phenoml 0.0.3 → 0.0.6

package/reference.md

@@ -50,7 +50,7 @@ await client.agent.create({
 <dl>
 <dd>
 
-**request:** `phenoml.agent.AgentCreateRequest`
+**request:** `phenoml.AgentCreateRequest`
 
 </dd>
 </dl>
@@ -97,7 +97,10 @@ Retrieves a list of PhenoAgents belonging to the authenticated user
 <dd>
 
 ```typescript
-await client.agent.list();
+await client.agent.list({
+    is_active: true,
+    tags: "tags",
+});
 ```
 
 </dd>
@@ -223,7 +226,11 @@ Updates an existing agent's configuration
 <dd>
 
 ```typescript
-await client.agent.update("id");
+await client.agent.update("id", {
+    name: "name",
+    prompts: ["prompt_123", "prompt_456"],
+    is_active: true,
+});
 ```
 
 </dd>
@@ -247,7 +254,7 @@ await client.agent.update("id");
 <dl>
 <dd>
 
-**request:** `phenoml.agent.AgentUpdateRequest`
+**request:** `phenoml.AgentCreateRequest`
 
 </dd>
 </dl>
@@ -511,6 +518,9 @@ Retrieves a list of chat messages for a given chat session
 ```typescript
 await client.agent.getChatMessages({
     chat_session_id: "chat_session_id",
+    num_messages: 1,
+    role: "role",
+    order: "asc",
 });
 ```
 
@@ -1346,9 +1356,9 @@ await client.construe.cohort({
 </dl>
 </details>
 
-## Lang2Fhir
+## Fhir
 
-<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">create</a>({ ...params }) -> phenoml.FhirResource</code></summary>
+<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">search</a>(fhirProviderId, fhirPath, { ...params }) -> phenoml.FhirSearchResponse</code></summary>
 <dl>
 <dd>
 
@@ -1360,7 +1370,9 @@ await client.construe.cohort({
 <dl>
 <dd>
 
-Converts natural language text into a structured FHIR resource
+Retrieves FHIR resources from the specified provider. Supports both individual resource retrieval and search operations based on the FHIR path and query parameters.
+
+The request is proxied to the configured FHIR server with appropriate authentication headers.
 
 </dd>
 </dl>
@@ -1376,10 +1388,8 @@ Converts natural language text into a structured FHIR resource
 <dd>
 
 ```typescript
-await client.lang2Fhir.create({
-    version: "R4",
-    resource: "auto",
-    text: "Patient has severe asthma with acute exacerbation",
+await client.fhir.search("550e8400-e29b-41d4-a716-446655440000", "Patient", {
+    "X-Phenoml-On-Behalf-Of": "user@example.com",
 });
 ```
 
@@ -1396,72 +1406,35 @@ await client.lang2Fhir.create({
 <dl>
 <dd>
 
-**request:** `phenoml.lang2Fhir.CreateRequest`
-
-</dd>
-</dl>
-
-<dl>
-<dd>
+**fhirProviderId:** `string`
 
-**requestOptions:** `Lang2Fhir.RequestOptions`
+The ID of the FHIR provider to use. Can be either:
 
-</dd>
-</dl>
-</dd>
-</dl>
+- A UUID representing the provider ID
+- A provider name (legacy support - will just use the most recently updated provider with this name)
 
 </dd>
 </dl>
-</details>
-
-<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">search</a>({ ...params }) -> phenoml.SearchResponse</code></summary>
-<dl>
-<dd>
-
-#### 📝 Description
-
-<dl>
-<dd>
 
 <dl>
 <dd>
 
-Converts natural language text into FHIR search parameters
-
-</dd>
-</dl>
-</dd>
-</dl>
-
-#### 🔌 Usage
-
-<dl>
-<dd>
+**fhirPath:** `string`
 
-<dl>
-<dd>
+The FHIR resource path to operate on. This follows FHIR RESTful API conventions.
+Examples:
 
-```typescript
-await client.lang2Fhir.search({
-    text: "Appointments between March 2-9, 2025",
-});
-```
+- "Patient" (for resource type operations)
+- "Patient/123" (for specific resource operations)
+- "Patient/123/\_history" (for history operations)
 
-</dd>
-</dl>
 </dd>
 </dl>
 
-#### ⚙️ Parameters
-
-<dl>
-<dd>
-
 <dl>
 <dd>
 
-**request:** `phenoml.lang2Fhir.SearchRequest`
+**request:** `phenoml.fhir.FhirSearchRequest`
 
 </dd>
 </dl>
@@ -1469,7 +1442,7 @@ await client.lang2Fhir.search({
 <dl>
 <dd>
 
-**requestOptions:** `Lang2Fhir.RequestOptions`
+**requestOptions:** `Fhir.RequestOptions`
 
 </dd>
 </dl>
@@ -1480,7 +1453,7 @@ await client.lang2Fhir.search({
 </dl>
 </details>
 
-<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">uploadProfile</a>({ ...params }) -> phenoml.Lang2FhirUploadProfileResponse</code></summary>
+<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">create</a>(fhirProviderId, fhirPath, { ...params }) -> phenoml.FhirResource</code></summary>
 <dl>
 <dd>
 
@@ -1492,7 +1465,9 @@ await client.lang2Fhir.search({
 <dl>
 <dd>
 
-Upload a custom FHIR StructureDefinition profile for use with the lang2fhir service
+Creates a new FHIR resource on the specified provider. The request body should contain a valid FHIR resource in JSON format.
+
+The request is proxied to the configured FHIR server with appropriate authentication headers.
 
