phenoml 5.3.0 → 6.0.0

package/dist/cjs/Client.js

@@ -52,8 +52,8 @@ class phenomlClient {
         this._options = Object.assign(Object.assign({}, _options), { headers: (0, headers_js_1.mergeHeaders)({
                 "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/auto",
                 "X-Fern-Runtime": core.RUNTIME.type,
                 "X-Fern-Runtime-Version": core.RUNTIME.version,
             }, _options === null || _options === void 0 ? void 0 : _options.headers) });

package/dist/cjs/api/resources/agent/types/ChatMessageTemplate.d.ts

@@ -17,8 +17,6 @@ export interface ChatMessageTemplate {
     created?: string;
     /** Message updated time */
     updated?: string;
-    /** User ID */
-    user_id?: string;
     /** Function name */
     function_name?: string;
     /** Function arguments */

package/dist/cjs/api/resources/agent/types/ChatSessionTemplate.d.ts

@@ -1,8 +1,6 @@
 export interface ChatSessionTemplate {
     /** Chat session ID */
     id?: string;
-    /** User ID */
-    user_id?: string;
     /** Chat session ID */
     session_id?: string;
     /** Chat session status */

package/dist/cjs/api/resources/construe/client/Client.d.ts

@@ -12,8 +12,9 @@ export declare class Construe {
     constructor(_options: Construe.Options);
     /**
      * 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.
@@ -27,12 +28,9 @@ export declare 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"
      *     })
      */
     uploadCodeSystem(request: phenoml.construe.UploadRequest, requestOptions?: Construe.RequestOptions): core.HttpResponsePromise<phenoml.construe.ConstrueUploadCodeSystemResponse>;
@@ -47,8 +45,10 @@ export declare class Construe {
      *
      * @throws {@link phenoml.construe.BadRequestError}
      * @throws {@link phenoml.construe.UnauthorizedError}
-     * @throws {@link phenoml.construe.FailedDependencyError}
+     * @throws {@link phenoml.construe.NotFoundError}
      * @throws {@link phenoml.construe.InternalServerError}
+     * @throws {@link phenoml.construe.ServiceUnavailableError}
+     * @throws {@link phenoml.construe.GatewayTimeoutError}
      *
      * @example
      *     await client.construe.extractCodes({
@@ -253,7 +253,6 @@ export declare class Construe {
      * @throws {@link phenoml.construe.NotFoundError}
      * @throws {@link phenoml.construe.InternalServerError}
      * @throws {@link phenoml.construe.NotImplementedError}
-     * @throws {@link phenoml.construe.ServiceUnavailableError}
      *
      * @example
      *     await client.construe.terminologyServerTextSearch("ICD-10-CM", {

package/dist/cjs/api/resources/construe/client/Client.js

@@ -55,8 +55,9 @@ 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.
@@ -70,12 +71,9 @@ 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"
      *     })
      */
     uploadCodeSystem(request, requestOptions) {
@@ -152,8 +150,10 @@ class Construe {
      *
      * @throws {@link phenoml.construe.BadRequestError}
      * @throws {@link phenoml.construe.UnauthorizedError}
-     * @throws {@link phenoml.construe.FailedDependencyError}
+     * @throws {@link phenoml.construe.NotFoundError}
      * @throws {@link phenoml.construe.InternalServerError}
+     * @throws {@link phenoml.construe.ServiceUnavailableError}
+     * @throws {@link phenoml.construe.GatewayTimeoutError}
      *
      * @example
      *     await client.construe.extractCodes({
@@ -188,10 +188,14 @@ class Construe {
                         throw new phenoml.construe.BadRequestError(_response.error.body, _response.rawResponse);
                     case 401:
                         throw new phenoml.construe.UnauthorizedError(_response.error.body, _response.rawResponse);
-                    case 424:
-                        throw new phenoml.construe.FailedDependencyError(_response.error.body, _response.rawResponse);
+                    case 404:
+                        throw new phenoml.construe.NotFoundError(_response.error.body, _response.rawResponse);
                     case 500:
                         throw new phenoml.construe.InternalServerError(_response.error.body, _response.rawResponse);
+                    case 503:
+                        throw new phenoml.construe.ServiceUnavailableError(_response.error.body, _response.rawResponse);
+                    case 504:
+                        throw new phenoml.construe.GatewayTimeoutError(_response.error.body, _response.rawResponse);
                     default:
                         throw new errors.phenomlError({
                             statusCode: _response.error.statusCode,
@@ -836,7 +840,6 @@ class Construe {
      * @throws {@link phenoml.construe.NotFoundError}
      * @throws {@link phenoml.construe.InternalServerError}
      * @throws {@link phenoml.construe.NotImplementedError}
-     * @throws {@link phenoml.construe.ServiceUnavailableError}
      *
      * @example
      *     await client.construe.terminologyServerTextSearch("ICD-10-CM", {
@@ -885,8 +888,6 @@ class Construe {
                         throw new phenoml.construe.InternalServerError(_response.error.body, _response.rawResponse);
                     case 501:
                         throw new phenoml.construe.NotImplementedError(_response.error.body, _response.rawResponse);
-                    case 503:
-                        throw new phenoml.construe.ServiceUnavailableError(_response.error.body, _response.rawResponse);
                     default:
                         throw new errors.phenomlError({
                             statusCode: _response.error.statusCode,

