Feat/healthinsights snippets

sdk/healthinsights/health-insights-cancerprofiling-rest/README.md

@@ -58,44 +58,50 @@ The Cancer Profiling model allows you to infer cancer attributes such as tumor s
 
 - [Infer Cancer Profiling](#cancer_profiling)
 
-```typescript
-const apiKey = process.env["HEALTH_INSIGHTS_API_KEY"] || "";
-const endpoint = process.env["HEALTH_INSIGHTS_ENDPOINT"] || "";
+```ts snippet:ReadmeSampleInferCanerProfiling
+import { AzureKeyCredential } from "@azure/core-auth";
+import CancerProfilingRestClient, {
+  OncoPhenotypeData,
+  isUnexpected,
+  getLongRunningPoller,
+} from "@azure-rest/health-insights-cancerprofiling";
+
+const endpoint = "https://<your-endpoint>";
+const apiKey = "<your-api-key>";
 const credential = new AzureKeyCredential(apiKey);
 const client = CancerProfilingRestClient(endpoint, credential);
 
-// Define patient information and clinical documents for the request body
+// Define patient information and clinical documents
 const patientInfo = {
   sex: "FEMALE",
   birthDate: new Date("1979-10-08T00:00:00.000Z"), // Note: Months are zero-based (11 represents December)
 };
 
-const doc1 = "15.8.2021";
-("Jane Doe 091175-8967");
-("42 year old female, married with 3 children, works as a nurse. ");
-("Healthy, no medications taken on a regular basis.");
-("PMHx is significant for migraines with aura, uses Mirena for contraception.");
-("Smoking history of 10 pack years (has stopped and relapsed several times).");
-("She is in c/o 2 weeks of productive cough and shortness of breath.");
-("She has a fever of 37.8 and general weakness. ");
-("Denies night sweats and rash. She denies symptoms of rhinosinusitis, asthma, and heartburn. ");
-("On PE:");
-("GENERAL: mild pallor, no cyanosis. Regular breathing rate. ");
-("LUNGS: decreased breath sounds on the base of the right lung. Vesicular breathing.");
-(" No crackles, rales, and wheezes. Resonant percussion. ");
-("PLAN: ");
-("Will be referred for a chest x-ray. ");
-("======================================");
-("CXR showed mild nonspecific opacities in right lung base. ");
-("PLAN:");
-("Findings are suggestive of a working diagnosis of pneumonia. The patient is referred to a ");
-("follow-up CXR in 2 weeks. ");
+const doc1 = `15.8.2021
+Jane Doe 091175-8967
+42 year old female, married with 3 children, works as a nurse.
+Healthy, no medications taken on a regular basis.
+PMHx is significant for migraines with aura, uses Mirena for contraception.
+Smoking history of 10 pack years (has stopped and relapsed several times).
+She is in c/o 2 weeks of productive cough and shortness of breath.
+She has a fever of 37.8 and general weakness.
+Denies night sweats and rash. She denies symptoms of rhinosinusitis, asthma, and heartburn.
+On PE:
+GENERAL: mild pallor, no cyanosis. Regular breathing rate.
+LUNGS: decreased breath sounds on the base of the right lung. Vesicular breathing.
+No crackles, rales, and wheezes. Resonant percussion.
+PLAN:
+Will be referred for a chest x-ray.
+======================================
+CXR showed mild nonspecific opacities in right lung base.
+PLAN:
+Findings are suggestive of a working diagnosis of pneumonia. The patient is referred to a
+follow-up CXR in 2 weeks.`;
 
 const docContent = {
   sourceType: "INLINE",
   value: doc1,
 };
-
 const patientDoc1 = {
   type: "NOTE",
   id: "doc1",
@@ -105,76 +111,77 @@ const patientDoc1 = {
   createdDateTime: new Date("2021-15-08T00:00:00.000Z"),
 };
 
