phenoml 14.0.0 → 16.0.0

package/reference.md

@@ -69,7 +69,7 @@ await client.agent.create({
 </dl>
 </details>
 
-<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">list</a>({ ...params }) -> phenoml.AgentListResponse</code></summary>
+<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">list</a>({ ...params }) -> phenoml.ListResponse</code></summary>
 <dl>
 <dd>
 
@@ -114,7 +114,7 @@ await client.agent.list({
 <dl>
 <dd>
 
-**request:** `phenoml.agent.AgentListRequest` 
+**request:** `phenoml.agent.ListRequest` 
     
 </dd>
 </dl>
@@ -274,7 +274,7 @@ await client.agent.update("id", {
 </dl>
 </details>
 
-<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">delete</a>(id) -> phenoml.AgentDeleteResponse</code></summary>
+<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">delete</a>(id) -> phenoml.DeleteResponse</code></summary>
 <dl>
 <dd>
 
@@ -559,7 +559,7 @@ for await (const item of response) {
 </dl>
 </details>
 
-<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">getChatMessages</a>({ ...params }) -> phenoml.AgentGetChatMessagesResponse</code></summary>
+<details><summary><code>client.agent.<a href="/src/api/resources/agent/client/Client.ts">getChatMessages</a>({ ...params }) -> phenoml.GetChatMessagesResponse</code></summary>
 <dl>
 <dd>
 
@@ -607,7 +607,7 @@ await client.agent.getChatMessages({
 <dl>
 <dd>
 
-**request:** `phenoml.agent.AgentGetChatMessagesRequest` 
+**request:** `phenoml.agent.GetChatMessagesRequest` 
     
 </dd>
 </dl>
@@ -1030,8 +1030,8 @@ await client.agent.prompts.patch("id", [{
 </dl>
 </details>
 
-## Authtoken Auth
-<details><summary><code>client.authtoken.auth.<a href="/src/api/resources/authtoken/resources/auth/client/Client.ts">getToken</a>({ ...params }) -> phenoml.TokenResponse</code></summary>
+## Authtoken
+<details><summary><code>client.authtoken.<a href="/src/api/resources/authtoken/client/Client.ts">getToken</a>({ ...params }) -> phenoml.TokenResponse</code></summary>
 <dl>
 <dd>
 
@@ -1061,7 +1061,7 @@ returns an access token with expiration information.
 <dd>
 
 ```typescript
-await client.authtoken.auth.getToken({
+await client.authtoken.getToken({
     client_id: "your_client_id",
     client_secret: "your_client_secret"
 });
@@ -1088,7 +1088,7 @@ await client.authtoken.auth.getToken({
 <dl>
 <dd>
 
-**requestOptions:** `AuthClient.RequestOptions` 
+**requestOptions:** `AuthtokenClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -1167,7 +1167,7 @@ await client.cohort.analyze({
 </details>
 
 ## Construe
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">uploadCodeSystem</a>({ ...params }) -> phenoml.ConstrueUploadCodeSystemResponse</code></summary>
+<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">uploadCodeSystem</a>({ ...params }) -> phenoml.UploadCodeSystemResponse</code></summary>
 <dl>
 <dd>
 
@@ -1315,7 +1315,7 @@ await client.construe.extractCodes({
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">listAvailableCodeSystems</a>() -> phenoml.ListCodeSystemsResponse</code></summary>
+<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">listCodeSystems</a>() -> phenoml.ListCodeSystemsResponse</code></summary>
 <dl>
 <dd>
 
@@ -1342,7 +1342,7 @@ Returns the terminology server's catalog of available code systems, including bo
 <dd>
 
 ```typescript
-await client.construe.listAvailableCodeSystems();
+await client.construe.listCodeSystems();
 
 ```
 </dd>
@@ -1370,7 +1370,7 @@ await client.construe.listAvailableCodeSystems();
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">getCodeSystemDetail</a>(codesystem, { ...params }) -> phenoml.GetCodeSystemDetailResponse</code></summary>
+<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">getCodeSystem</a>(codesystem, { ...params }) -> phenoml.GetCodeSystemDetailResponse</code></summary>
 <dl>
 <dd>
 
@@ -1397,7 +1397,7 @@ Returns full metadata for a single code system, including timestamps and builtin
 <dd>
 