 </dd>
 </dl>
@@ -1508,10 +1483,19 @@ Upload a custom FHIR StructureDefinition profile for use with the lang2fhir serv
 <dd>
 
 ```typescript
-await client.lang2Fhir.uploadProfile({
-    version: "version",
-    resource: "custom-patient",
-    profile: "profile",
+await client.fhir.create("550e8400-e29b-41d4-a716-446655440000", "Patient", {
+    "X-Phenoml-On-Behalf-Of": "user@example.com",
+    body: {
+        resourceType: "Patient",
+        name: [
+            {
+                family: "Doe",
+                given: ["Jane"],
+            },
+        ],
+        gender: "female",
+        birthDate: "1990-01-01",
+    },
 });
 ```
 
@@ -1528,7 +1512,12 @@ await client.lang2Fhir.uploadProfile({
 <dl>
 <dd>
 
-**request:** `phenoml.lang2Fhir.ProfileUploadRequest`
+**fhirProviderId:** `string`
+
+The ID of the FHIR provider to use. Can be either:
+
+- A UUID representing the provider ID
+- A provider name (legacy support - will just use the most recently updated provider with this name)
 
 </dd>
 </dl>
@@ -1536,7 +1525,30 @@ await client.lang2Fhir.uploadProfile({
 <dl>
 <dd>
 
-**requestOptions:** `Lang2Fhir.RequestOptions`
+**fhirPath:** `string`
+
+The FHIR resource path to operate on. This follows FHIR RESTful API conventions.
+Examples:
+
+- "Patient" (for resource type operations)
+- "Patient/123" (for specific resource operations)
+- "Patient/123/\_history" (for history operations)
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.fhir.FhirCreateRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Fhir.RequestOptions`
 
 </dd>
 </dl>
@@ -1547,7 +1559,7 @@ await client.lang2Fhir.uploadProfile({
 </dl>
 </details>
 
-<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">document</a>({ ...params }) -> phenoml.FhirResource</code></summary>
+<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">upsert</a>(fhirProviderId, fhirPath, { ...params }) -> phenoml.FhirResource</code></summary>
 <dl>
 <dd>
 
@@ -1559,7 +1571,9 @@ await client.lang2Fhir.uploadProfile({
 <dl>
 <dd>
 
-Extracts text from a document (PDF or image) and converts it into a structured FHIR resource
+Creates or updates a FHIR resource on the specified provider. If the resource exists, it will be updated; otherwise, it will be created.
+
+The request is proxied to the configured FHIR server with appropriate authentication headers.
 
 </dd>
 </dl>
@@ -1575,11 +1589,20 @@ Extracts text from a document (PDF or image) and converts it into a structured F
 <dd>
 
 ```typescript
-await client.lang2Fhir.document({
-    version: "R4",
-    resource: "questionnaire",
-    content: "content",
-    fileType: "application/pdf",
+await client.fhir.upsert("550e8400-e29b-41d4-a716-446655440000", "Patient", {
+    "X-Phenoml-On-Behalf-Of": "user@example.com",
+    body: {
+        resourceType: "Patient",
+        id: "123",
+        name: [
+            {
+                family: "Doe",
+                given: ["John", "Updated"],
+            },
+        ],
+        gender: "male",
+        birthDate: "1985-05-15",
+    },
 });
 ```
 
@@ -1596,7 +1619,12 @@ await client.lang2Fhir.document({
 <dl>
 <dd>
 
-**request:** `phenoml.lang2Fhir.DocumentRequest`
+**fhirProviderId:** `string`
+
+The ID of the FHIR provider to use. Can be either:
+
+- A UUID representing the provider ID
+- A provider name (legacy support - will just use the most recently updated provider with this name)
 
 </dd>
 </dl>
@@ -1604,7 +1632,30 @@ await client.lang2Fhir.document({
 <dl>
 <dd>
 
-**requestOptions:** `Lang2Fhir.RequestOptions`
+**fhirPath:** `string`
+
+The FHIR resource path to operate on. This follows FHIR RESTful API conventions.
+Examples:
+
+- "Patient" (for resource type operations)
+- "Patient/123" (for specific resource operations)
+- "Patient/123/\_history" (for history operations)
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.fhir.FhirUpsertRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Fhir.RequestOptions`
 
 </dd>
 </dl>
@@ -1615,9 +1666,7 @@ await client.lang2Fhir.document({
 </dl>
 </details>
 
-## Tools
-
-<details><summary><code>client.tools.<a href="/src/api/resources/tools/client/Client.ts">createFhirResource</a>({ ...params }) -> phenoml.Lang2FhirAndCreateResponse</code></summary>
+<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">delete</a>(fhirProviderId, fhirPath, { ...params }) -> Record<string, unknown></code></summary>
 <dl>
 <dd>
 
@@ -1629,7 +1678,9 @@ await client.lang2Fhir.document({
 <dl>
 <dd>
 
-Converts natural language to FHIR resource and optionally stores it in a FHIR server
+Deletes a FHIR resource from the specified provider.
+
+The request is proxied to the configured FHIR server with appropriate authentication headers.
 
