@omophub/omophub-mcp 1.3.0 → 1.4.0

package/README.md

@@ -2,7 +2,7 @@
 
 <p>
   <strong>Medical vocabularies for AI agents.</strong><br/>
-  Search, map, and navigate 5M+ OMOP concepts: SNOMED CT, ICD-10, RxNorm, LOINC, and more. Directly from Claude, Cursor, VS Code, or any MCP-compatible client.
+  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.
 </p>
 
 <p>
@@ -147,7 +147,7 @@ Connect MCP clients to `/` or `/mcp`. Useful for centralized deployments where m
 <details>
 <summary><strong>Hosted (mcp.omophub.com)</strong></summary>
 
-Connect directly to the OMOPHub-hosted MCP server — no installation required. Each client authenticates with their own API key via the `Authorization` header:
+Connect directly to the OMOPHub-hosted MCP server - no installation required. Each client authenticates with their own API key via the `Authorization` header:
 
 **Claude Code:**
 ```bash
@@ -189,7 +189,7 @@ claude mcp add omophub --transport http \
 <summary><strong>Docker</strong></summary>
 
 ```bash
-# HTTP mode (default in Docker) — serves MCP on port 3100
+# HTTP mode (default in Docker) - serves MCP on port 3100
 docker run -e OMOPHUB_API_KEY=oh_your_key_here -p 3100:3100 omophub/omophub-mcp
 
 # Stdio mode (for piping)
@@ -221,6 +221,8 @@ docker run -i -e OMOPHUB_API_KEY=oh_your_key_here omophub/omophub-mcp --transpor
 | `semantic_search` | Search using natural language with neural embeddings (understands clinical meaning) |
 | `find_similar_concepts` | Find concepts similar to a reference concept, name, or description |
 | `explore_concept` | Get concept details, hierarchy, and cross-vocabulary mappings in one call |
+| `fhir_resolve` | Resolve a FHIR coded value (system URI + code) to its OMOP standard concept and CDM target table |
+| `fhir_resolve_codeable_concept` | Resolve a FHIR CodeableConcept — picks the best match per OHDSI vocabulary preference |
 
 ### Resources
 
@@ -258,6 +260,12 @@ docker run -i -e OMOPHUB_API_KEY=oh_your_key_here omophub/omophub-mcp --transpor
 **Explore a concept →** `explore_concept`
 > "Give me everything about SNOMED concept 201826"
 
+**FHIR-to-OMOP resolution →** `fhir_resolve`
+> "Resolve FHIR SNOMED code 44054006 to OMOP — what table does it go in?"
+
+**CodeableConcept →** `fhir_resolve_codeable_concept`
+> "This CodeableConcept has both SNOMED 44054006 and ICD-10 E11.9 — which should I use for OMOP?"
+
 **Find similar →** `find_similar_concepts`
 > "What concepts are similar to 'Type 2 diabetes mellitus'?"
 
@@ -297,7 +305,7 @@ In **HTTP mode**, the health endpoint is available at `/health` on the same port
 ```bash
 npx @omophub/omophub-mcp --transport=http --port=3100 --api-key=oh_your_key
 curl http://localhost:3100/health
-# → {"status":"ok","version":"1.3.0","uptime_seconds":42}
+# → {"status":"ok","version":"1.3.1","uptime_seconds":42}
 ```
 
 In **stdio mode**, use `--health-port` for a standalone health endpoint:

package/dist/client/resolve.js

@@ -28,7 +28,7 @@ function pruneClientCache() {
  */
 export function resolveClient(extra, defaultClient) {
     const headers = extra?.requestInfo?.headers;
-    const rawHeader = headers?.['authorization'] ?? headers?.['Authorization'];
+    const rawHeader = headers?.authorization ?? headers?.Authorization;
     if (!rawHeader)
         return defaultClient;
     const authHeader = Array.isArray(rawHeader) ? rawHeader[0] : rawHeader;

package/dist/client/resolve.js.map

@@ -1 +1 @@
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package/dist/index.d.ts.map

@@ -1 +1 @@
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package/dist/index.js

@@ -2,6 +2,7 @@
 import { realpathSync } from 'node:fs';
 import url from 'node:url';
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js';
+import { OmopHubClient } from './client/api.js';
 import { startHealthServer } from './health.js';
 import { createServer } from './server.js';
 import { startHttpTransport } from './transports/http.js';
@@ -83,13 +84,14 @@ export async function main() {
     if (!apiKey) {
         logger.info('No default API key — hosted mode: all requests must include Authorization: Bearer header');
     }
-    const server = createServer(apiKey, args.baseUrl);
+    const defaultClient = new OmopHubClient(apiKey, args.baseUrl);
     if (transportType === 'http') {
         const port = resolvePort(args.port);
         logger.info('Starting OMOPHub MCP server (http transport)');
-        await startHttpTransport(server, port);
+        await startHttpTransport(createServer, defaultClient, port);
     }
     else {
+        const server = createServer(defaultClient);
         const transport = new StdioServerTransport();
         logger.info('Starting OMOPHub MCP server (stdio transport)');
         await server.connect(transport);

