refactor: simplify upload code system API and remove user_id fields

fern-api[bot] · web-flow · commit be125091bb06 · 2026-02-10T12:41:40.000Z
Major refactoring of the upload code system API to simplify the interface and improve consistency. The upload request structure has been consolidated and user ID references have been removed from multiple templates to support a more streamlined architecture.

Key changes:
- Unified upload request structure with simplified parameter handling
- Removed user_id fields from chat, workflow, FHIR provider, and other templates
- Updated upload code system to return asynchronous processing status
- Consolidated upload request types into a single interface
- Improved documentation for asynchronous processing workflow

🌿 Generated with Fern
diff --git a/changelog.md b/changelog.md
@@ -1,3 +1,14 @@
+## 6.0.0 - 2026-02-10
+* refactor: simplify upload code system API and remove user_id fields
+* Major refactoring of the upload code system API to simplify the interface and improve consistency. The upload request structure has been consolidated and user ID references have been removed from multiple templates to support a more streamlined architecture.
+* Key changes:
+* Unified upload request structure with simplified parameter handling
+* Removed user_id fields from chat, workflow, FHIR provider, and other templates
+* Updated upload code system to return asynchronous processing status
+* Consolidated upload request types into a single interface
+* Improved documentation for asynchronous processing workflow
+* 🌿 Generated with Fern
+
 ## 5.3.0 - 2026-02-09
 * feat: add custom code system export endpoint
 * Add new exportCustomCodeSystem method to the construe client that allows exporting custom (non-builtin) code systems as JSON files. This feature enables users to backup and transfer code systems between instances.
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
     "name": "phenoml",
-    "version": "5.3.0",
+    "version": "6.0.0",
     "private": false,
     "repository": "github:PhenoML/phenoml-ts-sdk",
     "type": "commonjs",
diff --git a/reference.md b/reference.md
@@ -1154,8 +1154,9 @@ await client.cohort.analyze({
 <dd>
 
 Upload a custom medical code system with codes and descriptions for use in code extraction. Requires a paid plan.
-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!)
+Returns 202 immediately; embedding generation runs asynchronously. Poll
+GET /construe/codes/systems/{codesystem}?version={version} to check when status
+transitions from "processing" to "ready" or "failed".
 </dd>
 </dl>
 </dd>
@@ -1171,12 +1172,9 @@ subsequently use the code system for construe/extract and lang2fhir/create (comi
 
 ```typescript
 await client.construe.uploadCodeSystem({
-    format: "csv",
     name: "CUSTOM_CODES",
     version: "1.0",
-    file: "file",
-    code_col: "code",
-    desc_col: "description"
+    format: "csv"
 });
 
 ```
@@ -1193,7 +1191,7 @@ await client.construe.uploadCodeSystem({
 <dl>
 <dd>
 
-**request:** `phenoml.UploadRequest` 
+**request:** `phenoml.construe.UploadRequest` 
     
 </dd>
 </dl>
diff --git a/src/Client.ts b/src/Client.ts
@@ -40,8 +40,8 @@ export class phenomlClient {
                 {
                     "X-Fern-Language": "JavaScript",
                     "X-Fern-SDK-Name": "phenoml",
-                    "X-Fern-SDK-Version": "5.3.0",
-                    "User-Agent": "phenoml/5.3.0",
+                    "X-Fern-SDK-Version": "6.0.0",
+                    "User-Agent": "phenoml/6.0.0",
                     "X-Fern-Runtime": core.RUNTIME.type,
                     "X-Fern-Runtime-Version": core.RUNTIME.version,
                 },
diff --git a/src/api/resources/agent/types/ChatMessageTemplate.ts b/src/api/resources/agent/types/ChatMessageTemplate.ts
@@ -19,8 +19,6 @@ export interface ChatMessageTemplate {
     created?: string;
     /** Message updated time */
     updated?: string;
-    /** User ID */
-    user_id?: string;
     /** Function name */
     function_name?: string;
     /** Function arguments */
diff --git a/src/api/resources/agent/types/ChatSessionTemplate.ts b/src/api/resources/agent/types/ChatSessionTemplate.ts
@@ -3,8 +3,6 @@
 export interface ChatSessionTemplate {
     /** Chat session ID */
     id?: string;
-    /** User ID */
-    user_id?: string;
     /** Chat session ID */
     session_id?: string;
     /** Chat session status */
diff --git a/src/api/resources/construe/client/Client.ts b/src/api/resources/construe/client/Client.ts
@@ -22,8 +22,9 @@ export class Construe {
 