 </dd>
 </dl>
@@ -1645,9 +1696,8 @@ Converts natural language to FHIR resource and optionally stores it in a FHIR se
 <dd>
 
 ```typescript
-await client.tools.createFhirResource({
-    resource: "auto",
-    text: "Patient John Doe has severe asthma with acute exacerbation",
+await client.fhir.delete("550e8400-e29b-41d4-a716-446655440000", "Patient", {
+    "X-Phenoml-On-Behalf-Of": "user@example.com",
 });
 ```
 
@@ -1664,7 +1714,12 @@ await client.tools.createFhirResource({
 <dl>
 <dd>
 
-**request:** `phenoml.tools.Lang2FhirAndCreateRequest`
+**fhirProviderId:** `string`
+
+The ID of the FHIR provider to use. Can be either:
+
+- A UUID representing the provider ID
+- A provider name (legacy support - will just use the most recently updated provider with this name)
 
 </dd>
 </dl>
@@ -1672,7 +1727,30 @@ await client.tools.createFhirResource({
 <dl>
 <dd>
 
-**requestOptions:** `Tools.RequestOptions`
+**fhirPath:** `string`
+
+The FHIR resource path to operate on. This follows FHIR RESTful API conventions.
+Examples:
+
+- "Patient" (for resource type operations)
+- "Patient/123" (for specific resource operations)
+- "Patient/123/\_history" (for history operations)
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.fhir.FhirDeleteRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Fhir.RequestOptions`
 
 </dd>
 </dl>
@@ -1683,7 +1761,7 @@ await client.tools.createFhirResource({
 </dl>
 </details>
 
-<details><summary><code>client.tools.<a href="/src/api/resources/tools/client/Client.ts">searchFhirResources</a>({ ...params }) -> phenoml.Lang2FhirAndSearchResponse</code></summary>
+<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">patch</a>(fhirProviderId, fhirPath, { ...params }) -> phenoml.FhirResource</code></summary>
 <dl>
 <dd>
 
@@ -1695,7 +1773,15 @@ await client.tools.createFhirResource({
 <dl>
 <dd>
 
-Converts natural language to FHIR search parameters and executes search in FHIR server
+Partially updates a FHIR resource on the specified provider using JSON Patch operations as defined in RFC 6902.
+
+The request body should contain an array of JSON Patch operations. Each operation specifies:
+
+- `op`: The operation type (add, remove, replace, move, copy, test)
+- `path`: JSON Pointer to the target location in the resource
+- `value`: The value to use (required for add, replace, and test operations)
+
+The request is proxied to the configured FHIR server with appropriate authentication headers.
 
 </dd>
 </dl>
@@ -1711,8 +1797,15 @@ Converts natural language to FHIR search parameters and executes search in FHIR
 <dd>
 
 ```typescript
-await client.tools.searchFhirResources({
-    text: "Find all appointments for patient John Doe next week",
+await client.fhir.patch("550e8400-e29b-41d4-a716-446655440000", "Patient", {
+    "X-Phenoml-On-Behalf-Of": "user@example.com",
+    body: [
+        {
+            op: "replace",
+            path: "/name/0/family",
+            value: "NewFamilyName",
+        },
+    ],
 });
 ```
 
@@ -1729,7 +1822,12 @@ await client.tools.searchFhirResources({
 <dl>
 <dd>
 
-**request:** `phenoml.tools.Lang2FhirAndSearchRequest`
+**fhirProviderId:** `string`
+
+The ID of the FHIR provider to use. Can be either:
+
+- A UUID representing the provider ID
+- A provider name (legacy support - will just use the most recently updated provider with this name)
 
 </dd>
 </dl>
@@ -1737,7 +1835,30 @@ await client.tools.searchFhirResources({
 <dl>
 <dd>
 
-**requestOptions:** `Tools.RequestOptions`
+**fhirPath:** `string`
+
+The FHIR resource path to operate on. This follows FHIR RESTful API conventions.
+Examples:
+
+- "Patient" (for resource type operations)
+- "Patient/123" (for specific resource operations)
+- "Patient/123/\_history" (for history operations)
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.fhir.FhirPatchRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Fhir.RequestOptions`
 
 </dd>
 </dl>
@@ -1748,7 +1869,7 @@ await client.tools.searchFhirResources({
 </dl>
 </details>
 
-<details><summary><code>client.tools.<a href="/src/api/resources/tools/client/Client.ts">analyzeCohort</a>({ ...params }) -> phenoml.CohortResponse</code></summary>
+<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">executeBundle</a>(fhirProviderId, { ...params }) -> phenoml.FhirBundle</code></summary>
 <dl>
 <dd>
 
@@ -1760,7 +1881,11 @@ await client.tools.searchFhirResources({
 <dl>
 <dd>
 
-Uses LLM to extract search concepts from natural language and builds patient cohorts with inclusion/exclusion criteria
+Executes a FHIR Bundle transaction or batch operation on the specified provider. This allows multiple FHIR resources to be processed in a single request.
+
+The request body should contain a valid FHIR Bundle resource with transaction or batch type.
+
+The request is proxied to the configured FHIR server with appropriate authentication headers.
 