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@@ -1 +1 @@
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+{"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"}

package/dist/server.d.ts

@@ -1,3 +1,4 @@
 import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
-export declare function createServer(apiKey: string | undefined, baseUrl?: string): McpServer;
+import type { OmopHubClient } from './client/api.js';
+export declare function createServer(client: OmopHubClient): McpServer;
 //# sourceMappingURL=server.d.ts.map

package/dist/server.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"server.d.ts","sourceRoot":"","sources":["../src/server.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAiBpE,wBAAgB,YAAY,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,EAAE,OAAO,CAAC,EAAE,MAAM,GAAG,SAAS,CA+BpF"}
+{"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"}

package/dist/server.js

@@ -1,17 +1,15 @@
 import { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
-import { OmopHubClient } from './client/api.js';
 import { registerPrompts } from './prompts/index.js';
 import { registerResources } from './resources/index.js';
-import { registerConceptTools, registerExploreTools, registerHierarchyTools, registerMappingTools, registerSearchTools, registerSemanticSearchTools, registerSimilarTools, registerVocabularyTools, } from './tools/index.js';
+import { registerConceptTools, registerExploreTools, registerFhirTools, registerHierarchyTools, registerMappingTools, registerSearchTools, registerSemanticSearchTools, registerSimilarTools, registerVocabularyTools, } from './tools/index.js';
 import { logger } from './utils/logger.js';
 import { VERSION } from './version.js';
-export function createServer(apiKey, baseUrl) {
+export function createServer(client) {
     const server = new McpServer({
         name: 'omophub',
         version: VERSION,
         description: 'Access OHDSI standardized medical vocabularies — search concepts, navigate hierarchies, and map between clinical coding systems like SNOMED CT, ICD-10, RxNorm, and LOINC.',
     });
-    const client = new OmopHubClient(apiKey, baseUrl);
     // Register tools
     registerSearchTools(server, client);
     registerSemanticSearchTools(server, client);
@@ -21,11 +19,12 @@ export function createServer(apiKey, baseUrl) {
     registerMappingTools(server, client);
     registerHierarchyTools(server, client);
     registerVocabularyTools(server, client);
+    registerFhirTools(server, client);
     // Register resources and prompts
     registerResources(server, client);
     registerPrompts(server);
     logger.info('OMOPHub MCP server initialized', {
-        tools: 9,
+        tools: 11,
         resources: 2,
         prompts: 2,
     });

package/dist/server.js.map

@@ -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,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"}

package/dist/tools/fhir.d.ts

@@ -0,0 +1,4 @@
+import type { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
+import type { OmopHubClient } from '../client/api.js';
+export declare function registerFhirTools(server: McpServer, client: OmopHubClient): void;
+//# sourceMappingURL=fhir.d.ts.map

package/dist/tools/fhir.d.ts.map

@@ -0,0 +1 @@
+{"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;AAiDtD,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,SAAS,EAAE,MAAM,EAAE,aAAa,GAAG,IAAI,CAsIhF"}