package/dist/cjs/api/resources/construe/client/requests/UploadRequest.d.ts

@@ -0,0 +1,55 @@
+import type * as phenoml from "../../../../index.js";
+/**
+ * @example
+ *     {
+ *         name: "CUSTOM_CODES",
+ *         version: "1.0",
+ *         format: "csv"
+ *     }
+ */
+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
+     * reserved and cannot be used for custom uploads; attempts return HTTP 403 Forbidden.
+     */
+    name: string;
+    /** Version of the code system */
+    version: string;
+    /** Optional revision number */
+    revision?: number;
+    /** Upload format */
+    format: UploadRequest.Format;
+    /**
+     * 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 (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.
+     */
+    codes?: phenoml.construe.CodeResponse[];
+    /**
+     * If true, replaces an existing code system with the same name and version.
+     * Builtin systems cannot be replaced; attempts to do so return HTTP 403 Forbidden.
+     * When false (default), uploading a duplicate returns 409 Conflict.
+     */
+    replace?: boolean;
+}
+export declare namespace UploadRequest {
+    /** Upload format */
+    const Format: {
+        readonly Csv: "csv";
+        readonly Json: "json";
+    };
+    type Format = (typeof Format)[keyof typeof Format];
+}

package/dist/cjs/api/resources/construe/client/requests/UploadRequest.js

@@ -0,0 +1,12 @@
+"use strict";
+// This file was auto-generated by Fern from our API Definition.
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.UploadRequest = void 0;
+var UploadRequest;
+(function (UploadRequest) {
+    /** Upload format */
+    UploadRequest.Format = {
+        Csv: "csv",
+        Json: "json",
+    };
+})(UploadRequest || (exports.UploadRequest = UploadRequest = {}));

package/dist/cjs/api/resources/construe/client/requests/index.d.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";

package/dist/cjs/api/resources/construe/errors/GatewayTimeoutError.d.ts

@@ -0,0 +1,5 @@
+import type * as core from "../../../../core/index.js";
+import * as errors from "../../../../errors/index.js";
+export declare class GatewayTimeoutError extends errors.phenomlError {
+    constructor(body?: unknown, rawResponse?: core.RawResponse);
+}

package/dist/cjs/api/resources/construe/errors/GatewayTimeoutError.js

@@ -0,0 +1,50 @@
+"use strict";
+// This file was auto-generated by Fern from our API Definition.
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.GatewayTimeoutError = void 0;
+const errors = __importStar(require("../../../../errors/index.js"));
+class GatewayTimeoutError extends errors.phenomlError {
+    constructor(body, rawResponse) {
+        super({
+            message: "GatewayTimeoutError",
+            statusCode: 504,
+            body: body,
+            rawResponse: rawResponse,
+        });
+        Object.setPrototypeOf(this, GatewayTimeoutError.prototype);
+    }
+}
+exports.GatewayTimeoutError = GatewayTimeoutError;