 </dd>
 </dl>
@@ -1776,9 +1901,41 @@ Uses LLM to extract search concepts from natural language and builds patient coh
 <dd>
 
 ```typescript
-await client.tools.analyzeCohort({
-    text: "female patients over 20 with diabetes but not hypertension",
-    provider: "medplum",
+await client.fhir.executeBundle("550e8400-e29b-41d4-a716-446655440000", {
+    "X-Phenoml-On-Behalf-Of": "user@example.com",
+    body: {
+        resourceType: "Bundle",
+        entry: [
+            {
+                resource: {
+                    resourceType: "Patient",
+                    name: [
+                        {
+                            family: "Doe",
+                            given: ["John"],
+                        },
+                    ],
+                },
+                request: {
+                    method: "POST",
+                    url: "Patient",
+                },
+            },
+            {
+                resource: {
+                    resourceType: "Observation",
+                    status: "final",
+                    subject: {
+                        reference: "Patient/123",
+                    },
+                },
+                request: {
+                    method: "POST",
+                    url: "Observation",
+                },
+            },
+        ],
+    },
 });
 ```
 
@@ -1795,7 +1952,12 @@ await client.tools.analyzeCohort({
 <dl>
 <dd>
 
-**request:** `phenoml.tools.CohortRequest`
+**fhirProviderId:** `string`
+
+The ID of the FHIR provider to use. Can be either:
+
+- A UUID representing the provider ID
+- A provider name (legacy support - will just use the most recently updated provider with this name)
 
 </dd>
 </dl>
@@ -1803,7 +1965,15 @@ await client.tools.analyzeCohort({
 <dl>
 <dd>
 
-**requestOptions:** `Tools.RequestOptions`
+**request:** `phenoml.fhir.FhirExecuteBundleRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Fhir.RequestOptions`
 
 </dd>
 </dl>
@@ -1814,9 +1984,9 @@ await client.tools.analyzeCohort({
 </dl>
 </details>
 
-## Tools McpServer
+## FhirProvider
 
-<details><summary><code>client.tools.mcpServer.<a href="/src/api/resources/tools/resources/mcpServer/client/Client.ts">create</a>({ ...params }) -> phenoml.McpServerResponse</code></summary>
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">create</a>({ ...params }) -> phenoml.FhirProviderResponse</code></summary>
 <dl>
 <dd>
 
@@ -1828,7 +1998,7 @@ await client.tools.analyzeCohort({
 <dl>
 <dd>
 
-Creates a new MCP server
+Creates a new FHIR provider configuration with authentication credentials
 
 </dd>
 </dl>
@@ -1844,9 +2014,11 @@ Creates a new MCP server
 <dd>
 
 ```typescript
-await client.tools.mcpServer.create({
-    name: "My MCP Server",
-    mcp_server_url: "https://mcp.example.com",
+await client.fhirProvider.create({
+    name: "Epic Sandbox",
+    provider: "athenahealth",
+    auth_method: "client_secret",
+    base_url: "https://fhir.epic.com/interconnect-fhir-oauth/api/FHIR/R4",
 });
 ```
 
@@ -1863,7 +2035,7 @@ await client.tools.mcpServer.create({
 <dl>
 <dd>
 
-**request:** `phenoml.tools.McpServerCreateRequest`
+**request:** `phenoml.fhirProvider.FhirProviderCreateRequest`
 
 </dd>
 </dl>
@@ -1871,7 +2043,7 @@ await client.tools.mcpServer.create({
 <dl>
 <dd>
 
-**requestOptions:** `McpServer.RequestOptions`
+**requestOptions:** `FhirProvider.RequestOptions`
 
 </dd>
 </dl>
@@ -1882,7 +2054,7 @@ await client.tools.mcpServer.create({
 </dl>
 </details>
 
-<details><summary><code>client.tools.mcpServer.<a href="/src/api/resources/tools/resources/mcpServer/client/Client.ts">list</a>() -> phenoml.McpServerResponse</code></summary>
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">list</a>() -> phenoml.FhirProviderListResponse</code></summary>
 <dl>
 <dd>
 
@@ -1894,7 +2066,7 @@ await client.tools.mcpServer.create({
 <dl>
 <dd>
 
-Lists all MCP servers for a specific user
+Retrieves a list of all active FHIR providers for the authenticated user
 
 </dd>
 </dl>
@@ -1910,7 +2082,7 @@ Lists all MCP servers for a specific user
 <dd>
 
 ```typescript
-await client.tools.mcpServer.list();
+await client.fhirProvider.list();
 ```
 
 </dd>
@@ -1926,7 +2098,7 @@ await client.tools.mcpServer.list();
 <dl>
 <dd>
 
-**requestOptions:** `McpServer.RequestOptions`
+**requestOptions:** `FhirProvider.RequestOptions`
 
 </dd>
 </dl>
@@ -1937,7 +2109,7 @@ await client.tools.mcpServer.list();
 </dl>
 </details>
 
-<details><summary><code>client.tools.mcpServer.<a href="/src/api/resources/tools/resources/mcpServer/client/Client.ts">get</a>(mcpServerId) -> phenoml.McpServerResponse</code></summary>
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">get</a>(fhirProviderId) -> phenoml.FhirProviderResponse</code></summary>
 <dl>
 <dd>
 
@@ -1949,7 +2121,7 @@ await client.tools.mcpServer.list();
 <dl>
 <dd>
 
-Gets a MCP server by ID
+Retrieves a specific FHIR provider configuration by its ID
 
 </dd>
 </dl>
@@ -1965,7 +2137,7 @@ Gets a MCP server by ID
 <dd>
 
 ```typescript
-await client.tools.mcpServer.get("mcp_server_id");
+await client.fhirProvider.get("fhir_provider_id");
 ```
 
 </dd>
@@ -1981,7 +2153,7 @@ await client.tools.mcpServer.get("mcp_server_id");
 <dl>
 <dd>
 