 ```typescript
-await client.construe.getCodeSystemDetail("ICD-10-CM", {
+await client.construe.getCodeSystem("ICD-10-CM", {
     version: "2025"
 });
 
@@ -1423,7 +1423,7 @@ await client.construe.getCodeSystemDetail("ICD-10-CM", {
 <dl>
 <dd>
 
-**request:** `phenoml.construe.GetConstrueCodesSystemsCodesystemRequest` 
+**request:** `phenoml.construe.GetCodeSystemRequest` 
     
 </dd>
 </dl>
@@ -1443,7 +1443,7 @@ await client.construe.getCodeSystemDetail("ICD-10-CM", {
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">deleteCustomCodeSystem</a>(codesystem, { ...params }) -> phenoml.DeleteCodeSystemResponse</code></summary>
+<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">deleteCodeSystem</a>(codesystem, { ...params }) -> phenoml.DeleteCodeSystemResponse</code></summary>
 <dl>
 <dd>
 
@@ -1471,7 +1471,7 @@ Only available on dedicated instances. Large systems may take up to a minute to
 <dd>
 
 ```typescript
-await client.construe.deleteCustomCodeSystem("CUSTOM_CODES", {
+await client.construe.deleteCodeSystem("CUSTOM_CODES", {
     version: "version"
 });
 
@@ -1497,7 +1497,7 @@ await client.construe.deleteCustomCodeSystem("CUSTOM_CODES", {
 <dl>
 <dd>
 
-**request:** `phenoml.construe.DeleteConstrueCodesSystemsCodesystemRequest` 
+**request:** `phenoml.construe.DeleteCodeSystemRequest` 
     
 </dd>
 </dl>
@@ -1517,7 +1517,7 @@ await client.construe.deleteCustomCodeSystem("CUSTOM_CODES", {
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">exportCustomCodeSystem</a>(codesystem, { ...params }) -> phenoml.ExportCodeSystemResponse</code></summary>
+<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">exportCodeSystem</a>(codesystem, { ...params }) -> phenoml.ExportCodeSystemResponse</code></summary>
 <dl>
 <dd>
 
@@ -1546,7 +1546,7 @@ Only available on dedicated instances. Builtin systems cannot be exported.
 <dd>
 
 ```typescript
-await client.construe.exportCustomCodeSystem("CUSTOM_CODES", {
+await client.construe.exportCodeSystem("CUSTOM_CODES", {
     version: "version"
 });
 
@@ -1572,7 +1572,7 @@ await client.construe.exportCustomCodeSystem("CUSTOM_CODES", {
 <dl>
 <dd>
 
-**request:** `phenoml.construe.GetConstrueCodesSystemsCodesystemExportRequest` 
+**request:** `phenoml.construe.ExportCodeSystemRequest` 
     
 </dd>
 </dl>
@@ -1592,7 +1592,7 @@ await client.construe.exportCustomCodeSystem("CUSTOM_CODES", {
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">listCodesInACodeSystem</a>(codesystem, { ...params }) -> phenoml.ListCodesResponse</code></summary>
+<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">listCodes</a>(codesystem, { ...params }) -> phenoml.ListCodesResponse</code></summary>
 <dl>
 <dd>
 