package/dist/cjs/api/resources/construe/errors/index.d.ts

@@ -2,6 +2,7 @@ export * from "./BadRequestError.js";
 export * from "./ConflictError.js";
 export * from "./FailedDependencyError.js";
 export * from "./ForbiddenError.js";
+export * from "./GatewayTimeoutError.js";
 export * from "./InternalServerError.js";
 export * from "./NotFoundError.js";
 export * from "./NotImplementedError.js";

package/dist/cjs/api/resources/construe/errors/index.js

@@ -18,6 +18,7 @@ __exportStar(require("./BadRequestError.js"), exports);
 __exportStar(require("./ConflictError.js"), exports);
 __exportStar(require("./FailedDependencyError.js"), exports);
 __exportStar(require("./ForbiddenError.js"), exports);
+__exportStar(require("./GatewayTimeoutError.js"), exports);
 __exportStar(require("./InternalServerError.js"), exports);
 __exportStar(require("./NotFoundError.js"), exports);
 __exportStar(require("./NotImplementedError.js"), exports);

package/dist/cjs/api/resources/construe/types/ConstrueUploadCodeSystemResponse.d.ts

@@ -1,3 +1,5 @@
 export interface ConstrueUploadCodeSystemResponse {
     status?: string;
+    name?: string;
+    version?: string;
 }

package/dist/cjs/api/resources/construe/types/ExtractedCodeResult.d.ts

@@ -6,10 +6,8 @@ export interface ExtractedCodeResult {
     description: string;
     /** Whether the code passed validation. Always true unless include_invalid is set to true, in which case invalid codes will have this set to false. */
     valid: boolean;
-    /** Long description of the code */
-    longDescription?: string;
     /** Explanation for why this code was extracted (if include_rationale is true) */
-    rationale?: string;
+    reason?: string;
     /**
      * Whether this code is an ancestor (parent) of an extracted code rather than directly extracted.
      * Only present when include_ancestors is true.

package/dist/cjs/api/resources/construe/types/GetCodeSystemDetailResponse.d.ts

@@ -9,9 +9,9 @@ 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 */
@@ -22,9 +22,9 @@ export interface GetCodeSystemDetailResponse {
 export declare 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)
      */
     const Status: {
         readonly Processing: "processing";

package/dist/cjs/api/resources/construe/types/GetCodeSystemDetailResponse.js

@@ -6,9 +6,9 @@ var GetCodeSystemDetailResponse;
 (function (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)
      */
     GetCodeSystemDetailResponse.Status = {
         Processing: "processing",

package/dist/cjs/api/resources/construe/types/index.d.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";

package/dist/cjs/api/resources/construe/types/index.js

@@ -33,6 +33,3 @@ __exportStar(require("./SemanticSearchResponse.js"), exports);
 __exportStar(require("./SemanticSearchResult.js"), exports);
 __exportStar(require("./TextSearchResponse.js"), exports);
 __exportStar(require("./TextSearchResult.js"), exports);
-__exportStar(require("./UploadRequest.js"), exports);
-__exportStar(require("./UploadRequestCsv.js"), exports);
-__exportStar(require("./UploadRequestJson.js"), exports);

package/dist/cjs/api/resources/fhirProvider/types/FhirProviderTemplate.d.ts

@@ -2,8 +2,6 @@ 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 */

package/dist/cjs/api/resources/summary/types/SummaryTemplate.d.ts

@@ -1,6 +1,5 @@
 export interface SummaryTemplate {
     id?: string;
-    user_id?: string;
     name?: string;
     description?: string;
     /** Template with {{resource.field}} placeholders */

package/dist/cjs/api/resources/tools/types/McpServerResponse.d.ts

@@ -13,8 +13,6 @@ export declare namespace McpServerResponse {
     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 */

package/dist/cjs/api/resources/tools/types/McpServerToolResponse.d.ts

@@ -13,8 +13,6 @@ export declare namespace McpServerToolResponse {
     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 */