     /**
      * Upload a custom medical code system with codes and descriptions for use in code extraction. Requires a paid plan.
-     * 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!)
+     * Returns 202 immediately; embedding generation runs asynchronously. Poll
+     * GET /construe/codes/systems/{codesystem}?version={version} to check when status
+     * transitions from "processing" to "ready" or "failed".
      *
      * @param {phenoml.construe.UploadRequest} request
      * @param {Construe.RequestOptions} requestOptions - Request-specific configuration.
@@ -37,12 +38,9 @@ export class Construe {
      *
      * @example
      *     await client.construe.uploadCodeSystem({
-     *         format: "csv",
      *         name: "CUSTOM_CODES",
      *         version: "1.0",
-     *         file: "file",
-     *         code_col: "code",
-     *         desc_col: "description"
+     *         format: "csv"
      *     })
      */
     public uploadCodeSystem(
diff --git a/src/api/resources/construe/client/requests/UploadRequest.ts b/src/api/resources/construe/client/requests/UploadRequest.ts
@@ -1,12 +1,16 @@
 // This file was auto-generated by Fern from our API Definition.
 
-import type * as phenoml from "../../../index.js";
+import type * as phenoml from "../../../../index.js";
 
 /**
- * Upload codes in JSON format. Either 'file' or 'codes' must be provided.
- * If both are provided, 'codes' takes precedence.
+ * @example
+ *     {
+ *         name: "CUSTOM_CODES",
+ *         version: "1.0",
+ *         format: "csv"
+ *     }
  */
-export interface UploadRequestJson {
+export interface UploadRequest {
     /**
      * Name of the code system. Names are case-insensitive and stored uppercase.
      * Builtin system names (e.g. ICD-10-CM, SNOMED_CT_US_LITE, LOINC, CPT, etc.) are
@@ -17,13 +21,22 @@ export interface UploadRequestJson {
     version: string;
     /** Optional revision number */
     revision?: number;
+    /** Upload format */
+    format: UploadRequest.Format;
     /**
-     * The file contents as a base64-encoded JSON array string.
-     * Prefer using 'codes' instead to pass the array directly without base64 encoding.
+     * The file contents as a base64-encoded string.
+     * For CSV format, this is the CSV file contents.
+     * For JSON format, this is a base64-encoded JSON array; prefer using 'codes' instead.
      */
     file?: string;
+    /** Column name containing codes (required for CSV format) */
+    code_col?: string;
+    /** Column name containing descriptions (required for CSV format) */
+    desc_col?: string;
+    /** Optional column name containing long definitions (for CSV format) */
+    defn_col?: string;
     /**
-     * The codes to upload as a JSON array.
+     * The codes to upload as a JSON array (JSON format only).
      * This is the preferred way to upload JSON codes, as it avoids unnecessary base64 encoding.
      * If both 'codes' and 'file' are provided, 'codes' takes precedence.
      */
@@ -34,10 +47,13 @@ export interface UploadRequestJson {
      * When false (default), uploading a duplicate returns 409 Conflict.
      */
     replace?: boolean;
-    /**
-     * If true, returns 202 Accepted immediately after validation and starts processing
-     * in the background. Poll GET /construe/codes/systems/{name}?version={version} to
-     * check when status transitions from "processing" to "ready" or "failed".
-     */
-    async?: boolean;
+}
+
+export namespace UploadRequest {
+    /** Upload format */
+    export const Format = {
+        Csv: "csv",
+        Json: "json",
+    } as const;
+    export type Format = (typeof Format)[keyof typeof Format];
 }
diff --git a/src/api/resources/construe/client/requests/index.ts b/src/api/resources/construe/client/requests/index.ts
@@ -6,3 +6,4 @@ export type { GetConstrueCodesCodesystemSearchSemanticRequest } from "./GetConst
 export type { GetConstrueCodesCodesystemSearchTextRequest } from "./GetConstrueCodesCodesystemSearchTextRequest.js";
 export type { GetConstrueCodesSystemsCodesystemExportRequest } from "./GetConstrueCodesSystemsCodesystemExportRequest.js";
 export type { GetConstrueCodesSystemsCodesystemRequest } from "./GetConstrueCodesSystemsCodesystemRequest.js";
+export type { UploadRequest } from "./UploadRequest.js";
diff --git a/src/api/resources/construe/types/ConstrueUploadCodeSystemResponse.ts b/src/api/resources/construe/types/ConstrueUploadCodeSystemResponse.ts
@@ -2,4 +2,6 @@
 