@@ -1621,7 +1621,7 @@ Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
 <dd>
 
 ```typescript
-await client.construe.listCodesInACodeSystem("ICD-10-CM", {
+await client.construe.listCodes("ICD-10-CM", {
     version: "2025",
     cursor: "cursor",
     limit: 1
@@ -1649,7 +1649,7 @@ await client.construe.listCodesInACodeSystem("ICD-10-CM", {
 <dl>
 <dd>
 
-**request:** `phenoml.construe.GetConstrueCodesCodesystemRequest` 
+**request:** `phenoml.construe.ListCodesRequest` 
     
 </dd>
 </dl>
@@ -1669,7 +1669,7 @@ await client.construe.listCodesInACodeSystem("ICD-10-CM", {
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">getASpecificCode</a>(codesystem, codeID, { ...params }) -> phenoml.GetCodeResponse</code></summary>
+<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">getCode</a>(codesystem, codeID, { ...params }) -> phenoml.GetCodeResponse</code></summary>
 <dl>
 <dd>
 
@@ -1698,7 +1698,7 @@ Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
 <dd>
 
 ```typescript
-await client.construe.getASpecificCode("ICD-10-CM", "E1165", {
+await client.construe.getCode("ICD-10-CM", "E1165", {
     version: "version"
 });
 
@@ -1735,7 +1735,7 @@ cosmetic dot (use "E1165", not "E11.65").
 <dl>
 <dd>
 
-**request:** `phenoml.construe.GetConstrueCodesCodesystemCodeIdRequest` 
+**request:** `phenoml.construe.GetCodeRequest` 
     
 </dd>
 </dl>
@@ -1755,7 +1755,7 @@ cosmetic dot (use "E1165", not "E11.65").
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">semanticSearchEmbeddingBased</a>(codesystem, { ...params }) -> phenoml.SemanticSearchResponse</code></summary>
+<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">searchSemantic</a>(codesystem, { ...params }) -> phenoml.SemanticSearchResponse</code></summary>
 <dl>
 <dd>
 
@@ -1800,7 +1800,7 @@ Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
 <dd>
 
 ```typescript
-await client.construe.semanticSearchEmbeddingBased("ICD-10-CM", {
+await client.construe.searchSemantic("ICD-10-CM", {
     text: "patient has trouble breathing at night and wakes up gasping",
     version: "version",
     limit: 1
@@ -1828,7 +1828,7 @@ await client.construe.semanticSearchEmbeddingBased("ICD-10-CM", {
 <dl>
 <dd>
 
-**request:** `phenoml.construe.GetConstrueCodesCodesystemSearchSemanticRequest` 
+**request:** `phenoml.construe.SearchSemanticRequest` 
     
 </dd>
 </dl>
@@ -1848,7 +1848,7 @@ await client.construe.semanticSearchEmbeddingBased("ICD-10-CM", {
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">submitFeedbackOnExtractionResults</a>({ ...params }) -> phenoml.FeedbackResponse</code></summary>
+<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">submitFeedback</a>({ ...params }) -> phenoml.FeedbackResponse</code></summary>
 <dl>
 <dd>
 
@@ -1876,7 +1876,7 @@ Feedback includes the full extraction result received and the result the user ex
 <dd>
 
 ```typescript
-await client.construe.submitFeedbackOnExtractionResults({
+await client.construe.submitFeedback({
     text: "Patient has type 2 diabetes with hyperglycemia",
     received_result: {
         system: {
@@ -1937,7 +1937,7 @@ await client.construe.submitFeedbackOnExtractionResults({
 </dl>
 </details>
 
-<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">terminologyServerTextSearch</a>(codesystem, { ...params }) -> phenoml.TextSearchResponse</code></summary>
+<details><summary><code>client.construe.<a href="/src/api/resources/construe/client/Client.ts">searchText</a>(codesystem, { ...params }) -> phenoml.TextSearchResponse</code></summary>
 <dl>
 <dd>
 