-**mcpServerId:** `string` — ID of the MCP server to retrieve
+**fhirProviderId:** `string` — ID of the FHIR provider to retrieve
 
 </dd>
 </dl>
@@ -1989,7 +2161,7 @@ await client.tools.mcpServer.get("mcp_server_id");
 <dl>
 <dd>
 
-**requestOptions:** `McpServer.RequestOptions`
+**requestOptions:** `FhirProvider.RequestOptions`
 
 </dd>
 </dl>
@@ -2000,7 +2172,7 @@ await client.tools.mcpServer.get("mcp_server_id");
 </dl>
 </details>
 
-<details><summary><code>client.tools.mcpServer.<a href="/src/api/resources/tools/resources/mcpServer/client/Client.ts">delete</a>(mcpServerId) -> phenoml.McpServerResponse</code></summary>
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">delete</a>(fhirProviderId) -> phenoml.FhirProviderDeleteResponse</code></summary>
 <dl>
 <dd>
 
@@ -2012,7 +2184,7 @@ await client.tools.mcpServer.get("mcp_server_id");
 <dl>
 <dd>
 
-Deletes a MCP server by ID
+Soft deletes a FHIR provider by setting is_active to false
 
 </dd>
 </dl>
@@ -2028,7 +2200,7 @@ Deletes a MCP server by ID
 <dd>
 
 ```typescript
-await client.tools.mcpServer.delete("mcp_server_id");
+await client.fhirProvider.delete("fhir_provider_id");
 ```
 
 </dd>
@@ -2044,7 +2216,7 @@ await client.tools.mcpServer.delete("mcp_server_id");
 <dl>
 <dd>
 
-**mcpServerId:** `string` — ID of the MCP server to delete
+**fhirProviderId:** `string` — ID of the FHIR provider to delete
 
 </dd>
 </dl>
@@ -2052,7 +2224,7 @@ await client.tools.mcpServer.delete("mcp_server_id");
 <dl>
 <dd>
 
-**requestOptions:** `McpServer.RequestOptions`
+**requestOptions:** `FhirProvider.RequestOptions`
 
 </dd>
 </dl>
@@ -2063,9 +2235,7 @@ await client.tools.mcpServer.delete("mcp_server_id");
 </dl>
 </details>
 
-## Tools McpServer Tools
-
-<details><summary><code>client.tools.mcpServer.tools.<a href="/src/api/resources/tools/resources/mcpServer/resources/tools/client/Client.ts">list</a>(mcpServerId) -> phenoml.McpServerToolResponse</code></summary>
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">addAuthConfig</a>(fhirProviderId, { ...params }) -> phenoml.FhirProviderResponse</code></summary>
 <dl>
 <dd>
 
@@ -2077,7 +2247,7 @@ await client.tools.mcpServer.delete("mcp_server_id");
 <dl>
 <dd>
 
-Lists all MCP server tools for a specific MCP server
+Adds a new authentication configuration to an existing FHIR provider. This enables key rotation and multiple auth configurations per provider.
 
 </dd>
 </dl>
@@ -2093,7 +2263,9 @@ Lists all MCP server tools for a specific MCP server
 <dd>
 
 ```typescript
-await client.tools.mcpServer.tools.list("mcp_server_id");
+await client.fhirProvider.addAuthConfig("1716d214-de93-43a4-aa6b-a878d864e2ad", {
+    auth_method: "client_secret",
+});
 ```
 
 </dd>
@@ -2109,7 +2281,7 @@ await client.tools.mcpServer.tools.list("mcp_server_id");
 <dl>
 <dd>
 
-**mcpServerId:** `string` — ID of the MCP server to list tools for
+**fhirProviderId:** `string` — ID of the FHIR provider to add auth config to
 
 </dd>
 </dl>
@@ -2117,7 +2289,15 @@ await client.tools.mcpServer.tools.list("mcp_server_id");
 <dl>
 <dd>
 
-**requestOptions:** `Tools.RequestOptions`
+**request:** `phenoml.fhirProvider.FhirProviderAddAuthConfigRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `FhirProvider.RequestOptions`
 
 </dd>
 </dl>
@@ -2128,7 +2308,7 @@ await client.tools.mcpServer.tools.list("mcp_server_id");
 </dl>
 </details>
 
-<details><summary><code>client.tools.mcpServer.tools.<a href="/src/api/resources/tools/resources/mcpServer/resources/tools/client/Client.ts">get</a>(mcpServerToolId) -> phenoml.McpServerToolResponse</code></summary>
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">setActiveAuthConfig</a>(fhirProviderId, { ...params }) -> phenoml.FhirProviderSetActiveAuthConfigResponse</code></summary>
 <dl>
 <dd>
 
@@ -2140,7 +2320,7 @@ await client.tools.mcpServer.tools.list("mcp_server_id");
 <dl>
 <dd>
 
-Gets a MCP server tool by ID
+Sets which authentication configuration should be active for a FHIR provider. Only one auth config can be active at a time.
 
