phenoml 13.0.0 → 14.0.0

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

@@ -30,7 +30,24 @@ export declare class ConstrueClient {
      *     await client.construe.uploadCodeSystem({
      *         name: "CUSTOM_CODES",
      *         version: "1.0",
-     *         format: "csv"
+     *         format: "json",
+     *         codes: [{
+     *                 code: "X001",
+     *                 description: "Example custom code 1"
+     *             }, {
+     *                 code: "X002",
+     *                 description: "Example custom code 2"
+     *             }]
+     *     })
+     *
+     * @example
+     *     await client.construe.uploadCodeSystem({
+     *         name: "CUSTOM_CODES",
+     *         version: "1.0",
+     *         format: "csv",
+     *         file: "Y29kZSxkZXNjcmlwdGlvbgpYMDAxLEV4YW1wbGUgY3VzdG9tIGNvZGUgMQo=",
+     *         code_col: "code",
+     *         desc_col: "description"
      *     })
      */
     uploadCodeSystem(request: phenoml.construe.UploadRequest, requestOptions?: ConstrueClient.RequestOptions): core.HttpResponsePromise<phenoml.construe.ConstrueUploadCodeSystemResponse>;
@@ -52,7 +69,66 @@ export declare class ConstrueClient {
      *
      * @example
      *     await client.construe.extractCodes({
-     *         text: "Patient is a 14-year-old female, previously healthy, who is here for evaluation of abnormal renal ultrasound with atrophic right kidney"
+     *         text: "Patient is a 14-year-old female, previously healthy, who is here for evaluation of abnormal renal ultrasound with atrophic right kidney.",
+     *         system: {
+     *             name: "ICD-10-CM",
+     *             version: "2025"
+     *         }
+     *     })
+     *
+     * @example
+     *     await client.construe.extractCodes({
+     *         text: "45-year-old male presents with chest pain radiating to left arm, shortness of breath, and diaphoresis. ECG shows ST elevation in leads II, III, and aVF.",
+     *         system: {
+     *             name: "SNOMED_CT_US_LITE",
+     *             version: "20240901"
+     *         },
+     *         config: {
+     *             chunking_method: "sentences",
+     *             validation_method: "simple",
+     *             include_rationale: true,
+     *             include_citations: true
+     *         }
+     *     })
+     *
+     * @example
+     *     await client.construe.extractCodes({
+     *         text: "Start Metformin 500mg twice daily for type 2 diabetes. Continue Lisinopril 10mg daily for hypertension. Add Atorvastatin 20mg at bedtime.",
+     *         system: {
+     *             name: "RXNORM",
+     *             version: "11042024"
+     *         },
+     *         config: {
+     *             validation_method: "medication_search",
+     *             include_rationale: true
+     *         }
+     *     })
+     *
+     * @example
+     *     await client.construe.extractCodes({
+     *         text: "Patient diagnosed with Type 2 diabetes mellitus with diabetic chronic kidney disease, stage 3.",
+     *         system: {
+     *             name: "ICD-10-CM",
+     *             version: "2025"
+     *         },
+     *         config: {
+     *             validation_method: "simple",
+     *             include_ancestors: true
+     *         }
+     *     })
+     *
+     * @example
+     *     await client.construe.extractCodes({
+     *         text: "5-year-old male with seizures, severe intellectual disability, microcephaly, and hypotonia.",
+     *         system: {
+     *             name: "HPO",
+     *             version: "2025"
+     *         },
+     *         config: {
+     *             chunking_method: "fasthpocr",
+     *             validation_method: "none",
+     *             include_rationale: false
+     *         }
      *     })
      */
     extractCodes(request: phenoml.construe.ExtractRequest, requestOptions?: ConstrueClient.RequestOptions): core.HttpResponsePromise<phenoml.construe.ExtractCodesResult>;
@@ -163,7 +239,8 @@ export declare class ConstrueClient {
      * Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
      *
      * @param {string} codesystem - Code system name
-     * @param {string} codeID - The code identifier
+     * @param {string} codeID - The code identifier. ICD-10-CM codes are stored without their
+     *                          cosmetic dot (use "E1165", not "E11.65").