@@ -1987,7 +1987,7 @@ Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
 <dd>
 
 ```typescript
-await client.construe.terminologyServerTextSearch("ICD-10-CM", {
+await client.construe.searchText("ICD-10-CM", {
     q: "E11.65",
     version: "version",
     limit: 1
@@ -2015,7 +2015,7 @@ await client.construe.terminologyServerTextSearch("ICD-10-CM", {
 <dl>
 <dd>
 
-**request:** `phenoml.construe.GetConstrueCodesCodesystemSearchTextRequest` 
+**request:** `phenoml.construe.SearchTextRequest` 
     
 </dd>
 </dl>
@@ -2036,7 +2036,7 @@ await client.construe.terminologyServerTextSearch("ICD-10-CM", {
 </details>
 
 ## Fhir
-<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">search</a>(fhir_provider_id, fhir_path, { ...params }) -> phenoml.FhirSearchResponse</code></summary>
+<details><summary><code>client.fhir.<a href="/src/api/resources/fhir/client/Client.ts">search</a>(fhir_provider_id, fhir_path, { ...params }) -> phenoml.SearchResponse</code></summary>
 <dl>
 <dd>
 
@@ -2110,7 +2110,7 @@ Examples:
 <dl>
 <dd>
 
-**request:** `phenoml.fhir.FhirSearchRequest` 
+**request:** `phenoml.fhir.SearchRequest` 
     
 </dd>
 </dl>
@@ -2207,7 +2207,7 @@ Examples:
 <dl>
 <dd>
 
-**request:** `phenoml.fhir.FhirCreateRequest` 
+**request:** `phenoml.fhir.CreateRequest` 
     
 </dd>
 </dl>
@@ -2305,7 +2305,7 @@ Examples:
 <dl>
 <dd>
 
-**request:** `phenoml.fhir.FhirUpsertRequest` 
+**request:** `phenoml.fhir.UpsertRequest` 
     
 </dd>
 </dl>
@@ -2399,7 +2399,7 @@ Examples:
 <dl>
 <dd>
 
-**request:** `phenoml.fhir.FhirDeleteRequest` 
+**request:** `phenoml.fhir.DeleteRequest` 
     
 </dd>
 </dl>
@@ -2503,7 +2503,7 @@ Examples:
 <dl>
 <dd>
 
-**request:** `phenoml.fhir.FhirPatchRequest` 
+**request:** `phenoml.fhir.PatchRequest` 
     
 </dd>
 </dl>
@@ -2617,7 +2617,7 @@ The ID of the FHIR provider to use. Can be either:
 <dl>
 <dd>
 
-**request:** `phenoml.fhir.FhirExecuteBundleRequest` 
+**request:** `phenoml.fhir.ExecuteBundleRequest` 
     
 </dd>
 </dl>
@@ -2837,7 +2837,7 @@ await client.fhirProvider.get("fhir_provider_id");
 </dl>
 </details>
 
-<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">delete</a>(fhir_provider_id) -> phenoml.FhirProviderDeleteResponse</code></summary>
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">delete</a>(fhir_provider_id) -> phenoml.DeleteResponse</code></summary>
 <dl>
 <dd>
 
@@ -3059,7 +3059,7 @@ await client.fhirProvider.setActiveAuthConfig("1716d214-de93-43a4-aa6b-a878d864e
 </dl>
 </details>
 
-<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">removeAuthConfig</a>(fhir_provider_id, { ...params }) -> phenoml.FhirProviderRemoveAuthConfigResponse</code></summary>
+<details><summary><code>client.fhirProvider.<a href="/src/api/resources/fhirProvider/client/Client.ts">removeAuthConfig</a>(fhir_provider_id, { ...params }) -> phenoml.RemoveAuthConfigResponse</code></summary>
 <dl>
 <dd>
 
@@ -3347,7 +3347,7 @@ 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.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">uploadProfile</a>({ ...params }) -> phenoml.UploadProfileResponse</code></summary>
 <dl>
 <dd>
 
@@ -3492,7 +3492,7 @@ await client.lang2Fhir.document({
 </dl>
 </details>
 
-<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">extractMultipleFhirResourcesFromADocument</a>({ ...params }) -> phenoml.DocumentMultiResponse</code></summary>
+<details><summary><code>client.lang2Fhir.<a href="/src/api/resources/lang2Fhir/client/Client.ts">documentMulti</a>({ ...params }) -> phenoml.DocumentMultiResponse</code></summary>
 <dl>
 <dd>
 
@@ -3524,7 +3524,7 @@ Resources are linked with proper references (e.g., Conditions reference the Pati
 <dd>
 