 export interface ConstrueUploadCodeSystemResponse {
     status?: string;
+    name?: string;
+    version?: string;
 }
diff --git a/src/api/resources/construe/types/GetCodeSystemDetailResponse.ts b/src/api/resources/construe/types/GetCodeSystemDetailResponse.ts
@@ -11,9 +11,9 @@ export interface GetCodeSystemDetailResponse {
     builtin: boolean;
     /**
      * Processing status of the code system.
-     * - "processing": embeddings are being generated (async upload in progress)
+     * - "processing": embeddings are being generated
      * - "ready": code system is ready for use
-     * - "failed": async processing failed (re-upload with replace=true to retry)
+     * - "failed": processing failed (re-upload with replace=true to retry)
      */
     status: GetCodeSystemDetailResponse.Status;
     /** When the code system was created */
@@ -25,9 +25,9 @@ export interface GetCodeSystemDetailResponse {
 export namespace GetCodeSystemDetailResponse {
     /**
      * Processing status of the code system.
-     * - "processing": embeddings are being generated (async upload in progress)
+     * - "processing": embeddings are being generated
      * - "ready": code system is ready for use
-     * - "failed": async processing failed (re-upload with replace=true to retry)
+     * - "failed": processing failed (re-upload with replace=true to retry)
      */
     export const Status = {
         Processing: "processing",
diff --git a/src/api/resources/construe/types/UploadRequest.ts b/src/api/resources/construe/types/UploadRequest.ts
diff --git a/src/api/resources/construe/types/UploadRequestCsv.ts b/src/api/resources/construe/types/UploadRequestCsv.ts
diff --git a/src/api/resources/construe/types/index.ts b/src/api/resources/construe/types/index.ts
@@ -17,6 +17,3 @@ export * from "./SemanticSearchResponse.js";
 export * from "./SemanticSearchResult.js";
 export * from "./TextSearchResponse.js";
 export * from "./TextSearchResult.js";
-export * from "./UploadRequest.js";
-export * from "./UploadRequestCsv.js";
-export * from "./UploadRequestJson.js";
diff --git a/src/api/resources/fhirProvider/types/FhirProviderTemplate.ts b/src/api/resources/fhirProvider/types/FhirProviderTemplate.ts
@@ -5,8 +5,6 @@ import type * as phenoml from "../../../index.js";
 export interface FhirProviderTemplate {
     /** Unique identifier for the FHIR provider */
     id?: string;
-    /** ID of the user who owns this FHIR provider */
-    user_id?: string;
     /** Display name for the FHIR provider */
     name?: string;
     /** Optional description of the FHIR provider */
diff --git a/src/api/resources/summary/types/SummaryTemplate.ts b/src/api/resources/summary/types/SummaryTemplate.ts
@@ -2,7 +2,6 @@
 