      * @param {phenoml.construe.GetConstrueCodesCodesystemCodeIdRequest} request
      * @param {ConstrueClient.RequestOptions} requestOptions - Request-specific configuration.
      *
@@ -173,7 +250,7 @@ export declare class ConstrueClient {
      * @throws {@link phenoml.construe.InternalServerError}
      *
      * @example
-     *     await client.construe.getASpecificCode("ICD-10-CM", "E11.65", {
+     *     await client.construe.getASpecificCode("ICD-10-CM", "E1165", {
      *         version: "version"
      *     })
      */
@@ -234,21 +311,28 @@ export declare class ConstrueClient {
      *     await client.construe.submitFeedbackOnExtractionResults({
      *         text: "Patient has type 2 diabetes with hyperglycemia",
      *         received_result: {
-     *             system: {},
+     *             system: {
+     *                 name: "ICD-10-CM",
+     *                 version: "2025"
+     *             },
      *             codes: [{
-     *                     code: "195967001",
-     *                     description: "Asthma",
+     *                     code: "E11.9",
+     *                     description: "Type 2 diabetes mellitus without complications",
      *                     valid: true
      *                 }]
      *         },
      *         expected_result: {
-     *             system: {},
+     *             system: {
+     *                 name: "ICD-10-CM",
+     *                 version: "2025"
+     *             },
      *             codes: [{
-     *                     code: "195967001",
-     *                     description: "Asthma",
+     *                     code: "E11.65",
+     *                     description: "Type 2 diabetes mellitus with hyperglycemia",
      *                     valid: true
      *                 }]
-     *         }
+     *         },
+     *         detail: "Expected code E11.65 because the text mentions hyperglycemia"
      *     })
      */
     submitFeedbackOnExtractionResults(request: phenoml.construe.FeedbackRequest, requestOptions?: ConstrueClient.RequestOptions): core.HttpResponsePromise<phenoml.construe.FeedbackResponse>;

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

@@ -75,7 +75,24 @@ class ConstrueClient {
      *     await client.construe.uploadCodeSystem({
      *         name: "CUSTOM_CODES",
      *         version: "1.0",
-     *         format: "csv"
+     *         format: "json",
+     *         codes: [{
+     *                 code: "X001",
+     *                 description: "Example custom code 1"
+     *             }, {
+     *                 code: "X002",
+     *                 description: "Example custom code 2"
+     *             }]
+     *     })
+     *
+     * @example
+     *     await client.construe.uploadCodeSystem({
+     *         name: "CUSTOM_CODES",
+     *         version: "1.0",
+     *         format: "csv",
+     *         file: "Y29kZSxkZXNjcmlwdGlvbgpYMDAxLEV4YW1wbGUgY3VzdG9tIGNvZGUgMQo=",
+     *         code_col: "code",
+     *         desc_col: "description"
      *     })
      */
     uploadCodeSystem(request, requestOptions) {
@@ -91,7 +108,7 @@ class ConstrueClient {
                 method: "POST",
                 headers: _headers,
                 contentType: "application/json",
-                queryParameters: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams,
+                queryString: core.url.queryBuilder().mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams).build(),
                 requestType: "json",
                 body: request,
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
@@ -148,7 +165,66 @@ class ConstrueClient {
      *
      * @example
      *     await client.construe.extractCodes({
-     *         text: "Patient is a 14-year-old female, previously healthy, who is here for evaluation of abnormal renal ultrasound with atrophic right kidney"
+     *         text: "Patient is a 14-year-old female, previously healthy, who is here for evaluation of abnormal renal ultrasound with atrophic right kidney.",
+     *         system: {
+     *             name: "ICD-10-CM",
+     *             version: "2025"
+     *         }
+     *     })
+     *
+     * @example
+     *     await client.construe.extractCodes({