 ```typescript
-await client.lang2Fhir.extractMultipleFhirResourcesFromADocument({
+await client.lang2Fhir.documentMulti({
     version: "R4",
     content: "JVBERi0xLjQKJeLjz9MK...(base64-encoded PDF or image bytes)",
     provider: "medplum"
@@ -3565,7 +3565,7 @@ await client.lang2Fhir.extractMultipleFhirResourcesFromADocument({
 </details>
 
 ## Summary
-<details><summary><code>client.summary.<a href="/src/api/resources/summary/client/Client.ts">listTemplates</a>() -> phenoml.SummaryListTemplatesResponse</code></summary>
+<details><summary><code>client.summary.<a href="/src/api/resources/summary/client/Client.ts">create</a>({ ...params }) -> phenoml.CreateSummaryResponse</code></summary>
 <dl>
 <dd>
 
@@ -3577,7 +3577,10 @@ await client.lang2Fhir.extractMultipleFhirResourcesFromADocument({
 <dl>
 <dd>
 
-Retrieves all summary templates for the authenticated user
+Creates a summary from FHIR resources using one of three modes:
+- **narrative**: Uses a template to substitute FHIR data into placeholders (requires template_id)
+- **flatten**: Flattens FHIR resources into a searchable format for RAG/search (no template needed)
+- **ips**: Generates an International Patient Summary (IPS) narrative per ISO 27269/HL7 FHIR IPS IG. Requires a Bundle with exactly one Patient resource (returns 400 error if no Patient or multiple Patients are present). Automatically filters resources to those referencing the patient and generates sections for allergies, medications, problems, immunizations, procedures, and vital signs.
 </dd>
 </dl>
 </dd>
@@ -3592,7 +3595,40 @@ Retrieves all summary templates for the authenticated user
 <dd>
 
 ```typescript
-await client.summary.listTemplates();
+await client.summary.create({
+    mode: "narrative",
+    template_id: "a1b2c3d4-e5f6-7890-abcd-ef1234567890",
+    fhir_resources: {
+        "resourceType": "Bundle",
+        "type": "collection",
+        "entry": [
+            {
+                "resource": {
+                    "resourceType": "Patient",
+                    "name": [
+                        {
+                            "given": [
+                                "John"
+                            ],
+                            "family": "Doe"
+                        }
+                    ],
+                    "gender": "male",
+                    "birthDate": "1979-03-15"
+                }
+            },
+            {
+                "resource": {
+                    "resourceType": "Condition",
+                    "code": {
+                        "text": "Type 2 Diabetes Mellitus"
+                    },
+                    "onsetDateTime": "2024-01-15"
+                }
+            }
+        ]
+    }
+});
 
 ```
 </dd>
@@ -3608,6 +3644,14 @@ await client.summary.listTemplates();
 <dl>
 <dd>
 
+**request:** `phenoml.summary.CreateSummaryRequest` 
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
 **requestOptions:** `SummaryClient.RequestOptions` 
     
 </dd>
@@ -3620,7 +3664,8 @@ await client.summary.listTemplates();
 </dl>
 </details>
 
-<details><summary><code>client.summary.<a href="/src/api/resources/summary/client/Client.ts">createTemplate</a>({ ...params }) -> phenoml.CreateSummaryTemplateResponse</code></summary>
+## Summary Templates
+<details><summary><code>client.summary.templates.<a href="/src/api/resources/summary/resources/templates/client/Client.ts">list</a>() -> phenoml.TemplatesListResponse</code></summary>
 <dl>
 <dd>
 