package/dist/tools/fhir.js

@@ -0,0 +1,147 @@
+import { z } from 'zod';
+import { resolveClient } from '../client/resolve.js';
+import { formatErrorForMcp } from '../utils/errors.js';
+function formatResolution(res) {
+    const lines = [
+        `Resolved: ${res.standard_concept.concept_name} (ID: ${res.standard_concept.concept_id})`,
+        `Vocabulary: ${res.vocabulary_id ?? 'N/A'} | Type: ${res.mapping_type}`,
+        `Target table: ${res.target_table ?? 'unknown'} | Alignment: ${res.domain_resource_alignment}`,
+    ];
+    if (res.similarity_score !== undefined) {
+        lines.push(`Similarity: ${res.similarity_score.toFixed(2)}`);
+    }
+    if (res.mapping_quality) {
+        lines.push(`Quality: ${res.mapping_quality}`);
+    }
+    if (res.recommendations && res.recommendations.length > 0) {
+        lines.push(`Recommendations (${res.recommendations.length}):`);
+        for (const rec of res.recommendations.slice(0, 5)) {
+            lines.push(`  - ${rec.concept_name} (${rec.concept_id}) via ${rec.relationship_id}`);
+        }
+    }
+    return lines.join('\n');
+}
+export function registerFhirTools(server, client) {
+    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.", {
+        system: z
+            .string()
+            .optional()
+            .describe('FHIR code system URI (e.g. http://snomed.info/sct, http://loinc.org)'),
+        code: z.string().optional().describe('Code value from the FHIR Coding'),
+        display: z
+            .string()
+            .optional()
+            .describe('Display text for semantic search fallback when code is unavailable'),
+        vocabulary_id: z
+            .string()
+            .optional()
+            .describe('Direct OMOP vocabulary_id (e.g. SNOMED, ICD10CM), bypasses URI resolution'),
+        resource_type: z
+            .string()
+            .optional()
+            .describe('FHIR resource type (Condition, Observation, MedicationRequest, Procedure, etc.)'),
+        include_recommendations: z
+            .boolean()
+            .optional()
+            .default(false)
+            .describe('Include Phoebe-recommended related concepts'),
+        include_quality: z
+            .boolean()
+            .optional()
+            .default(false)
+            .describe('Include mapping quality signal (high/medium/low/manual_review)'),
+    }, async (params, extra) => {
+        try {
+            const rc = resolveClient(extra, client);
+            const body = {};
+            if (params.system)
+                body.system = params.system;
+            if (params.code)
+                body.code = params.code;
+            if (params.display)
+                body.display = params.display;
+            if (params.vocabulary_id)
+                body.vocabulary_id = params.vocabulary_id;
+            if (params.resource_type)
+                body.resource_type = params.resource_type;
+            if (params.include_recommendations)
+                body.include_recommendations = true;
+            if (params.include_quality)
+                body.include_quality = true;
+            const response = await rc.post('/fhir/resolve', body, 'fhir_resolve');
+            const res = response.data?.resolution;
+            const text = res ? formatResolution(res) : 'Resolution failed — no data returned';
+            return {
+                content: [
+                    { type: 'text', text },
+                    { type: 'text', text: JSON.stringify(response, null, 2) },
+                ],
+            };
+        }
+        catch (error) {
+            const { text, json } = formatErrorForMcp(error, 'fhir_resolve');
+            return {
+                content: [
+                    { type: 'text', text },
+                    { type: 'text', text: json },
+                ],
+                isError: true,
+            };
+        }
+    });
+    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.', {
+        coding: z
+            .array(z.object({
+            system: z.string().describe('FHIR code system URI'),
+            code: z.string().describe('Code value'),
+            display: z.string().optional().describe('Display text'),
+        }))
+            .min(1)
+            .max(20)
+            .describe('Array of FHIR Coding entries from the CodeableConcept'),
+        text: z
+            .string()
+            .optional()
+            .describe('CodeableConcept.text — semantic fallback if no coding resolves'),
+        resource_type: z.string().optional().describe('FHIR resource type'),
+        include_recommendations: z.boolean().optional().default(false),
+        include_quality: z.boolean().optional().default(false),
+    }, async (params, extra) => {
+        try {
+            const rc = resolveClient(extra, client);
+            const body = { coding: params.coding };
+            if (params.text)
+                body.text = params.text;
+            if (params.resource_type)
+                body.resource_type = params.resource_type;
+            if (params.include_recommendations)
+                body.include_recommendations = true;
+            if (params.include_quality)
+                body.include_quality = true;
+            const response = await rc.post('/fhir/resolve/codeable-concept', body, 'fhir_resolve_codeable_concept');
+            const best = response.data?.best_match?.resolution;
+            const altCount = response.data?.alternatives?.length ?? 0;
+            const text = best
+                ? `Best match: ${best.standard_concept.concept_name} (${best.source_concept.vocabulary_id})\n` +
+                    `Target table: ${best.target_table ?? 'unknown'} | Alternatives: ${altCount}`
+                : 'No resolution found — all codings failed to resolve';
+            return {
+                content: [
+                    { type: 'text', text },
+                    { type: 'text', text: JSON.stringify(response, null, 2) },
+                ],
+            };
+        }
+        catch (error) {
+            const { text, json } = formatErrorForMcp(error, 'fhir_resolve_codeable_concept');
+            return {
+                content: [
+                    { type: 'text', text },
+                    { type: 'text', text: json },
+                ],
+                isError: true,
+            };
+        }
+    });
+}
+//# sourceMappingURL=fhir.js.map

package/dist/tools/fhir.js.map

@@ -0,0 +1 @@
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package/dist/tools/index.d.ts