+     *         text: "45-year-old male presents with chest pain radiating to left arm, shortness of breath, and diaphoresis. ECG shows ST elevation in leads II, III, and aVF.",
+     *         system: {
+     *             name: "SNOMED_CT_US_LITE",
+     *             version: "20240901"
+     *         },
+     *         config: {
+     *             chunking_method: "sentences",
+     *             validation_method: "simple",
+     *             include_rationale: true,
+     *             include_citations: true
+     *         }
+     *     })
+     *
+     * @example
+     *     await client.construe.extractCodes({
+     *         text: "Start Metformin 500mg twice daily for type 2 diabetes. Continue Lisinopril 10mg daily for hypertension. Add Atorvastatin 20mg at bedtime.",
+     *         system: {
+     *             name: "RXNORM",
+     *             version: "11042024"
+     *         },
+     *         config: {
+     *             validation_method: "medication_search",
+     *             include_rationale: true
+     *         }
+     *     })
+     *
+     * @example
+     *     await client.construe.extractCodes({
+     *         text: "Patient diagnosed with Type 2 diabetes mellitus with diabetic chronic kidney disease, stage 3.",
+     *         system: {
+     *             name: "ICD-10-CM",
+     *             version: "2025"
+     *         },
+     *         config: {
+     *             validation_method: "simple",
+     *             include_ancestors: true
+     *         }
+     *     })
+     *
+     * @example
+     *     await client.construe.extractCodes({
+     *         text: "5-year-old male with seizures, severe intellectual disability, microcephaly, and hypotonia.",
+     *         system: {
+     *             name: "HPO",
+     *             version: "2025"
+     *         },
+     *         config: {
+     *             chunking_method: "fasthpocr",
+     *             validation_method: "none",
+     *             include_rationale: false
+     *         }
      *     })
      */
     extractCodes(request, requestOptions) {
@@ -164,7 +240,7 @@ class ConstrueClient {
                 method: "POST",
                 headers: _headers,
                 contentType: "application/json",
-                queryParameters: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams,
+                queryString: core.url.queryBuilder().mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams).build(),
                 requestType: "json",
                 body: request,
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
@@ -224,7 +300,7 @@ class ConstrueClient {
                 url: core.url.join((_d = (_c = (yield core.Supplier.get(this._options.baseUrl))) !== null && _c !== void 0 ? _c : (yield core.Supplier.get(this._options.environment))) !== null && _d !== void 0 ? _d : environments.phenomlEnvironment.Default, "construe/codes/systems"),
                 method: "GET",
                 headers: _headers,
-                queryParameters: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams,
+                queryString: core.url.queryBuilder().mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams).build(),
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
                 maxRetries: (_h = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.maxRetries) !== null && _h !== void 0 ? _h : (_j = this._options) === null || _j === void 0 ? void 0 : _j.maxRetries,
                 abortSignal: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.abortSignal,
@@ -287,7 +363,11 @@ class ConstrueClient {
                 url: core.url.join((_d = (_c = (yield core.Supplier.get(this._options.baseUrl))) !== null && _c !== void 0 ? _c : (yield core.Supplier.get(this._options.environment))) !== null && _d !== void 0 ? _d : environments.phenomlEnvironment.Default, `construe/codes/systems/${core.url.encodePathParam(codesystem)}`),
                 method: "GET",
                 headers: _headers,
-                queryParameters: Object.assign(Object.assign({}, _queryParams), requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams),
+                queryString: core.url
+                    .queryBuilder()
+                    .addMany(_queryParams)
+                    .mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams)
+                    .build(),
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