@@ -3632,7 +3677,7 @@ await client.summary.listTemplates();
 <dl>
 <dd>
 
-Creates a summary template from an example using LLM function calling
+Retrieves all summary templates for the authenticated user
 </dd>
 </dl>
 </dd>
@@ -3647,12 +3692,7 @@ Creates a summary template from an example using LLM function calling
 <dd>
 
 ```typescript
-await client.summary.createTemplate({
-    name: "Discharge Summary",
-    example_summary: "Patient John Doe, age 45, was admitted on 2024-01-10 with Type 2 Diabetes. Discharged on 2024-01-15 with Metformin 500mg BID.",
-    target_resources: ["Patient", "Condition", "MedicationRequest"],
-    mode: "narrative"
-});
+await client.summary.templates.list();
 
 ```
 </dd>
@@ -3668,15 +3708,7 @@ await client.summary.createTemplate({
 <dl>
 <dd>
 
-**request:** `phenoml.summary.CreateSummaryTemplateRequest` 
-    
-</dd>
-</dl>
-
-<dl>
-<dd>
-
-**requestOptions:** `SummaryClient.RequestOptions` 
+**requestOptions:** `TemplatesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -3688,7 +3720,7 @@ await client.summary.createTemplate({
 </dl>
 </details>
 
-<details><summary><code>client.summary.<a href="/src/api/resources/summary/client/Client.ts">getTemplate</a>(id) -> phenoml.SummaryGetTemplateResponse</code></summary>
+<details><summary><code>client.summary.templates.<a href="/src/api/resources/summary/resources/templates/client/Client.ts">create</a>({ ...params }) -> phenoml.CreateSummaryTemplateResponse</code></summary>
 <dl>
 <dd>
 
@@ -3700,7 +3732,7 @@ await client.summary.createTemplate({
 <dl>
 <dd>
 
-Retrieves a specific summary template
+Creates a summary template from an example using LLM function calling
 </dd>
 </dl>
 </dd>
@@ -3715,7 +3747,12 @@ Retrieves a specific summary template
 <dd>
 
 ```typescript
-await client.summary.getTemplate("id");
+await client.summary.templates.create({
+    name: "Discharge Summary",
+    example_summary: "Patient John Doe, age 45, was admitted on 2024-01-10 with Type 2 Diabetes. Discharged on 2024-01-15 with Metformin 500mg BID.",
+    target_resources: ["Patient", "Condition", "MedicationRequest"],
+    mode: "narrative"
+});
 
 ```
 </dd>
@@ -3731,7 +3768,7 @@ await client.summary.getTemplate("id");
 <dl>
 <dd>
 
-**id:** `string` — Template ID
+**request:** `phenoml.summary.CreateSummaryTemplateRequest` 
     
 </dd>
 </dl>
@@ -3739,7 +3776,7 @@ await client.summary.getTemplate("id");
 <dl>
 <dd>
 
-**requestOptions:** `SummaryClient.RequestOptions` 
+**requestOptions:** `TemplatesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -3751,7 +3788,7 @@ await client.summary.getTemplate("id");
 </dl>
 </details>
 
-<details><summary><code>client.summary.<a href="/src/api/resources/summary/client/Client.ts">updateTemplate</a>(id, { ...params }) -> phenoml.SummaryUpdateTemplateResponse</code></summary>
+<details><summary><code>client.summary.templates.<a href="/src/api/resources/summary/resources/templates/client/Client.ts">get</a>(id) -> phenoml.TemplatesGetResponse</code></summary>
 <dl>
 <dd>
 
@@ -3763,7 +3800,7 @@ await client.summary.getTemplate("id");
 <dl>
 <dd>
 
-Updates an existing summary template
+Retrieves a specific summary template
 </dd>
 </dl>
 </dd>
@@ -3778,12 +3815,7 @@ Updates an existing summary template
 <dd>
 
 ```typescript
-await client.summary.updateTemplate("id", {
-    name: "Discharge Summary",
-    template: "Patient {{Patient.name[0].text}} was discharged on {{Encounter[0].period.end}} with {{MedicationRequest[0].medicationCodeableConcept.coding[0].display}} {{MedicationRequest[0].dosageInstruction[0].text}}.",
-    target_resources: ["Patient", "Encounter", "MedicationRequest"],
-    mode: "narrative"
-});
+await client.summary.templates.get("id");
 