@@ -1,5 +1,6 @@
 export { registerConceptTools } from './concepts.js';
 export { registerExploreTools } from './explore.js';
+export { registerFhirTools } from './fhir.js';
 export { registerHierarchyTools } from './hierarchy.js';
 export { registerMappingTools } from './mappings.js';
 export { registerSearchTools } from './search.js';

package/dist/tools/index.d.ts.map

@@ -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"}
+{"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

@@ -1,5 +1,6 @@
 export { registerConceptTools } from './concepts.js';
 export { registerExploreTools } from './explore.js';
+export { registerFhirTools } from './fhir.js';
 export { registerHierarchyTools } from './hierarchy.js';
 export { registerMappingTools } from './mappings.js';
 export { registerSearchTools } from './search.js';

package/dist/tools/index.js.map

@@ -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"}
+{"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"}

package/dist/transports/http.d.ts

@@ -1,8 +1,9 @@
 import { type Server } from 'node:http';
 import type { McpServer } from '@modelcontextprotocol/sdk/server/mcp.js';
+import type { OmopHubClient } from '../client/api.js';
 /**
- * Starts an HTTP server with Streamable HTTP MCP transport on /
+ * Starts an HTTP server with per-session MCP transports on /
  * and a health endpoint on /health.
  */
-export declare function startHttpTransport(mcpServer: McpServer, port: number): Promise<Server>;
+export declare function startHttpTransport(serverFactory: (client: OmopHubClient) => McpServer, defaultClient: OmopHubClient, port: number): Promise<Server>;
 //# sourceMappingURL=http.d.ts.map

package/dist/transports/http.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"http.d.ts","sourceRoot":"","sources":["../../src/transports/http.ts"],"names":[],"mappings":"AAAA,OAAO,EAAsC,KAAK,MAAM,EAAuB,MAAM,WAAW,CAAC;AACjG,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAkBzE;;;GAGG;AACH,wBAAsB,kBAAkB,CAAC,SAAS,EAAE,SAAS,EAAE,IAAI,EAAE,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,CAqD5F"}
+{"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