package/dist/cjs/api/resources/workflows/types/WorkflowDefinition.d.ts

@@ -2,8 +2,6 @@ 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 */

package/dist/cjs/api/resources/workflows/types/WorkflowResponse.d.ts

@@ -5,8 +5,6 @@ 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 */

package/dist/cjs/version.d.ts

@@ -1 +1 @@
-export declare const SDK_VERSION = "5.3.0";
+export declare const SDK_VERSION = "6.0.0";

package/dist/cjs/version.js

@@ -1,4 +1,4 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.SDK_VERSION = void 0;
-exports.SDK_VERSION = "5.3.0";
+exports.SDK_VERSION = "6.0.0";

package/dist/esm/Client.mjs

@@ -16,8 +16,8 @@ export class phenomlClient {
         this._options = Object.assign(Object.assign({}, _options), { headers: mergeHeaders({
                 "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/auto",
                 "X-Fern-Runtime": core.RUNTIME.type,
                 "X-Fern-Runtime-Version": core.RUNTIME.version,
             }, _options === null || _options === void 0 ? void 0 : _options.headers) });

package/dist/esm/api/resources/agent/types/ChatMessageTemplate.d.mts

@@ -17,8 +17,6 @@ export interface ChatMessageTemplate {
     created?: string;
     /** Message updated time */
     updated?: string;
-    /** User ID */
-    user_id?: string;
     /** Function name */
     function_name?: string;
     /** Function arguments */

package/dist/esm/api/resources/agent/types/ChatSessionTemplate.d.mts

@@ -1,8 +1,6 @@
 export interface ChatSessionTemplate {
     /** Chat session ID */
     id?: string;
-    /** User ID */
-    user_id?: string;
     /** Chat session ID */
     session_id?: string;
     /** Chat session status */

package/dist/esm/api/resources/construe/client/Client.d.mts

@@ -12,8 +12,9 @@ export declare class Construe {
     constructor(_options: Construe.Options);
     /**
      * 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.
@@ -27,12 +28,9 @@ export declare 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"
      *     })
      */
     uploadCodeSystem(request: phenoml.construe.UploadRequest, requestOptions?: Construe.RequestOptions): core.HttpResponsePromise<phenoml.construe.ConstrueUploadCodeSystemResponse>;
@@ -47,8 +45,10 @@ export declare class Construe {
      *
      * @throws {@link phenoml.construe.BadRequestError}
      * @throws {@link phenoml.construe.UnauthorizedError}
-     * @throws {@link phenoml.construe.FailedDependencyError}
+     * @throws {@link phenoml.construe.NotFoundError}
      * @throws {@link phenoml.construe.InternalServerError}
+     * @throws {@link phenoml.construe.ServiceUnavailableError}
+     * @throws {@link phenoml.construe.GatewayTimeoutError}
      *
      * @example
      *     await client.construe.extractCodes({
@@ -253,7 +253,6 @@ export declare class Construe {
      * @throws {@link phenoml.construe.NotFoundError}
      * @throws {@link phenoml.construe.InternalServerError}
      * @throws {@link phenoml.construe.NotImplementedError}
-     * @throws {@link phenoml.construe.ServiceUnavailableError}
      *
      * @example
      *     await client.construe.terminologyServerTextSearch("ICD-10-CM", {