 ```
 </dd>
@@ -3807,15 +3839,7 @@ await client.summary.updateTemplate("id", {
 <dl>
 <dd>
 
-**request:** `phenoml.summary.UpdateSummaryTemplateRequest` 
-    
-</dd>
-</dl>
-
-<dl>
-<dd>
-
-**requestOptions:** `SummaryClient.RequestOptions` 
+**requestOptions:** `TemplatesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -3827,7 +3851,7 @@ await client.summary.updateTemplate("id", {
 </dl>
 </details>
 
-<details><summary><code>client.summary.<a href="/src/api/resources/summary/client/Client.ts">deleteTemplate</a>(id) -> phenoml.SummaryDeleteTemplateResponse</code></summary>
+<details><summary><code>client.summary.templates.<a href="/src/api/resources/summary/resources/templates/client/Client.ts">update</a>(id, { ...params }) -> phenoml.TemplatesUpdateResponse</code></summary>
 <dl>
 <dd>
 
@@ -3839,7 +3863,7 @@ await client.summary.updateTemplate("id", {
 <dl>
 <dd>
 
-Deletes a summary template
+Updates an existing summary template
 </dd>
 </dl>
 </dd>
@@ -3854,7 +3878,12 @@ Deletes a summary template
 <dd>
 
 ```typescript
-await client.summary.deleteTemplate("id");
+await client.summary.templates.update("id", {
+    name: "Discharge Summary",
+    template: "Patient {{Patient.name[0].text}} was discharged on {{Encounter[0].period.end}} with {{MedicationRequest[0].medicationCodeableConcept.coding[0].display}} {{MedicationRequest[0].dosageInstruction[0].text}}.",
+    target_resources: ["Patient", "Encounter", "MedicationRequest"],
+    mode: "narrative"
+});
 
 ```
 </dd>
@@ -3878,7 +3907,15 @@ await client.summary.deleteTemplate("id");
 <dl>
 <dd>
 
-**requestOptions:** `SummaryClient.RequestOptions` 
+**request:** `phenoml.summary.UpdateSummaryTemplateRequest` 
+    
+</dd>
+</dl>
+
+<dl>
+<dd>
+
+**requestOptions:** `TemplatesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -3890,7 +3927,7 @@ await client.summary.deleteTemplate("id");
 </dl>
 </details>
 
-<details><summary><code>client.summary.<a href="/src/api/resources/summary/client/Client.ts">create</a>({ ...params }) -> phenoml.CreateSummaryResponse</code></summary>
+<details><summary><code>client.summary.templates.<a href="/src/api/resources/summary/resources/templates/client/Client.ts">delete</a>(id) -> phenoml.TemplatesDeleteResponse</code></summary>
 <dl>
 <dd>
 
@@ -3902,10 +3939,7 @@ await client.summary.deleteTemplate("id");
 <dl>
 <dd>
 
-Creates a summary from FHIR resources using one of three modes:
-- **narrative**: Uses a template to substitute FHIR data into placeholders (requires template_id)
-- **flatten**: Flattens FHIR resources into a searchable format for RAG/search (no template needed)
-- **ips**: Generates an International Patient Summary (IPS) narrative per ISO 27269/HL7 FHIR IPS IG. Requires a Bundle with exactly one Patient resource (returns 400 error if no Patient or multiple Patients are present). Automatically filters resources to those referencing the patient and generates sections for allergies, medications, problems, immunizations, procedures, and vital signs.
+Deletes a summary template
 </dd>
 </dl>
 </dd>
@@ -3920,40 +3954,7 @@ Creates a summary from FHIR resources using one of three modes:
 <dd>
 
 ```typescript
-await client.summary.create({
-    mode: "narrative",
-    template_id: "a1b2c3d4-e5f6-7890-abcd-ef1234567890",
-    fhir_resources: {
-        "resourceType": "Bundle",
-        "type": "collection",
-        "entry": [
-            {
-                "resource": {
-                    "resourceType": "Patient",
-                    "name": [
-                        {
-                            "given": [
-                                "John"
-                            ],
-                            "family": "Doe"
-                        }
-                    ],
-                    "gender": "male",
-                    "birthDate": "1979-03-15"
-                }
-            },
-            {
-                "resource": {
-                    "resourceType": "Condition",
-                    "code": {
-                        "text": "Type 2 Diabetes Mellitus"
-                    },
-                    "onsetDateTime": "2024-01-15"
-                }
-            }
-        ]
-    }
-});
+await client.summary.templates.delete("id");
 
