;GAGG;AACH,wBAAsB,kBAAkB,CACtC,aAAa,EAAE,CAAC,MAAM,EAAE,aAAa,KAAK,SAAS,EACnD,aAAa,EAAE,aAAa,EAC5B,IAAI,EAAE,MAAM,GACX,OAAO,CAAC,MAAM,CAAC,CAgKjB"}
|
package/dist/transports/http.js
CHANGED
|
@@ -45,6 +45,8 @@ export async function startHttpTransport(serverFactory, defaultClient, port) {
|
|
|
45
45
|
if (req.method === 'GET' || req.method === 'DELETE') {
|
|
46
46
|
if (sessionId && sessions.has(sessionId)) {
|
|
47
47
|
const transport = sessions.get(sessionId);
|
|
48
|
+
if (!transport)
|
|
49
|
+
return;
|
|
48
50
|
try {
|
|
49
51
|
await transport.handleRequest(req, res);
|
|
50
52
|
}
|
|
@@ -105,6 +107,8 @@ export async function startHttpTransport(serverFactory, defaultClient, port) {
|
|
|
105
107
|
// Existing session
|
|
106
108
|
if (sessionId && sessions.has(sessionId)) {
|
|
107
109
|
const transport = sessions.get(sessionId);
|
|
110
|
+
if (!transport)
|
|
111
|
+
return;
|
|
108
112
|
try {
|
|
109
113
|
await transport.handleRequest(req, res, parsedBody);
|
|
110
114
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@omophub/omophub-mcp",
|
|
3
|
-
"version": "1.
|
|
3
|
+
"version": "1.5.0",
|
|
4
4
|
"mcpName": "io.github.OMOPHub/omophub-mcp",
|
|
5
5
|
"description": "MCP server for OHDSI OMOP standardized medical vocabularies - search, lookup, map, and navigate concepts via AI agents",
|
|
6
6
|
"type": "module",
|