package/dist/esm/api/resources/construe/client/Client.mjs

@@ -19,8 +19,9 @@ 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.
@@ -34,12 +35,9 @@ 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"
      *     })
      */
     uploadCodeSystem(request, requestOptions) {
@@ -116,8 +114,10 @@ export class Construe {
      *
      * @throws {@link phenoml.construe.BadRequestError}
      * @throws {@link phenoml.construe.UnauthorizedError}
-     * @throws {@link phenoml.construe.FailedDependencyError}
+     * @throws {@link phenoml.construe.NotFoundError}
      * @throws {@link phenoml.construe.InternalServerError}
+     * @throws {@link phenoml.construe.ServiceUnavailableError}
+     * @throws {@link phenoml.construe.GatewayTimeoutError}
      *
      * @example
      *     await client.construe.extractCodes({
@@ -152,10 +152,14 @@ export class Construe {
                         throw new phenoml.construe.BadRequestError(_response.error.body, _response.rawResponse);
                     case 401:
                         throw new phenoml.construe.UnauthorizedError(_response.error.body, _response.rawResponse);
-                    case 424:
-                        throw new phenoml.construe.FailedDependencyError(_response.error.body, _response.rawResponse);
+                    case 404:
+                        throw new phenoml.construe.NotFoundError(_response.error.body, _response.rawResponse);
                     case 500:
                         throw new phenoml.construe.InternalServerError(_response.error.body, _response.rawResponse);
+                    case 503:
+                        throw new phenoml.construe.ServiceUnavailableError(_response.error.body, _response.rawResponse);
+                    case 504:
+                        throw new phenoml.construe.GatewayTimeoutError(_response.error.body, _response.rawResponse);
                     default:
                         throw new errors.phenomlError({
                             statusCode: _response.error.statusCode,
@@ -800,7 +804,6 @@ export class Construe {
      * @throws {@link phenoml.construe.NotFoundError}
      * @throws {@link phenoml.construe.InternalServerError}
      * @throws {@link phenoml.construe.NotImplementedError}
-     * @throws {@link phenoml.construe.ServiceUnavailableError}
      *
      * @example
      *     await client.construe.terminologyServerTextSearch("ICD-10-CM", {
@@ -849,8 +852,6 @@ export class Construe {
                         throw new phenoml.construe.InternalServerError(_response.error.body, _response.rawResponse);
                     case 501:
                         throw new phenoml.construe.NotImplementedError(_response.error.body, _response.rawResponse);
-                    case 503:
-                        throw new phenoml.construe.ServiceUnavailableError(_response.error.body, _response.rawResponse);
                     default:
                         throw new errors.phenomlError({
                             statusCode: _response.error.statusCode,

package/dist/esm/api/resources/construe/client/requests/UploadRequest.d.mts

@@ -0,0 +1,55 @@
+import type * as phenoml from "../../../../index.mjs";
+/**
+ * @example
+ *     {
+ *         name: "CUSTOM_CODES",
+ *         version: "1.0",
+ *         format: "csv"
+ *     }
+ */
+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
+     * reserved and cannot be used for custom uploads; attempts return HTTP 403 Forbidden.
+     */
+    name: string;
+    /** Version of the code system */
+    version: string;
+    /** Optional revision number */
+    revision?: number;
+    /** Upload format */
+    format: UploadRequest.Format;
+    /**
+     * 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 (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.
+     */
+    codes?: phenoml.construe.CodeResponse[];
+    /**
+     * If true, replaces an existing code system with the same name and version.
+     * Builtin systems cannot be replaced; attempts to do so return HTTP 403 Forbidden.
+     * When false (default), uploading a duplicate returns 409 Conflict.
+     */
+    replace?: boolean;
+}
+export declare namespace UploadRequest {
+    /** Upload format */
+    const Format: {
+        readonly Csv: "csv";
+        readonly Json: "json";
+    };
+    type Format = (typeof Format)[keyof typeof Format];
+}

package/dist/esm/api/resources/construe/client/requests/UploadRequest.mjs

@@ -0,0 +1,9 @@
+// This file was auto-generated by Fern from our API Definition.
+export var UploadRequest;
+(function (UploadRequest) {
+    /** Upload format */
+    UploadRequest.Format = {
+        Csv: "csv",
+        Json: "json",
+    };
+})(UploadRequest || (UploadRequest = {}));

package/dist/esm/api/resources/construe/client/requests/index.d.mts

@@ -6,3 +6,4 @@ export type { GetConstrueCodesCodesystemSearchSemanticRequest } from "./GetConst
 export type { GetConstrueCodesCodesystemSearchTextRequest } from "./GetConstrueCodesCodesystemSearchTextRequest.mjs";
 export type { GetConstrueCodesSystemsCodesystemExportRequest } from "./GetConstrueCodesSystemsCodesystemExportRequest.mjs";
 export type { GetConstrueCodesSystemsCodesystemRequest } from "./GetConstrueCodesSystemsCodesystemRequest.mjs";
+export type { UploadRequest } from "./UploadRequest.mjs";