                 maxRetries: (_h = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.maxRetries) !== null && _h !== void 0 ? _h : (_j = this._options) === null || _j === void 0 ? void 0 : _j.maxRetries,
                 abortSignal: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.abortSignal,
@@ -356,7 +436,11 @@ class ConstrueClient {
                 url: core.url.join((_d = (_c = (yield core.Supplier.get(this._options.baseUrl))) !== null && _c !== void 0 ? _c : (yield core.Supplier.get(this._options.environment))) !== null && _d !== void 0 ? _d : environments.phenomlEnvironment.Default, `construe/codes/systems/${core.url.encodePathParam(codesystem)}`),
                 method: "DELETE",
                 headers: _headers,
-                queryParameters: Object.assign(Object.assign({}, _queryParams), requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams),
+                queryString: core.url
+                    .queryBuilder()
+                    .addMany(_queryParams)
+                    .mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams)
+                    .build(),
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
                 maxRetries: (_h = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.maxRetries) !== null && _h !== void 0 ? _h : (_j = this._options) === null || _j === void 0 ? void 0 : _j.maxRetries,
                 abortSignal: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.abortSignal,
@@ -430,7 +514,11 @@ class ConstrueClient {
                 url: core.url.join((_d = (_c = (yield core.Supplier.get(this._options.baseUrl))) !== null && _c !== void 0 ? _c : (yield core.Supplier.get(this._options.environment))) !== null && _d !== void 0 ? _d : environments.phenomlEnvironment.Default, `construe/codes/systems/${core.url.encodePathParam(codesystem)}/export`),
                 method: "GET",
                 headers: _headers,
-                queryParameters: Object.assign(Object.assign({}, _queryParams), requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams),
+                queryString: core.url
+                    .queryBuilder()
+                    .addMany(_queryParams)
+                    .mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams)
+                    .build(),
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
                 maxRetries: (_h = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.maxRetries) !== null && _h !== void 0 ? _h : (_j = this._options) === null || _j === void 0 ? void 0 : _j.maxRetries,
                 abortSignal: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.abortSignal,
@@ -509,7 +597,11 @@ class ConstrueClient {
                 url: core.url.join((_d = (_c = (yield core.Supplier.get(this._options.baseUrl))) !== null && _c !== void 0 ? _c : (yield core.Supplier.get(this._options.environment))) !== null && _d !== void 0 ? _d : environments.phenomlEnvironment.Default, `construe/codes/${core.url.encodePathParam(codesystem)}`),
                 method: "GET",
                 headers: _headers,
-                queryParameters: Object.assign(Object.assign({}, _queryParams), requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams),
+                queryString: core.url
+                    .queryBuilder()
+                    .addMany(_queryParams)
+                    .mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams)
+                    .build(),
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
                 maxRetries: (_h = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.maxRetries) !== null && _h !== void 0 ? _h : (_j = this._options) === null || _j === void 0 ? void 0 : _j.maxRetries,
                 abortSignal: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.abortSignal,
@@ -546,7 +638,8 @@ class ConstrueClient {
      * Usage of CPT is subject to AMA requirements: see PhenoML Terms of Service.
      *
      * @param {string} codesystem - Code system name
-     * @param {string} codeID - The code identifier
+     * @param {string} codeID - The code identifier. ICD-10-CM codes are stored without their
+     *                          cosmetic dot (use "E1165", not "E11.65").
      * @param {phenoml.construe.GetConstrueCodesCodesystemCodeIdRequest} request
      * @param {ConstrueClient.RequestOptions} requestOptions - Request-specific configuration.
