phenoml 0.0.2

package/reference.md

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+# Reference
+
+## Agent
+
+<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">create</a>({ ...params }) -> phenoml.AgentResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Creates a new PhenoAgent with specified configuration
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.agent.create({
+    name: "name",
+    prompts: ["prompt_123", "prompt_456"],
+    is_active: true,
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.agent.AgentCreateRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Agent.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">list</a>({ ...params }) -> phenoml.AgentListResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Retrieves a list of PhenoAgents belonging to the authenticated user
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.agent.list();
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.agent.AgentListRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Agent.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">get</a>(id) -> phenoml.AgentResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Retrieves a specific agent by its ID
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.agent.get("id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**id:** `string` — Agent ID
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Agent.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">update</a>(id, { ...params }) -> phenoml.AgentResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Updates an existing agent's configuration
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.agent.update("id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**id:** `string` — Agent ID
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.agent.AgentUpdateRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Agent.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">delete</a>(id) -> phenoml.AgentDeleteResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Deletes an existing agent
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.agent.delete("id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**id:** `string` — Agent ID
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Agent.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">patch</a>(id, { ...params }) -> phenoml.AgentResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Patches an existing agent's configuration
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.agent.patch("id", [
+    {
+        op: "replace",
+        path: "/name",
+        value: "Updated Agent Name",
+    },
+    {
+        op: "add",
+        path: "/tags/-",
+        value: "new-tag",
+    },
+    {
+        op: "remove",
+        path: "/description",
+    },
+]);
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**id:** `string` — Agent ID
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.JsonPatch`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Agent.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">chat</a>({ ...params }) -> phenoml.AgentChatResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Send a message to an agent and receive a response
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.agent.chat({
+    message: "What is the patient's current condition?",
+    agent_id: "agent-123",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.agent.AgentChatRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Agent.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">getChatMessages</a>({ ...params }) -> phenoml.AgentGetChatMessagesResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Retrieves a list of chat messages for a given chat session
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.agent.getChatMessages({
+    chat_session_id: "chat_session_id",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.agent.AgentGetChatMessagesRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Agent.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+## Agent Prompts
+
+<details><summary><code>client.agent.prompts.<a href="/src/api/resources/agent/resources/prompts/client/Client.ts">create</a>({ ...params }) -> phenoml.AgentPromptsResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Creates a new agent prompt
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.agent.prompts.create({
+    name: "Medical Assistant System Prompt",
+    content: "You are a helpful medical assistant specialized in FHIR data processing...",
+    is_active: true,
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.agent.AgentPromptsCreateRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Prompts.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.agent.prompts.<a href="/src/api/resources/agent/resources/prompts/client/Client.ts">list</a>() -> phenoml.PromptsListResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Retrieves a list of agent prompts belonging to the authenticated user
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.agent.prompts.list();
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**requestOptions:** `Prompts.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.agent.prompts.<a href="/src/api/resources/agent/resources/prompts/client/Client.ts">get</a>(id) -> phenoml.AgentPromptsResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Retrieves a specific prompt by its ID
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.agent.prompts.get("id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**id:** `string` — Prompt ID
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Prompts.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.agent.prompts.<a href="/src/api/resources/agent/resources/prompts/client/Client.ts">update</a>(id, { ...params }) -> phenoml.AgentPromptsResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Updates an existing prompt
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.agent.prompts.update("id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**id:** `string` — Prompt ID
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.agent.AgentPromptsUpdateRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Prompts.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.agent.prompts.<a href="/src/api/resources/agent/resources/prompts/client/Client.ts">delete</a>(id) -> phenoml.PromptsDeleteResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Soft deletes a prompt by setting is_active to false
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.agent.prompts.delete("id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**id:** `string` — Prompt ID
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Prompts.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.agent.prompts.<a href="/src/api/resources/agent/resources/prompts/client/Client.ts">patch</a>(id, { ...params }) -> phenoml.AgentPromptsResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Patches an existing prompt
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.agent.prompts.patch("id", [
+    {
+        op: "replace",
+        path: "/name",
+        value: "Updated Agent Name",
+    },
+    {
+        op: "add",
+        path: "/tags/-",
+        value: "new-tag",
+    },
+    {
+        op: "remove",
+        path: "/description",
+    },
+]);
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**id:** `string` — Agent Prompt ID
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.JsonPatch`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Prompts.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.agent.prompts.<a href="/src/api/resources/agent/resources/prompts/client/Client.ts">loadDefaults</a>() -> phenoml.SuccessResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Loads default agent prompts for the authenticated user
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.agent.prompts.loadDefaults();
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**requestOptions:** `Prompts.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+## Authtoken Auth
+
+<details><summary><code>client.authtoken.auth.<a href="/src/api/resources/authtoken/resources/auth/client/Client.ts">generateToken</a>({ ...params }) -> phenoml.AuthGenerateTokenResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Obtain an access token using client credentials
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.authtoken.auth.generateToken({
+    username: "username",
+    password: "password",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.authtoken.AuthGenerateTokenRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Auth.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+## Cohort
+
+<details><summary><code>client.cohort.<a href="/src/api/resources/cohort/client/Client.ts">analyze</a>({ ...params }) -> phenoml.CohortResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Converts natural language text into structured FHIR search queries for patient cohort analysis
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.cohort.analyze({
+    text: "female patients over 65 with diabetes but not hypertension",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.cohort.CohortRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Cohort.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+## Construe
+
+<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">uploadCodeSystem</a>({ ...params }) -> phenoml.ConstrueUploadCodeSystemResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Upload a custom medical code system with codes and descriptions for use in code extraction.
+Upon upload, construe generates embeddings for all of the codes in the code system and stores them in the vector database so you can
+subsequently use the code system for construe/extract and lang2fhir/create (coming soon!)
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.construe.uploadCodeSystem({
+    name: "CUSTOM_CODES",
+    version: "1.0",
+    format: "json",
+    file: "file",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.construe.UploadRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Construe.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">extractCodes</a>({ ...params }) -> phenoml.ExtractCodesResult</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Converts natural language text into structured medical codes
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.construe.extractCodes({
+    text: "Patient is a 14-year-old female, previously healthy, who is here for evaluation of abnormal renal ultrasound with atrophic right kidney",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.construe.ExtractRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Construe.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">cohort</a>({ ...params }) -> phenoml.ConstrueCohortResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Creates a patient cohort based on a natural language description.
+Translates the description into FHIR search queries and optional SQL queries.
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.construe.cohort({
+    text: "Between 20 and 40 years old with hyperlipidemia",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.construe.ConstrueCohortRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Construe.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+## Lang2Fhir
+
+<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">create</a>({ ...params }) -> phenoml.FhirResource</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Converts natural language text into a structured FHIR resource
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.lang2Fhir.create({
+    version: "R4",
+    resource: "auto",
+    text: "Patient has severe asthma with acute exacerbation",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.lang2Fhir.CreateRequest`
+
+</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">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: "medplum",
+});
+```
+
+</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>