package/dist/esm/api/resources/construe/errors/GatewayTimeoutError.d.mts

@@ -0,0 +1,5 @@
+import type * as core from "../../../../core/index.mjs";
+import * as errors from "../../../../errors/index.mjs";
+export declare class GatewayTimeoutError extends errors.phenomlError {
+    constructor(body?: unknown, rawResponse?: core.RawResponse);
+}

package/dist/esm/api/resources/construe/errors/GatewayTimeoutError.mjs

@@ -0,0 +1,13 @@
+// This file was auto-generated by Fern from our API Definition.
+import * as errors from "../../../../errors/index.mjs";
+export class GatewayTimeoutError extends errors.phenomlError {
+    constructor(body, rawResponse) {
+        super({
+            message: "GatewayTimeoutError",
+            statusCode: 504,
+            body: body,
+            rawResponse: rawResponse,
+        });
+        Object.setPrototypeOf(this, GatewayTimeoutError.prototype);
+    }
+}

package/dist/esm/api/resources/construe/errors/index.d.mts

@@ -2,6 +2,7 @@ export * from "./BadRequestError.mjs";
 export * from "./ConflictError.mjs";
 export * from "./FailedDependencyError.mjs";
 export * from "./ForbiddenError.mjs";
+export * from "./GatewayTimeoutError.mjs";
 export * from "./InternalServerError.mjs";
 export * from "./NotFoundError.mjs";
 export * from "./NotImplementedError.mjs";

package/dist/esm/api/resources/construe/errors/index.mjs

@@ -2,6 +2,7 @@ export * from "./BadRequestError.mjs";
 export * from "./ConflictError.mjs";
 export * from "./FailedDependencyError.mjs";
 export * from "./ForbiddenError.mjs";
+export * from "./GatewayTimeoutError.mjs";
 export * from "./InternalServerError.mjs";
 export * from "./NotFoundError.mjs";
 export * from "./NotImplementedError.mjs";

package/dist/esm/api/resources/construe/types/ConstrueUploadCodeSystemResponse.d.mts

@@ -1,3 +1,5 @@
 export interface ConstrueUploadCodeSystemResponse {
     status?: string;
+    name?: string;
+    version?: string;
 }

package/dist/esm/api/resources/construe/types/ExtractedCodeResult.d.mts

@@ -6,10 +6,8 @@ export interface ExtractedCodeResult {
     description: string;
     /** Whether the code passed validation. Always true unless include_invalid is set to true, in which case invalid codes will have this set to false. */
     valid: boolean;
-    /** Long description of the code */
-    longDescription?: string;
     /** Explanation for why this code was extracted (if include_rationale is true) */
-    rationale?: string;
+    reason?: string;
     /**
      * Whether this code is an ancestor (parent) of an extracted code rather than directly extracted.
      * Only present when include_ancestors is true.

package/dist/esm/api/resources/construe/types/GetCodeSystemDetailResponse.d.mts

@@ -9,9 +9,9 @@ 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 */
@@ -22,9 +22,9 @@ export interface GetCodeSystemDetailResponse {
 export declare 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)
      */
     const Status: {
         readonly Processing: "processing";

package/dist/esm/api/resources/construe/types/GetCodeSystemDetailResponse.mjs

@@ -3,9 +3,9 @@ export var GetCodeSystemDetailResponse;
 (function (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)
      */
     GetCodeSystemDetailResponse.Status = {
         Processing: "processing",

package/dist/esm/api/resources/construe/types/index.d.mts

@@ -17,6 +17,3 @@ export * from "./SemanticSearchResponse.mjs";
 export * from "./SemanticSearchResult.mjs";
 export * from "./TextSearchResponse.mjs";
 export * from "./TextSearchResult.mjs";
-export * from "./UploadRequest.mjs";
-export * from "./UploadRequestCsv.mjs";
-export * from "./UploadRequestJson.mjs";