      *
@@ -556,7 +649,7 @@ class ConstrueClient {
      * @throws {@link phenoml.construe.InternalServerError}
      *
      * @example
-     *     await client.construe.getASpecificCode("ICD-10-CM", "E11.65", {
+     *     await client.construe.getASpecificCode("ICD-10-CM", "E1165", {
      *         version: "version"
      *     })
      */
@@ -576,7 +669,11 @@ class ConstrueClient {
                 url: core.url.join((_d = (_c = (yield core.Supplier.get(this._options.baseUrl))) !== null && _c !== void 0 ? _c : (yield core.Supplier.get(this._options.environment))) !== null && _d !== void 0 ? _d : environments.phenomlEnvironment.Default, `construe/codes/${core.url.encodePathParam(codesystem)}/${core.url.encodePathParam(codeID)}`),
                 method: "GET",
                 headers: _headers,
-                queryParameters: Object.assign(Object.assign({}, _queryParams), requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams),
+                queryString: core.url
+                    .queryBuilder()
+                    .addMany(_queryParams)
+                    .mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams)
+                    .build(),
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
                 maxRetries: (_h = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.maxRetries) !== null && _h !== void 0 ? _h : (_j = this._options) === null || _j === void 0 ? void 0 : _j.maxRetries,
                 abortSignal: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.abortSignal,
@@ -662,7 +759,11 @@ class ConstrueClient {
                 url: core.url.join((_d = (_c = (yield core.Supplier.get(this._options.baseUrl))) !== null && _c !== void 0 ? _c : (yield core.Supplier.get(this._options.environment))) !== null && _d !== void 0 ? _d : environments.phenomlEnvironment.Default, `construe/codes/${core.url.encodePathParam(codesystem)}/search/semantic`),
                 method: "GET",
                 headers: _headers,
-                queryParameters: Object.assign(Object.assign({}, _queryParams), requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams),
+                queryString: core.url
+                    .queryBuilder()
+                    .addMany(_queryParams)
+                    .mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams)
+                    .build(),
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
                 maxRetries: (_h = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.maxRetries) !== null && _h !== void 0 ? _h : (_j = this._options) === null || _j === void 0 ? void 0 : _j.maxRetries,
                 abortSignal: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.abortSignal,
@@ -712,21 +813,28 @@ class ConstrueClient {
      *     await client.construe.submitFeedbackOnExtractionResults({
      *         text: "Patient has type 2 diabetes with hyperglycemia",
      *         received_result: {
-     *             system: {},
+     *             system: {
+     *                 name: "ICD-10-CM",
+     *                 version: "2025"
+     *             },
      *             codes: [{
-     *                     code: "195967001",
-     *                     description: "Asthma",
+     *                     code: "E11.9",
+     *                     description: "Type 2 diabetes mellitus without complications",
      *                     valid: true
      *                 }]
      *         },
      *         expected_result: {
-     *             system: {},
+     *             system: {
+     *                 name: "ICD-10-CM",
+     *                 version: "2025"
+     *             },
      *             codes: [{
-     *                     code: "195967001",
-     *                     description: "Asthma",
+     *                     code: "E11.65",
+     *                     description: "Type 2 diabetes mellitus with hyperglycemia",
      *                     valid: true
      *                 }]
-     *         }
+     *         },
+     *         detail: "Expected code E11.65 because the text mentions hyperglycemia"
      *     })
      */
     submitFeedbackOnExtractionResults(request, requestOptions) {
@@ -742,7 +850,7 @@ class ConstrueClient {
                 method: "POST",
                 headers: _headers,
                 contentType: "application/json",
-                queryParameters: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams,
+                queryString: core.url.queryBuilder().mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams).build(),
                 requestType: "json",
                 body: request,
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
@@ -836,7 +944,11 @@ class ConstrueClient {
                 url: core.url.join((_d = (_c = (yield core.Supplier.get(this._options.baseUrl))) !== null && _c !== void 0 ? _c : (yield core.Supplier.get(this._options.environment))) !== null && _d !== void 0 ? _d : environments.phenomlEnvironment.Default, `construe/codes/${core.url.encodePathParam(codesystem)}/search/text`),
