refactor: refactor code upload system and remove user_id fields

fern-api[bot] · web-flow · commit aa3b0d9dcb95 · 2026-02-10T18:59:40.000Z
Refactored the Construe uploadCodeSystem API to simplify the request structure and improve asynchronous processing behavior. Updated the upload request interface to use a single unified structure instead of separate CSV and JSON variants. Also removed user_id fields across multiple resource templates to streamline data models.

Key changes:
- Unified UploadRequest interface with simplified structure and format enum
- Updated uploadCodeSystem to return immediately with 202 status and process asynchronously
- Removed user_id fields from ChatMessageTemplate, ChatSessionTemplate, FhirProviderTemplate, SummaryTemplate, McpServerResponse, WorkflowDefinition, and WorkflowResponse
- Added name and version fields to upload response for better tracking
- Updated documentation to reflect async processing pattern
- Reorganized construe types and moved UploadRequest to client/requests directory

🌿 Generated with Fern
diff --git a/changelog.md b/changelog.md
@@ -1,3 +1,15 @@
+## 6.0.0 - 2026-02-10
+* refactor: refactor code upload system and remove user_id fields
+* Refactored the Construe uploadCodeSystem API to simplify the request structure and improve asynchronous processing behavior. Updated the upload request interface to use a single unified structure instead of separate CSV and JSON variants. Also removed user_id fields across multiple resource templates to streamline data models.
+* Key changes:
+* Unified UploadRequest interface with simplified structure and format enum
+* Updated uploadCodeSystem to return immediately with 202 status and process asynchronously
+* Removed user_id fields from ChatMessageTemplate, ChatSessionTemplate, FhirProviderTemplate, SummaryTemplate, McpServerResponse, WorkflowDefinition, and WorkflowResponse
+* Added name and version fields to upload response for better tracking
+* Updated documentation to reflect async processing pattern
+* Reorganized construe types and moved UploadRequest to client/requests directory
+* 🌿 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`	`}`