package/dist/esm/api/resources/construe/types/index.mjs

@@ -17,6 +17,3 @@ export * from "./SemanticSearchResponse.mjs";
 export * from "./SemanticSearchResult.mjs";
 export * from "./TextSearchResponse.mjs";
 export * from "./TextSearchResult.mjs";
-export * from "./UploadRequest.mjs";
-export * from "./UploadRequestCsv.mjs";
-export * from "./UploadRequestJson.mjs";

package/dist/esm/api/resources/fhirProvider/types/FhirProviderTemplate.d.mts

@@ -2,8 +2,6 @@ import type * as phenoml from "../../../index.mjs";
 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 */

package/dist/esm/api/resources/summary/types/SummaryTemplate.d.mts

@@ -1,6 +1,5 @@
 export interface SummaryTemplate {
     id?: string;
-    user_id?: string;
     name?: string;
     description?: string;
     /** Template with {{resource.field}} placeholders */

package/dist/esm/api/resources/tools/types/McpServerResponse.d.mts

@@ -13,8 +13,6 @@ export declare namespace McpServerResponse {
     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 */

package/dist/esm/api/resources/tools/types/McpServerToolResponse.d.mts

@@ -13,8 +13,6 @@ export declare namespace McpServerToolResponse {
     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 */

package/dist/esm/api/resources/workflows/types/WorkflowDefinition.d.mts

@@ -2,8 +2,6 @@ import type * as phenoml from "../../../index.mjs";
 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 */

package/dist/esm/api/resources/workflows/types/WorkflowResponse.d.mts

@@ -5,8 +5,6 @@ import type * as phenoml from "../../../index.mjs";
 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 */

package/dist/esm/version.d.mts

@@ -1 +1 @@
-export declare const SDK_VERSION = "5.3.0";
+export declare const SDK_VERSION = "6.0.0";

package/dist/esm/version.mjs

@@ -1 +1 @@
-export const SDK_VERSION = "5.3.0";
+export const SDK_VERSION = "6.0.0";

package/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",

package/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>

package/dist/cjs/api/resources/construe/types/UploadRequest.d.ts

@@ -1,10 +0,0 @@
-import type * as phenoml from "../../../index.js";
-export type UploadRequest = phenoml.construe.UploadRequest.Csv | phenoml.construe.UploadRequest.Json;
-export declare namespace UploadRequest {
-    interface Csv extends phenoml.construe.UploadRequestCsv {
-        format: "csv";
-    }
-    interface Json extends phenoml.construe.UploadRequestJson {
-        format: "json";
-    }
-}

package/dist/cjs/api/resources/construe/types/UploadRequest.js

@@ -1,3 +0,0 @@
-"use strict";
-// This file was auto-generated by Fern from our API Definition.
-Object.defineProperty(exports, "__esModule", { value: true });

package/dist/cjs/api/resources/construe/types/UploadRequestCsv.d.ts

@@ -1,32 +0,0 @@
-export interface UploadRequestCsv {
-    /**
-     * 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
-     * reserved and cannot be used for custom uploads; attempts return HTTP 403 Forbidden.
-     */
-    name: string;
-    /** Version of the code system */
-    version: string;
-    /** Optional revision number */
-    revision?: number;
-    /** The CSV file contents as a base64-encoded string. */
-    file: string;
-    /** Column name containing codes */
-    code_col: string;
-    /** Column name containing descriptions */
-    desc_col: string;
-    /** Optional column name containing long definitions */
-    defn_col?: string;
-    /**
-     * If true, replaces an existing code system with the same name and version.
-     * Builtin systems cannot be replaced; attempts to do so return HTTP 403 Forbidden.
-     * 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;
-}

package/dist/cjs/api/resources/construe/types/UploadRequestCsv.js

@@ -1,3 +0,0 @@
-"use strict";
-// This file was auto-generated by Fern from our API Definition.
-Object.defineProperty(exports, "__esModule", { value: true });