                 method: "GET",
                 headers: _headers,
-                queryParameters: Object.assign(Object.assign({}, _queryParams), requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams),
+                queryString: core.url
+                    .queryBuilder()
+                    .addMany(_queryParams)
+                    .mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams)
+                    .build(),
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
                 maxRetries: (_h = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.maxRetries) !== null && _h !== void 0 ? _h : (_j = this._options) === null || _j === void 0 ? void 0 : _j.maxRetries,
                 abortSignal: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.abortSignal,

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

@@ -2,7 +2,66 @@ import type * as phenoml from "../../../../index.js";
 /**
  * @example
  *     {
- *         text: "Patient is a 14-year-old female, previously healthy, who is here for evaluation of abnormal renal ultrasound with atrophic right kidney"
+ *         text: "Patient is a 14-year-old female, previously healthy, who is here for evaluation of abnormal renal ultrasound with atrophic right kidney.",
+ *         system: {
+ *             name: "ICD-10-CM",
+ *             version: "2025"
+ *         }
+ *     }
+ *
+ * @example
+ *     {
+ *         text: "45-year-old male presents with chest pain radiating to left arm, shortness of breath, and diaphoresis. ECG shows ST elevation in leads II, III, and aVF.",
+ *         system: {
+ *             name: "SNOMED_CT_US_LITE",
+ *             version: "20240901"
+ *         },
+ *         config: {
+ *             chunking_method: "sentences",
+ *             validation_method: "simple",
+ *             include_rationale: true,
+ *             include_citations: true
+ *         }
+ *     }
+ *
+ * @example
+ *     {
+ *         text: "Start Metformin 500mg twice daily for type 2 diabetes. Continue Lisinopril 10mg daily for hypertension. Add Atorvastatin 20mg at bedtime.",
+ *         system: {
+ *             name: "RXNORM",
+ *             version: "11042024"
+ *         },
+ *         config: {
+ *             validation_method: "medication_search",
+ *             include_rationale: true
+ *         }
+ *     }
+ *
+ * @example
+ *     {
+ *         text: "Patient diagnosed with Type 2 diabetes mellitus with diabetic chronic kidney disease, stage 3.",
+ *         system: {
+ *             name: "ICD-10-CM",
+ *             version: "2025"
+ *         },
+ *         config: {
+ *             validation_method: "simple",
+ *             include_ancestors: true
+ *         }
+ *     }
+ *
+ * @example
+ *     {
+ *         text: "5-year-old male with seizures, severe intellectual disability, microcephaly, and hypotonia.",
+ *         system: {
+ *             name: "HPO",
+ *             version: "2025"
+ *         },
+ *         config: {
+ *             chunking_method: "fasthpocr",
+ *             validation_method: "none",
+ *             include_rationale: false
+ *         }
  *     }
  */
 export interface ExtractRequest {

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

@@ -4,21 +4,28 @@ import type * as phenoml from "../../../../index.js";
  *     {
  *         text: "Patient has type 2 diabetes with hyperglycemia",
  *         received_result: {
- *             system: {},
+ *             system: {
+ *                 name: "ICD-10-CM",
+ *                 version: "2025"
+ *             },
  *             codes: [{
- *                     code: "195967001",
- *                     description: "Asthma",
+ *                     code: "E11.9",
+ *                     description: "Type 2 diabetes mellitus without complications",
  *                     valid: true
  *                 }]
  *         },
  *         expected_result: {
- *             system: {},
+ *             system: {
+ *                 name: "ICD-10-CM",
+ *                 version: "2025"
+ *             },
  *             codes: [{
- *                     code: "195967001",
- *                     description: "Asthma",
+ *                     code: "E11.65",
+ *                     description: "Type 2 diabetes mellitus with hyperglycemia",
  *                     valid: true
  *                 }]
- *         }
+ *         },
+ *         detail: "Expected code E11.65 because the text mentions hyperglycemia"
  *     }
  */
 export interface FeedbackRequest {

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

@@ -4,7 +4,24 @@ import type * as phenoml from "../../../../index.js";
  *     {
  *         name: "CUSTOM_CODES",
  *         version: "1.0",
- *         format: "csv"
+ *         format: "json",
+ *         codes: [{
+ *                 code: "X001",
+ *                 description: "Example custom code 1"
+ *             }, {
