phenoml 0.0.3 → 0.0.4

package/reference.md

@@ -50,7 +50,7 @@ await client.agent.create({
 <dl>
 <dd>
 
-**request:** `phenoml.agent.AgentCreateRequest`
+**request:** `phenoml.AgentCreateRequest`
 
 </dd>
 </dl>
@@ -223,7 +223,11 @@ 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 +251,7 @@ await client.agent.update("id");
 <dl>
 <dd>
 
-**request:** `phenoml.agent.AgentUpdateRequest`
+**request:** `phenoml.AgentCreateRequest`
 
 </dd>
 </dl>
@@ -1346,6 +1350,1088 @@ await client.construe.cohort({
 </dl>
 </details>
 
+## Fhir
+
+<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>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+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>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.fhir.search("550e8400-e29b-41d4-a716-446655440000", "Patient", {
+    "X-Phenoml-On-Behalf-Of": "user@example.com",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**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>
+
+<dl>
+<dd>
+
+**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.FhirSearchRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Fhir.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<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>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+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>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.fhir.create("550e8400-e29b-41d4-a716-446655440000", "Patient", {
+    "X-Phenoml-On-Behalf-Of": "user@example.com",
+    body: {
+        resourceType: "Patient",
+    },
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**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>
+
+<dl>
+<dd>
+
+**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>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<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>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+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>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.fhir.upsert("550e8400-e29b-41d4-a716-446655440000", "Patient", {
+    "X-Phenoml-On-Behalf-Of": "user@example.com",
+    body: {
+        resourceType: "Patient",
+        id: "123",
+    },
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**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>
+
+<dl>
+<dd>
+
+**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>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<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>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Deletes a FHIR resource from the specified provider.
+
+The request is proxied to the configured FHIR server with appropriate authentication headers.
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.fhir.delete("550e8400-e29b-41d4-a716-446655440000", "Patient", {
+    "X-Phenoml-On-Behalf-Of": "user@example.com",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**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>
+
+<dl>
+<dd>
+
+**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>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<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>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+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>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+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",
+        },
+    ],
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**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>
+
+<dl>
+<dd>
+
+**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>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">executeBundle</a>(fhirProviderId, { ...params }) -> phenoml.FhirBundle</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+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>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+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",
+                },
+            },
+        ],
+    },
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**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>
+
+<dl>
+<dd>
+
+**request:** `phenoml.fhir.FhirExecuteBundleRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `Fhir.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+## FhirProvider
+
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">create</a>({ ...params }) -> phenoml.FhirProviderResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Creates a new FHIR provider configuration with authentication credentials
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+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",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**request:** `phenoml.fhirProvider.FhirProviderCreateRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `FhirProvider.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">list</a>() -> phenoml.FhirProviderListResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Retrieves a list of all active FHIR providers for the authenticated user
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.fhirProvider.list();
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**requestOptions:** `FhirProvider.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">get</a>(fhirProviderId) -> phenoml.FhirProviderResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Retrieves a specific FHIR provider configuration by its ID
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.fhirProvider.get("fhir_provider_id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**fhirProviderId:** `string` — ID of the FHIR provider to retrieve
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `FhirProvider.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">delete</a>(fhirProviderId) -> phenoml.FhirProviderDeleteResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Soft deletes a FHIR provider by setting is_active to false
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.fhirProvider.delete("fhir_provider_id");
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**fhirProviderId:** `string` — ID of the FHIR provider to delete
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `FhirProvider.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">addAuthConfig</a>(fhirProviderId, { ...params }) -> phenoml.FhirProviderResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Adds a new authentication configuration to an existing FHIR provider. This enables key rotation and multiple auth configurations per provider.
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.fhirProvider.addAuthConfig("1716d214-de93-43a4-aa6b-a878d864e2ad", {
+    auth_method: "client_secret",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**fhirProviderId:** `string` — ID of the FHIR provider to add auth config to
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.fhirProvider.FhirProviderAddAuthConfigRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `FhirProvider.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">setActiveAuthConfig</a>(fhirProviderId, { ...params }) -> phenoml.FhirProviderSetActiveAuthConfigResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Sets which authentication configuration should be active for a FHIR provider. Only one auth config can be active at a time.
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.fhirProvider.setActiveAuthConfig("1716d214-de93-43a4-aa6b-a878d864e2ad", {
+    auth_config_id: "auth-config-123",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**fhirProviderId:** `string` — ID of the FHIR provider
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.fhirProvider.FhirProviderSetActiveAuthConfigRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `FhirProvider.RequestOptions`
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+</dd>
+</dl>
+</details>
+
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">removeAuthConfig</a>(fhirProviderId, { ...params }) -> phenoml.FhirProviderRemoveAuthConfigResponse</code></summary>
+<dl>
+<dd>
+
+#### 📝 Description
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+Removes an authentication configuration from a FHIR provider. Cannot remove the currently active auth configuration.
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### 🔌 Usage
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+```typescript
+await client.fhirProvider.removeAuthConfig("1716d214-de93-43a4-aa6b-a878d864e2ad", {
+    auth_config_id: "auth-config-123",
+});
+```
+
+</dd>
+</dl>
+</dd>
+</dl>
+
+#### ⚙️ Parameters
+
+<dl>
+<dd>
+
+<dl>
+<dd>
+
+**fhirProviderId:** `string` — ID of the FHIR provider
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**request:** `phenoml.fhirProvider.FhirProviderRemoveAuthConfigRequest`
+
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `FhirProvider.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>
@@ -1778,7 +2864,7 @@ Uses LLM to extract search concepts from natural language and builds patient coh
 ```typescript
 await client.tools.analyzeCohort({
     text: "female patients over 20 with diabetes but not hypertension",
-    provider: "medplum",
+    provider: "550e8400-e29b-41d4-a716-446655440000",
 });
 ```