package/dist/cjs/api/resources/construe/types/UploadRequestJson.d.ts

@@ -1,40 +0,0 @@
-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.
- */
-export interface UploadRequestJson {
-    /**
-     * 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
-     * reserved and cannot be used for custom uploads; attempts return HTTP 403 Forbidden.
-     */
-    name: string;
-    /** Version of the code system */
-    version: string;
-    /** Optional revision number */
-    revision?: number;
-    /**
-     * The file contents as a base64-encoded JSON array string.
-     * Prefer using 'codes' instead to pass the array directly without base64 encoding.
-     */
-    file?: string;
-    /**
-     * The codes to upload as a JSON array.
-     * 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.
-     */
-    codes?: phenoml.construe.CodeResponse[];
-    /**
-     * If true, replaces an existing code system with the same name and version.
-     * Builtin systems cannot be replaced; attempts to do so return HTTP 403 Forbidden.
-     * 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;
-}

package/dist/cjs/api/resources/construe/types/UploadRequestJson.js

@@ -1,3 +0,0 @@
-"use strict";
-// This file was auto-generated by Fern from our API Definition.
-Object.defineProperty(exports, "__esModule", { value: true });

package/dist/esm/api/resources/construe/types/UploadRequest.d.mts

@@ -1,10 +0,0 @@
-import type * as phenoml from "../../../index.mjs";
-export type UploadRequest = phenoml.construe.UploadRequest.Csv | phenoml.construe.UploadRequest.Json;
-export declare namespace UploadRequest {
-    interface Csv extends phenoml.construe.UploadRequestCsv {
-        format: "csv";
-    }
-    interface Json extends phenoml.construe.UploadRequestJson {
-        format: "json";
-    }
-}

package/dist/esm/api/resources/construe/types/UploadRequest.mjs

@@ -1,2 +0,0 @@
-// This file was auto-generated by Fern from our API Definition.
-export {};

package/dist/esm/api/resources/construe/types/UploadRequestCsv.d.mts

@@ -1,32 +0,0 @@
-export interface UploadRequestCsv {
-    /**
-     * 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
-     * reserved and cannot be used for custom uploads; attempts return HTTP 403 Forbidden.
-     */
-    name: string;
-    /** Version of the code system */
-    version: string;
-    /** Optional revision number */
-    revision?: number;
-    /** The CSV file contents as a base64-encoded string. */
-    file: string;
-    /** Column name containing codes */
-    code_col: string;
-    /** Column name containing descriptions */
-    desc_col: string;
-    /** Optional column name containing long definitions */
-    defn_col?: string;
-    /**
-     * If true, replaces an existing code system with the same name and version.
-     * Builtin systems cannot be replaced; attempts to do so return HTTP 403 Forbidden.
-     * 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;
-}

package/dist/esm/api/resources/construe/types/UploadRequestCsv.mjs

@@ -1,2 +0,0 @@
-// This file was auto-generated by Fern from our API Definition.
-export {};

package/dist/esm/api/resources/construe/types/UploadRequestJson.d.mts

@@ -1,40 +0,0 @@
-import type * as phenoml from "../../../index.mjs";
-/**
- * Upload codes in JSON format. Either 'file' or 'codes' must be provided.
- * If both are provided, 'codes' takes precedence.
- */
-export interface UploadRequestJson {
-    /**
-     * 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
-     * reserved and cannot be used for custom uploads; attempts return HTTP 403 Forbidden.
-     */
-    name: string;
-    /** Version of the code system */
-    version: string;
-    /** Optional revision number */
-    revision?: number;
-    /**
-     * The file contents as a base64-encoded JSON array string.
-     * Prefer using 'codes' instead to pass the array directly without base64 encoding.
-     */
-    file?: string;
-    /**
-     * The codes to upload as a JSON array.
-     * 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.
-     */
-    codes?: phenoml.construe.CodeResponse[];
-    /**
-     * If true, replaces an existing code system with the same name and version.
-     * Builtin systems cannot be replaced; attempts to do so return HTTP 403 Forbidden.
-     * 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;
-}

package/dist/esm/api/resources/construe/types/UploadRequestJson.mjs

@@ -1,2 +0,0 @@
-// This file was auto-generated by Fern from our API Definition.
-export {};