 </dd>
 </dl>
@@ -2156,7 +2336,9 @@ Gets a MCP server tool by ID
 <dd>
 
 ```typescript
-await client.tools.mcpServer.tools.get("mcp_server_tool_id");
+await client.fhirProvider.setActiveAuthConfig("1716d214-de93-43a4-aa6b-a878d864e2ad", {
+    auth_config_id: "auth-config-123",
+});
 ```
 
 </dd>
@@ -2172,7 +2354,7 @@ await client.tools.mcpServer.tools.get("mcp_server_tool_id");
 <dl>
 <dd>
 
-**mcpServerToolId:** `string` — ID of the MCP server tool to retrieve
+**fhirProviderId:** `string` — ID of the FHIR provider
 
 </dd>
 </dl>
@@ -2180,7 +2362,15 @@ await client.tools.mcpServer.tools.get("mcp_server_tool_id");
 <dl>
 <dd>
 
-**requestOptions:** `Tools.RequestOptions`
+**request:** `phenoml.fhirProvider.FhirProviderSetActiveAuthConfigRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `FhirProvider.RequestOptions`
 
 </dd>
 </dl>
@@ -2191,7 +2381,7 @@ await client.tools.mcpServer.tools.get("mcp_server_tool_id");
 </dl>
 </details>
 
-<details><summary><code>client.tools.mcpServer.tools.<a href="/src/api/resources/tools/resources/mcpServer/resources/tools/client/Client.ts">delete</a>(mcpServerToolId) -> phenoml.McpServerToolResponse</code></summary>
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">removeAuthConfig</a>(fhirProviderId, { ...params }) -> phenoml.FhirProviderRemoveAuthConfigResponse</code></summary>
 <dl>
 <dd>
 
@@ -2203,7 +2393,7 @@ await client.tools.mcpServer.tools.get("mcp_server_tool_id");
 <dl>
 <dd>
 
-Deletes a MCP server tool by ID
+Removes an authentication configuration from a FHIR provider. Cannot remove the currently active auth configuration.
 
 </dd>
 </dl>
@@ -2219,7 +2409,9 @@ Deletes a MCP server tool by ID
 <dd>
 
 ```typescript
-await client.tools.mcpServer.tools.delete("mcp_server_tool_id");
+await client.fhirProvider.removeAuthConfig("1716d214-de93-43a4-aa6b-a878d864e2ad", {
+    auth_config_id: "auth-config-123",
+});
 ```
 
 </dd>
@@ -2235,7 +2427,7 @@ await client.tools.mcpServer.tools.delete("mcp_server_tool_id");
 <dl>
 <dd>
 
-**mcpServerToolId:** `string` — ID of the MCP server tool to delete
+**fhirProviderId:** `string` — ID of the FHIR provider
 
 </dd>
 </dl>
@@ -2243,7 +2435,15 @@ await client.tools.mcpServer.tools.delete("mcp_server_tool_id");
 <dl>
 <dd>
 
-**requestOptions:** `Tools.RequestOptions`
+**request:** `phenoml.fhirProvider.FhirProviderRemoveAuthConfigRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `FhirProvider.RequestOptions`
 
 </dd>
 </dl>
@@ -2254,7 +2454,9 @@ await client.tools.mcpServer.tools.delete("mcp_server_tool_id");
 </dl>
 </details>
 
-<details><summary><code>client.tools.mcpServer.tools.<a href="/src/api/resources/tools/resources/mcpServer/resources/tools/client/Client.ts">call</a>(mcpServerToolId, { ...params }) -> phenoml.McpServerToolCallResponse</code></summary>
+## Lang2Fhir
+
+<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">create</a>({ ...params }) -> phenoml.FhirResource</code></summary>
 <dl>
 <dd>
 
@@ -2266,7 +2468,7 @@ await client.tools.mcpServer.tools.delete("mcp_server_tool_id");
 <dl>
 <dd>
 
-Calls a MCP server tool
+Converts natural language text into a structured FHIR resource
 
 </dd>
 </dl>
@@ -2282,10 +2484,10 @@ Calls a MCP server tool
 <dd>
 
 ```typescript
-await client.tools.mcpServer.tools.call("mcp_server_tool_id", {
-    arguments: {
-        title: "PhenoML Agent API",
-    },
+await client.lang2Fhir.create({
+    version: "R4",
+    resource: "auto",
+    text: "Patient has severe asthma with acute exacerbation",
 });
 ```
 
@@ -2302,7 +2504,7 @@ await client.tools.mcpServer.tools.call("mcp_server_tool_id", {
 <dl>
 <dd>
 
-**mcpServerToolId:** `string` — ID of the MCP server tool to call
+**request:** `phenoml.lang2Fhir.CreateRequest`
 
 </dd>
 </dl>
@@ -2310,7 +2512,1842 @@ await client.tools.mcpServer.tools.call("mcp_server_tool_id", {
 <dl>
 <dd>
 