-const doc1 = `15.8.2021
-        Jane Doe 091175-8967
-        42 year old female, married with 3 children, works as a nurse. 
-        Healthy, no medications taken on a regular basis.
-        PMHx is significant for migraines with aura, uses Mirena for contraception.
-        Smoking history of 10 pack years (has stopped and relapsed several times).
-        She is in c/o 2 weeks of productive cough and shortness of breath.
-        She has a fever of 37.8 and general weakness. 
-        Denies night sweats and rash. She denies symptoms of rhinosinusitis, asthma, and heartburn. 
-        On PE:
-        GENERAL: mild pallor, no cyanosis. Regular breathing rate. 
-        LUNGS: decreased breath sounds on the base of the right lung. Vesicular breathing.
-         No crackles, rales, and wheezes. Resonant percussion. 
-        PLAN: 
-        Will be referred for a chest x-ray. 
-        ======================================
-        CXR showed mild nonspecific opacities in right lung base. 
-        PLAN:
-        Findings are suggestive of a working diagnosis of pneumonia. The patient is referred to a 
-        follow-up CXR in 2 weeks. `;
+// Define patientDoc2 and patientDoc3 similarly
+const doc2 = `Oncology Clinic
+20.10.2021
+Jane Doe 091175-8967
+42-year-old healthy female who works as a nurse in the ER of this hospital.
+First menstruation at 11 years old. First delivery- 27 years old. She has 3 children.
+Didn’t breastfeed.
+Contraception- Mirena.
+Smoking- 10 pack years.
+Mother- Belarusian. Father- Georgian.
+About 3 months prior to admission, she stated she had SOB and was febrile.
+She did a CXR as an outpatient which showed a finding in the base of the right lung-
+possibly an infiltrate.
+She was treated with antibiotics with partial response.
+6 weeks later a repeat CXR was performed- a few solid dense findings in the right lung.
+Therefore, she was referred for a PET-CT which demonstrated increased uptake in the right
+breast, lymph nodes on the right a few areas in the lungs and liver.
+On biopsy from the lesion in the right breast- triple negative adenocarcinoma. Genetic
+testing has not been done thus far.
+Genetic counseling- the patient denies a family history of breast, ovary, uterus,
+and prostate cancer. Her mother has chronic lymphocytic leukemia (CLL).
+She is planned to undergo genetic tests because the aggressive course of the disease,
+and her young age.
+Impression:
+Stage 4 triple negative breast adenocarcinoma.
+Could benefit from biological therapy.
+Different treatment options were explained- the patient wants to get a second opinion.`;
 
-const docContent = {
+const docContent2 = {
   sourceType: "INLINE",
-  value: doc1,
+  value: doc2,
 };
 
-const patientDoc1 = {
+const patientDoc2 = {
   type: "NOTE",
-  id: "doc1",
-  content: docContent,
-  clinicalType: "IMAGING",
+  id: "doc2",
+  content: docContent2,
+  clinicalType: "PATHOLOGY",
   language: "en",
-  createdDateTime: new Date("2021-15-08T00:00:00.000Z"),
+  createdDateTime: new Date("2021-10-20T00:00:00.000Z"),
 };
 
-const doc2 = `Oncology Clinic 
-       20.10.2021
-       Jane Doe 091175-8967
-       42-year-old healthy female who works as a nurse in the ER of this hospital. 
-       First menstruation at 11 years old. First delivery- 27 years old. She has 3 children.
-       Didn’t breastfeed. 
-       Contraception- Mirena.
-       Smoking- 10 pack years. 
-       Mother- Belarusian. Father- Georgian. 
-       About 3 months prior to admission, she stated she had SOB and was febrile. 
-       She did a CXR as an outpatient which showed a finding in the base of the right lung- 
-       possibly an infiltrate.
-       She was treated with antibiotics with partial response. 
-       6 weeks later a repeat CXR was performed- a few solid dense findings in the right lung. 
-       Therefore, she was referred for a PET-CT which demonstrated increased uptake in the right 
-       breast, lymph nodes on the right a few areas in the lungs and liver. 
-       On biopsy from the lesion in the right breast- triple negative adenocarcinoma. Genetic 
-       testing has not been done thus far. 
-       Genetic counseling- the patient denies a family history of breast, ovary, uterus, 
-       and prostate cancer. Her mother has chronic lymphocytic leukemia (CLL). 
-       She is planned to undergo genetic tests because the aggressive course of the disease, 
-       and her young age. 
-       Impression:
-       Stage 4 triple negative breast adenocarcinoma. 
-       Could benefit from biological therapy. 
-       Different treatment options were explained- the patient wants to get a second opinion.`;
-
-const docContent2 = {
+const doc3 = `PATHOLOGY REPORT
+                          Clinical Information
+Ultrasound-guided biopsy; A. 18 mm mass; most likely diagnosis based on imaging:  IDC
+                              Diagnosis
+A.  BREAST, LEFT AT 2:00 4 CM FN; ULTRASOUND-GUIDED NEEDLE CORE BIOPSIES:
+- Invasive carcinoma of no special type (invasive ductal carcinoma), grade 1
+Nottingham histologic grade:  1/3 (tubules 2; nuclear grade 2; mitotic rate 1;
+total score; 5/9)
+Fragments involved by invasive carcinoma:  2
+Largest measurement of invasive carcinoma on a single fragment:  7 mm
+Ductal carcinoma in situ (DCIS):  Present
+Architectural pattern:  Cribriform
+Nuclear grade:  2-
+                  -intermediate
+Necrosis:  Not identified
+Fragments involved by DCIS:  1
+Largest measurement of DCIS on a single fragment:  Span 2 mm
+Microcalcifications:  Present in benign breast tissue and invasive carcinoma
+Blocks with invasive carcinoma:  A1
+Special studies: Pending`;
+
+const docContent3 = {
   sourceType: "INLINE",
-  value: doc2,
+  value: doc3,
 };
 