 ```
 </dd>
@@ -3969,7 +3970,7 @@ await client.summary.create({
 <dl>
 <dd>
 
-**request:** `phenoml.summary.CreateSummaryRequest` 
+**id:** `string` — Template ID
     
 </dd>
 </dl>
@@ -3977,7 +3978,7 @@ await client.summary.create({
 <dl>
 <dd>
 
-**requestOptions:** `SummaryClient.RequestOptions` 
+**requestOptions:** `TemplatesClient.RequestOptions` 
     
 </dd>
 </dl>
@@ -4703,81 +4704,6 @@ await client.tools.mcpServer.tools.delete("mcp_server_tool_id");
 </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>(mcp_server_tool_id, { ...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>
-
-**mcp_server_tool_id:** `string` — ID of the MCP server tool to call
-    
-</dd>
-</dl>
-
-<dl>
-<dd>
-
-**request:** `phenoml.tools.mcpServer.McpServerToolCallRequest` 
-    
-</dd>
-</dl>
-
-<dl>
-<dd>
-
-**requestOptions:** `ToolsClient.RequestOptions` 
-    
-</dd>
-</dl>
-</dd>
-</dl>
-
-
 </dd>
 </dl>
 </details>
@@ -4828,7 +4754,7 @@ await client.workflows.list({
 <dl>
 <dd>
 
-**request:** `phenoml.workflows.WorkflowsListRequest` 
+**request:** `phenoml.workflows.ListRequest` 
     
 </dd>
 </dl>
@@ -4922,7 +4848,7 @@ await client.workflows.create({
 </dl>
 </details>
 
-<details><summary><code>client.workflows.<a href="/src/api/resources/workflows/client/Client.ts">get</a>(id, { ...params }) -> phenoml.WorkflowsGetResponse</code></summary>
+<details><summary><code>client.workflows.<a href="/src/api/resources/workflows/client/Client.ts">get</a>(id, { ...params }) -> phenoml.GetResponse</code></summary>
 <dl>
 <dd>
 
@@ -4975,7 +4901,7 @@ await client.workflows.get("id", {
 <dl>
 <dd>
 
-**request:** `phenoml.workflows.WorkflowsGetRequest` 
+**request:** `phenoml.workflows.GetRequest` 
     
 </dd>
 </dl>
@@ -4995,7 +4921,7 @@ await client.workflows.get("id", {
 </dl>
 </details>
 
-<details><summary><code>client.workflows.<a href="/src/api/resources/workflows/client/Client.ts">update</a>(id, { ...params }) -> phenoml.WorkflowsUpdateResponse</code></summary>
+<details><summary><code>client.workflows.<a href="/src/api/resources/workflows/client/Client.ts">update</a>(id, { ...params }) -> phenoml.UpdateResponse</code></summary>
 <dl>
 <dd>
 
@@ -5077,7 +5003,7 @@ await client.workflows.update("id", {
 </dl>
 </details>
 
-<details><summary><code>client.workflows.<a href="/src/api/resources/workflows/client/Client.ts">delete</a>(id) -> phenoml.WorkflowsDeleteResponse</code></summary>
+<details><summary><code>client.workflows.<a href="/src/api/resources/workflows/client/Client.ts">delete</a>(id) -> phenoml.DeleteResponse</code></summary>
 <dl>
 <dd>