-**request:** `phenoml.tools.mcpServer.McpServerToolCallRequest`
+**requestOptions:** `Lang2Fhir.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">search</a>({ ...params }) -> phenoml.SearchResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Converts natural language text into FHIR search parameters
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.lang2Fhir.search({
+    text: "Appointments between March 2-9, 2025",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.lang2Fhir.SearchRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Lang2Fhir.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">uploadProfile</a>({ ...params }) -> phenoml.Lang2FhirUploadProfileResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Upload a custom FHIR StructureDefinition profile for use with the lang2fhir service
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.lang2Fhir.uploadProfile({
+    version: "version",
+    resource: "custom-patient",
+    profile: "profile",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.lang2Fhir.ProfileUploadRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Lang2Fhir.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">document</a>({ ...params }) -> phenoml.FhirResource</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Extracts text from a document (PDF or image) and converts it into a structured FHIR resource
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.lang2Fhir.document({
+    version: "R4",
+    resource: "questionnaire",
+    content: "content",
+    fileType: "application/pdf",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.lang2Fhir.DocumentRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Lang2Fhir.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+## Tools
+
+<details><summary><code>client.tools.<a href="/src/api/resources/tools/client/Client.ts">createFhirResource</a>({ ...params }) -> phenoml.Lang2FhirAndCreateResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Converts natural language to FHIR resource and optionally stores it in a FHIR server
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.tools.createFhirResource({
+    resource: "auto",
+    text: "Patient John Doe has severe asthma with acute exacerbation",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.tools.Lang2FhirAndCreateRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Tools.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.tools.<a href="/src/api/resources/tools/client/Client.ts">searchFhirResources</a>({ ...params }) -> phenoml.Lang2FhirAndSearchResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Converts natural language to FHIR search parameters and executes search in FHIR server
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.tools.searchFhirResources({
+    text: "Find all appointments for patient John Doe next week",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.tools.Lang2FhirAndSearchRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Tools.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.tools.<a href="/src/api/resources/tools/client/Client.ts">analyzeCohort</a>({ ...params }) -> phenoml.CohortResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Uses LLM to extract search concepts from natural language and builds patient cohorts with inclusion/exclusion criteria
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.tools.analyzeCohort({
+    text: "female patients over 20 with diabetes but not hypertension",
+    provider: "550e8400-e29b-41d4-a716-446655440000",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.tools.CohortRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Tools.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+## Tools McpServer
+
+<details><summary><code>client.tools.mcpServer.<a href="/src/api/resources/tools/resources/mcpServer/client/Client.ts">create</a>({ ...params }) -> phenoml.McpServerResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Creates a new MCP server
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.tools.mcpServer.create({
+    name: "My MCP Server",
+    mcp_server_url: "https://mcp.example.com",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.tools.McpServerCreateRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `McpServer.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.tools.mcpServer.<a href="/src/api/resources/tools/resources/mcpServer/client/Client.ts">list</a>() -> phenoml.McpServerResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Lists all MCP servers for a specific user
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.tools.mcpServer.list();
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**requestOptions:** `McpServer.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.tools.mcpServer.<a href="/src/api/resources/tools/resources/mcpServer/client/Client.ts">get</a>(mcpServerId) -> phenoml.McpServerResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Gets a MCP server by ID
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.tools.mcpServer.get("mcp_server_id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**mcpServerId:** `string` — ID of the MCP server to retrieve
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `McpServer.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.tools.mcpServer.<a href="/src/api/resources/tools/resources/mcpServer/client/Client.ts">delete</a>(mcpServerId) -> phenoml.McpServerResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Deletes a MCP server by ID
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.tools.mcpServer.delete("mcp_server_id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**mcpServerId:** `string` — ID of the MCP server to delete
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `McpServer.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+## Tools McpServer Tools
+
+<details><summary><code>client.tools.mcpServer.tools.<a href="/src/api/resources/tools/resources/mcpServer/resources/tools/client/Client.ts">list</a>(mcpServerId) -> phenoml.McpServerToolResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Lists all MCP server tools for a specific MCP server
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.tools.mcpServer.tools.list("mcp_server_id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**mcpServerId:** `string` — ID of the MCP server to list tools for
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Tools.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.tools.mcpServer.tools.<a href="/src/api/resources/tools/resources/mcpServer/resources/tools/client/Client.ts">get</a>(mcpServerToolId) -> phenoml.McpServerToolResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Gets a MCP server tool by ID
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.tools.mcpServer.tools.get("mcp_server_tool_id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**mcpServerToolId:** `string` — ID of the MCP server tool to retrieve
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Tools.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.tools.mcpServer.tools.<a href="/src/api/resources/tools/resources/mcpServer/resources/tools/client/Client.ts">delete</a>(mcpServerToolId) -> phenoml.McpServerToolResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Deletes a MCP server tool by ID
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.tools.mcpServer.tools.delete("mcp_server_tool_id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**mcpServerToolId:** `string` — ID of the MCP server tool to delete
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Tools.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.tools.mcpServer.tools.<a href="/src/api/resources/tools/resources/mcpServer/resources/tools/client/Client.ts">call</a>(mcpServerToolId, { ...params }) -> phenoml.McpServerToolCallResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Calls a MCP server tool
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.tools.mcpServer.tools.call("mcp_server_tool_id", {
+    arguments: {
+        title: "PhenoML Agent API",
+    },
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**mcpServerToolId:** `string` — ID of the MCP server tool to call
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.tools.mcpServer.McpServerToolCallRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Tools.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+## Workflows
+
+<details><summary><code>client.workflows.<a href="/src/api/resources/workflows/client/Client.ts">createFhirResource</a>() -> void</code></summary>
+<dl>
+<dd>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.createFhirResource();