+ *                 code: "X002",
+ *                 description: "Example custom code 2"
+ *             }]
+ *     }
+ *
+ * @example
+ *     {
+ *         name: "CUSTOM_CODES",
+ *         version: "1.0",
+ *         format: "csv",
+ *         file: "Y29kZSxkZXNjcmlwdGlvbgpYMDAxLEV4YW1wbGUgY3VzdG9tIGNvZGUgMQo=",
+ *         code_col: "code",
+ *         desc_col: "description"
  *     }
  */
 export interface UploadRequest {

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

@@ -105,7 +105,11 @@ class FhirClient {
                 url: core.url.join((_d = (_c = (yield core.Supplier.get(this._options.baseUrl))) !== null && _c !== void 0 ? _c : (yield core.Supplier.get(this._options.environment))) !== null && _d !== void 0 ? _d : environments.phenomlEnvironment.Default, `fhir-provider/${core.url.encodePathParam(fhir_provider_id)}/fhir/${core.url.encodePathParam(fhir_path)}`),
                 method: "GET",
                 headers: _headers,
-                queryParameters: Object.assign(Object.assign({}, _queryParams), requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams),
+                queryString: core.url
+                    .queryBuilder()
+                    .addMany(_queryParams)
+                    .mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams)
+                    .build(),
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
                 maxRetries: (_h = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.maxRetries) !== null && _h !== void 0 ? _h : (_j = this._options) === null || _j === void 0 ? void 0 : _j.maxRetries,
                 abortSignal: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.abortSignal,
@@ -191,7 +195,7 @@ class FhirClient {
                 method: "POST",
                 headers: _headers,
                 contentType: "application/fhir+json",
-                queryParameters: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams,
+                queryString: core.url.queryBuilder().mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams).build(),
                 requestType: "json",
                 body: _body,
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
@@ -278,7 +282,7 @@ class FhirClient {
                 method: "PUT",
                 headers: _headers,
                 contentType: "application/fhir+json",
-                queryParameters: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams,
+                queryString: core.url.queryBuilder().mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams).build(),
                 requestType: "json",
                 body: _body,
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
@@ -361,7 +365,7 @@ class FhirClient {
                 url: core.url.join((_d = (_c = (yield core.Supplier.get(this._options.baseUrl))) !== null && _c !== void 0 ? _c : (yield core.Supplier.get(this._options.environment))) !== null && _d !== void 0 ? _d : environments.phenomlEnvironment.Default, `fhir-provider/${core.url.encodePathParam(fhir_provider_id)}/fhir/${core.url.encodePathParam(fhir_path)}`),
                 method: "DELETE",
                 headers: _headers,
-                queryParameters: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams,
+                queryString: core.url.queryBuilder().mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams).build(),
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
                 maxRetries: (_h = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.maxRetries) !== null && _h !== void 0 ? _h : (_j = this._options) === null || _j === void 0 ? void 0 : _j.maxRetries,
                 abortSignal: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.abortSignal,
@@ -506,7 +510,7 @@ class FhirClient {
                 method: "PATCH",
                 headers: _headers,
                 contentType: "application/json-patch+json",
-                queryParameters: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams,
+                queryString: core.url.queryBuilder().mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams).build(),
                 requestType: "json",
                 body: _body,
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,
@@ -620,7 +624,7 @@ class FhirClient {
                 method: "POST",
                 headers: _headers,
                 contentType: "application/fhir+json",
-                queryParameters: requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams,
+                queryString: core.url.queryBuilder().mergeAdditional(requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.queryParams).build(),
                 requestType: "json",
                 body: _body,
                 timeoutMs: ((_g = (_e = requestOptions === null || requestOptions === void 0 ? void 0 : requestOptions.timeoutInSeconds) !== null && _e !== void 0 ? _e : (_f = this._options) === null || _f === void 0 ? void 0 : _f.timeoutInSeconds) !== null && _g !== void 0 ? _g : 60) * 1000,