@@ -1,5 +1,7 @@
+import { randomUUID } from 'node:crypto';
 import { createServer } from 'node:http';
 import { StreamableHTTPServerTransport } from '@modelcontextprotocol/sdk/server/streamableHttp.js';
+import { isInitializeRequest } from '@modelcontextprotocol/sdk/types.js';
 import { handleHealthRequest } from '../health.js';
 import { logger } from '../utils/logger.js';
 const CORS_HEADERS = {
@@ -13,42 +15,150 @@ function setCorsHeaders(res) {
         res.setHeader(key, value);
     }
 }
+// Active sessions — each client gets its own transport + server
+const sessions = new Map();
+const MAX_BODY_SIZE = 1_048_576; // 1 MB
+const JSON_RPC_INTERNAL_ERROR = JSON.stringify({
+    jsonrpc: '2.0',
+    error: { code: -32603, message: 'Internal server error' },
+    id: null,
+});
 /**
- * Starts an HTTP server with Streamable HTTP MCP transport on /
+ * Starts an HTTP server with per-session MCP transports on /
  * and a health endpoint on /health.
  */
-export async function startHttpTransport(mcpServer, port) {
-    const transport = new StreamableHTTPServerTransport({
-        sessionIdGenerator: undefined,
-    });
-    await mcpServer.connect(transport);
+export async function startHttpTransport(serverFactory, defaultClient, port) {
     const httpServer = createServer(async (req, res) => {
         setCorsHeaders(res);
-        // Handle CORS preflight
         if (req.method === 'OPTIONS') {
             res.writeHead(204);
             res.end();
             return;
         }
-        // Health endpoint
         if (handleHealthRequest(req, res))
             return;
-        // MCP endpoint (/ for hosted, /mcp for self-hosted backward compat)
         const pathname = new URL(req.url ?? '/', 'http://localhost').pathname;
         if (pathname === '/' || pathname === '/mcp') {
+            const rawSessionId = req.headers['mcp-session-id'];
+            const sessionId = Array.isArray(rawSessionId) ? rawSessionId[0] : rawSessionId;
+            // GET (SSE stream) and DELETE (session close) carry no body — route directly
+            if (req.method === 'GET' || req.method === 'DELETE') {
+                if (sessionId && sessions.has(sessionId)) {
+                    const transport = sessions.get(sessionId);
+                    if (!transport)
+                        return;
+                    try {
+                        await transport.handleRequest(req, res);
+                    }
+                    catch (error) {
+                        logger.error('MCP transport error', { error: String(error), sessionId });
+                        if (!res.headersSent) {
+                            res.writeHead(500, { 'Content-Type': 'application/json' });
+                            res.end(JSON_RPC_INTERNAL_ERROR);
+                        }
+                    }
+                }
+                else {
+                    res.writeHead(400, { 'Content-Type': 'application/json' });
+                    res.end(JSON.stringify({
+                        jsonrpc: '2.0',
+                        error: { code: -32000, message: 'Bad Request: No valid session ID provided' },
+                        id: null,
+                    }));
+                }
+                return;
+            }
+            // POST — read body with size limit
+            const chunks = [];
+            let totalBytes = 0;
+            let aborted = false;
+            for await (const chunk of req) {
+                const buf = typeof chunk === 'string' ? Buffer.from(chunk) : chunk;
+                totalBytes += buf.length;
+                if (totalBytes > MAX_BODY_SIZE) {
+                    req.destroy();
+                    res.writeHead(413, { 'Content-Type': 'application/json' });
+                    res.end(JSON.stringify({
+                        jsonrpc: '2.0',
+                        error: { code: -32000, message: 'Payload too large' },
+                        id: null,
+                    }));
+                    aborted = true;
+                    break;
+                }
+                chunks.push(buf);
+            }
+            if (aborted)
+                return;
+            const body = Buffer.concat(chunks).toString();
+            let parsedBody;
             try {
-                await transport.handleRequest(req, res);
+                parsedBody = JSON.parse(body);
             }
-            catch (error) {
-                logger.error('MCP transport error', { error: String(error) });
-                if (!res.headersSent) {
-                    res.writeHead(500, { 'Content-Type': 'application/json' });
-                    res.end(JSON.stringify({ error: 'Internal server error' }));
+            catch {
+                res.writeHead(400, { 'Content-Type': 'application/json' });
+                res.end(JSON.stringify({
+                    jsonrpc: '2.0',
+                    error: { code: -32700, message: 'Parse error' },
+                    id: null,
+                }));
+                return;
+            }
+            // Existing session
+            if (sessionId && sessions.has(sessionId)) {
+                const transport = sessions.get(sessionId);
+                if (!transport)
+                    return;
+                try {
+                    await transport.handleRequest(req, res, parsedBody);
+                }
+                catch (error) {
+                    logger.error('MCP transport error', { error: String(error), sessionId });
+                    if (!res.headersSent) {
+                        res.writeHead(500, { 'Content-Type': 'application/json' });
+                        res.end(JSON_RPC_INTERNAL_ERROR);
+                    }
+                }
+                return;
+            }
+            // New session (initialize request)
+            if (!sessionId && isInitializeRequest(parsedBody)) {
+                const transport = new StreamableHTTPServerTransport({
+                    sessionIdGenerator: () => randomUUID(),
+                    onsessioninitialized: (id) => {
+                        sessions.set(id, transport);
+                        logger.info('MCP session created', { sessionId: id });
+                    },
+                });
+                transport.onclose = () => {
+                    if (transport.sessionId) {
+                        sessions.delete(transport.sessionId);
+                        logger.info('MCP session closed', { sessionId: transport.sessionId });
+                    }
+                };
+                const server = serverFactory(defaultClient);
+                await server.connect(transport);
+                try {
+                    await transport.handleRequest(req, res, parsedBody);
+                }
+                catch (error) {
+                    logger.error('MCP transport error (init)', { error: String(error) });
+                    if (!res.headersSent) {
+                        res.writeHead(500, { 'Content-Type': 'application/json' });
+                        res.end(JSON_RPC_INTERNAL_ERROR);
+                    }
                 }
+                return;
             }
+            // Invalid request — no session and not an initialize
+            res.writeHead(400, { 'Content-Type': 'application/json' });
+            res.end(JSON.stringify({
+                jsonrpc: '2.0',
+                error: { code: -32000, message: 'Bad Request: No valid session ID provided' },
+                id: null,
+            }));
             return;
         }
-        // Not found
         res.writeHead(404, { 'Content-Type': 'application/json' });
         res.end(JSON.stringify({ error: 'Not found' }));
     });

package/dist/transports/http.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,8 +1,8 @@
 {
   "name": "@omophub/omophub-mcp",
-  "version": "1.3.0",
+  "version": "1.4.0",
   "mcpName": "io.github.OMOPHub/omophub-mcp",
-  "description": "MCP server for OHDSI OMOP standardized medical vocabularies — search, lookup, map, and navigate concepts via AI agents",
+  "description": "MCP server for OHDSI OMOP standardized medical vocabularies - search, lookup, map, and navigate concepts via AI agents",
   "type": "module",
   "main": "dist/index.js",
   "bin": {