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**requestOptions:** `Workflows.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.workflows.<a href="/src/api/resources/workflows/client/Client.ts">searchFhirResources</a>() -> void</code></summary>
+<dl>
+<dd>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.searchFhirResources();
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**requestOptions:** `Workflows.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.workflows.<a href="/src/api/resources/workflows/client/Client.ts">analyzeCohort</a>() -> void</code></summary>
+<dl>
+<dd>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.analyzeCohort();
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**requestOptions:** `Workflows.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+## Workflows Workflows
+
+<details><summary><code>client.workflows.workflows.<a href="/src/api/resources/workflows/resources/workflows/client/Client.ts">list</a>({ ...params }) -> phenoml.ListWorkflowsResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Retrieves all workflow definitions for the authenticated user
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.workflows.list({
+    verbose: true,
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.workflows.WorkflowsListRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Workflows.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.workflows.workflows.<a href="/src/api/resources/workflows/resources/workflows/client/Client.ts">create</a>({ ...params }) -> phenoml.CreateWorkflowResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Creates a new workflow definition with graph generation from workflow instructions
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.workflows.create({
+    verbose: true,
+    name: "Patient Data Mapping Workflow",
+    workflow_instructions: "Given diagnosis data, find the patient and create condition record",
+    sample_data: {
+        patient_last_name: "Rippin",
+        patient_first_name: "Clay",
+        diagnosis_code: "I10",
+    },
+    fhir_provider_id: "550e8400-e29b-41d4-a716-446655440000",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.workflows.CreateWorkflowRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Workflows.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.workflows.workflows.<a href="/src/api/resources/workflows/resources/workflows/client/Client.ts">get</a>(id, { ...params }) -> phenoml.WorkflowsGetResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Retrieves a workflow definition by its ID
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.workflows.get("id", {
+    verbose: true,
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**id:** `string` — ID of the workflow to retrieve
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.workflows.WorkflowsGetRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Workflows.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.workflows.workflows.<a href="/src/api/resources/workflows/resources/workflows/client/Client.ts">update</a>(id, { ...params }) -> phenoml.WorkflowsUpdateResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Updates an existing workflow definition
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.workflows.update("id", {
+    verbose: true,
+    name: "Updated Patient Data Mapping Workflow",
+    workflow_instructions: "Given diagnosis data, find the patient and create condition record",
+    sample_data: {
+        patient_last_name: "Smith",
+        patient_first_name: "John",
+        diagnosis_code: "E11",
+    },
+    fhir_provider_id: "550e8400-e29b-41d4-a716-446655440000",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**id:** `string` — ID of the workflow to update
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.workflows.UpdateWorkflowRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Workflows.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.workflows.workflows.<a href="/src/api/resources/workflows/resources/workflows/client/Client.ts">delete</a>(id) -> phenoml.WorkflowsDeleteResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Deletes a workflow definition by its ID
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.workflows.delete("id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**id:** `string` — ID of the workflow to delete
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Workflows.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.workflows.workflows.<a href="/src/api/resources/workflows/resources/workflows/client/Client.ts">execute</a>(id, { ...params }) -> phenoml.ExecuteWorkflowResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Executes a workflow with provided input data and returns results
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.workflows.execute("id", {
+    input_data: {
+        patient_last_name: "Johnson",
+        patient_first_name: "Mary",
+        diagnosis_code: "M79.3",
+        encounter_date: "2024-01-15",
+    },
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**id:** `string` — ID of the workflow to execute
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.workflows.ExecuteWorkflowRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Workflows.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+## Workflows McpServer
+
+<details><summary><code>client.workflows.mcpServer.<a href="/src/api/resources/workflows/resources/mcpServer/client/Client.ts">create</a>() -> void</code></summary>
+<dl>
+<dd>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.mcpServer.create();
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**requestOptions:** `McpServer.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.workflows.mcpServer.<a href="/src/api/resources/workflows/resources/mcpServer/client/Client.ts">list</a>() -> void</code></summary>
+<dl>
+<dd>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.mcpServer.list();
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**requestOptions:** `McpServer.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.workflows.mcpServer.<a href="/src/api/resources/workflows/resources/mcpServer/client/Client.ts">get</a>(mcpServerId) -> void</code></summary>
+<dl>
+<dd>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.mcpServer.get("mcp_server_id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**mcpServerId:** `string`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `McpServer.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.workflows.mcpServer.<a href="/src/api/resources/workflows/resources/mcpServer/client/Client.ts">delete</a>(mcpServerId) -> void</code></summary>
+<dl>
+<dd>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.mcpServer.delete("mcp_server_id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**mcpServerId:** `string`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `McpServer.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+## Workflows McpServer Tools
+
+<details><summary><code>client.workflows.mcpServer.tools.<a href="/src/api/resources/workflows/resources/mcpServer/resources/tools/client/Client.ts">list</a>(mcpServerId) -> void</code></summary>
+<dl>
+<dd>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.mcpServer.tools.list("mcp_server_id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**mcpServerId:** `string`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Tools.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.workflows.mcpServer.tools.<a href="/src/api/resources/workflows/resources/mcpServer/resources/tools/client/Client.ts">get</a>(mcpServerToolId) -> void</code></summary>
+<dl>
+<dd>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.mcpServer.tools.get("mcp_server_tool_id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**mcpServerToolId:** `string`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Tools.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.workflows.mcpServer.tools.<a href="/src/api/resources/workflows/resources/mcpServer/resources/tools/client/Client.ts">delete</a>(mcpServerToolId) -> void</code></summary>
+<dl>
+<dd>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.mcpServer.tools.delete("mcp_server_tool_id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**mcpServerToolId:** `string`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Tools.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.workflows.mcpServer.tools.<a href="/src/api/resources/workflows/resources/mcpServer/resources/tools/client/Client.ts">call</a>(mcpServerToolId) -> void</code></summary>
+<dl>
+<dd>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.workflows.mcpServer.tools.call("mcp_server_tool_id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**mcpServerToolId:** `string`
 
 </dd>
 </dl>