 export interface SummaryTemplate {
     id?: string;
-    user_id?: string;
     name?: string;
     description?: string;
     /** Template with {{resource.field}} placeholders */
diff --git a/src/api/resources/tools/types/McpServerResponse.ts b/src/api/resources/tools/types/McpServerResponse.ts
@@ -16,8 +16,6 @@ export namespace McpServerResponse {
     export interface Data {
         /** ID of the MCP server */
         id?: string;
-        /** ID of the user who created the MCP server */
-        user_id?: string;
         /** Name of the MCP server */
         name?: string;
         /** Description of the MCP server */
diff --git a/src/api/resources/tools/types/McpServerToolResponse.ts b/src/api/resources/tools/types/McpServerToolResponse.ts
@@ -16,8 +16,6 @@ export namespace McpServerToolResponse {
     export interface Data {
         /** ID of the MCP server tool */
         id?: string;
-        /** ID of the user who created the MCP server tool */
-        user_id?: string;
         /** Name of the MCP server tool */
         name?: string;
         /** Description of the MCP server tool */
diff --git a/src/api/resources/workflows/types/WorkflowDefinition.ts b/src/api/resources/workflows/types/WorkflowDefinition.ts
@@ -5,8 +5,6 @@ import type * as phenoml from "../../../index.js";
 export interface WorkflowDefinition {
     /** Unique identifier for the workflow */
     id?: string;
-    /** ID of the user who created the workflow */
-    user_id?: string;
     /** Human-readable name for the workflow */
     name?: string;
     /** Natural language instructions that define the workflow logic */
diff --git a/src/api/resources/workflows/types/WorkflowResponse.ts b/src/api/resources/workflows/types/WorkflowResponse.ts
@@ -8,8 +8,6 @@ import type * as phenoml from "../../../index.js";
 export interface WorkflowResponse {
     /** Unique identifier for the workflow */
     id?: string;
-    /** ID of the user who created the workflow */
-    user_id?: string;
     /** Human-readable name for the workflow */
     name?: string;
     /** Natural language instructions that define the workflow logic */
diff --git a/src/version.ts b/src/version.ts
@@ -1 +1 @@
-export const SDK_VERSION = "5.3.0";
+export const SDK_VERSION = "6.0.0";
diff --git a/tests/wire/agent/main.test.ts b/tests/wire/agent/main.test.ts
@@ -892,7 +892,6 @@ describe("Agent", () => {
                     content: "Hello, how are you?",
                     created: "2021-01-01T00:00:00Z",
                     updated: "2021-01-01T00:00:00Z",
-                    user_id: "user_123",
                     function_name: "get_patient_info",
                     function_args: { patient_id: "123" },
                     function_result: { name: "John Doe" },
@@ -925,7 +924,6 @@ describe("Agent", () => {
                     content: "Hello, how are you?",
                     created: "2021-01-01T00:00:00Z",
                     updated: "2021-01-01T00:00:00Z",
-                    user_id: "user_123",
                     function_name: "get_patient_info",
                     function_args: {
                         patient_id: "123",
diff --git a/tests/wire/construe/main.test.ts b/tests/wire/construe/main.test.ts
diff --git a/tests/wire/fhir_provider/main.test.ts b/tests/wire/fhir_provider/main.test.ts
diff --git a/tests/wire/summary/main.test.ts b/tests/wire/summary/main.test.ts
diff --git a/tests/wire/tools/mcpServer.test.ts b/tests/wire/tools/mcpServer.test.ts
diff --git a/tests/wire/tools/mcpServer/tools.test.ts b/tests/wire/tools/mcpServer/tools.test.ts
diff --git a/tests/wire/workflows/main.test.ts b/tests/wire/workflows/main.test.ts

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`{`
`2`	`2`	`"name": "phenoml",`
`3`		`- "version": "5.3.0",`
	`3`	`+ "version": "6.0.0",`
`4`	`4`	`"private": false,`
`5`	`5`	`"repository": "github:PhenoML/phenoml-ts-sdk",`
`6`	`6`	`"type": "commonjs",`
Original file line number	Diff line number	Diff line change
`@@ -2,4 +2,6 @@`
`2`	`2`
`3`	`3`	`export interface ConstrueUploadCodeSystemResponse {`
`4`	`4`	`status?: string;`
	`5`	`+ name?: string;`
	`6`	`+ version?: string;`
`5`	`7`	`}`