-const patientDoc2 = {
+const patientDoc3 = {
   type: "NOTE",
-  id: "doc2",
+  id: "doc3",
   content: docContent3,
   clinicalType: "PATHOLOGY",
   language: "en",
@@ -184,7 +191,7 @@ const patientDoc2 = {
 const patient1 = {
   id: "patient_id",
   info: patientInfo,
-  data: [patientDoc1, patientDoc2],
+  data: [patientDoc1, patientDoc2, patientDoc3],
 };
 
 const cancerProfilingData: OncoPhenotypeData = {
@@ -199,41 +206,34 @@ const parameters = {
 // Initiate cancer profiling job and retrieve results
 const initialResponse = await client.path("/oncophenotype/jobs").post(parameters);
 if (isUnexpected(initialResponse)) {
-  throw initialResponse;
+  throw initialResponse.body.error;
 }
+
 const poller = await getLongRunningPoller(client, initialResponse);
 const cancerProfilingResult = await poller.pollUntilDone();
 if (isUnexpected(cancerProfilingResult)) {
-  throw cancerProfilingResult;
+  throw cancerProfilingResult.body.error;
 }
+
 const resultBody = cancerProfilingResult.body;
 // Print the inference results for a patient's cancer attributes
-if (cancerProfilingResult.status === "succeeded") {
-  const results = cancerProfilingResult.results;
-  if (results) {
-    for (const patientResult of results.patients) {
-      console.log(`Inferences of Patient ${patientResult.id}`);
-      for (const { type, value, confidenceScore, evidence } of patientResult.inferences) {
-        console.log(
-          `Clinical Type: ${String(type)} Value: ${value}, ConfidenceScore: ${confidenceScore}`,
-        );
-        for (const { patientDataEvidence } of evidence || []) {
-          if (patientDataEvidence) {
-            console.log(
-              `Evidence: ${patientDataEvidence.id} ${patientDataEvidence.offset} ${patientDataEvidence.length} ${patientDataEvidence.text}`,
-            );
-          }
+const results = resultBody.results;
+if (results) {
+  for (const patientResult of results.patients) {
+    console.log(`Inferences of Patient ${patientResult.id}`);
+    for (const { type, value, confidenceScore, evidence } of patientResult.inferences) {
+      console.log(
+        `Clinical Type: ${String(type)} Value: ${value}, ConfidenceScore: ${confidenceScore}`,
+      );
+      for (const { patientDataEvidence } of evidence || []) {
+        if (patientDataEvidence) {
+          console.log(
+            `Evidence: ${patientDataEvidence.id} ${patientDataEvidence.offset} ${patientDataEvidence.length} ${patientDataEvidence.text}`,
+          );
         }
       }
     }
   }
-} else {
-  const errors = cancerProfilingResult.errors;
-  if (errors) {
-    for (const error of errors) {
-      console.log(error.code, ":", error.message);
-    }
-  }
 }
 ```
 
@@ -243,8 +243,8 @@ if (cancerProfilingResult.status === "succeeded") {
 
 Enabling logging may help uncover useful information about failures. In order to see a log of HTTP requests and responses, set the `AZURE_LOG_LEVEL` environment variable to `info`. Alternatively, logging can be enabled at runtime by calling `setLogLevel` in the `@azure/logger`:
 
-```javascript
-const { setLogLevel } = require("@azure/logger");
+```ts snippet:SetLogLevel
+import { setLogLevel } from "@azure/logger";
 
 setLogLevel("info");
 ```

sdk/healthinsights/health-insights-cancerprofiling-rest/package.json

@@ -53,7 +53,7 @@
     "unit-test": "npm run unit-test:node && npm run unit-test:browser",
     "unit-test:browser": "npm run clean && dev-tool run build-package && dev-tool run build-test && dev-tool run test:vitest --browser",
     "unit-test:node": "dev-tool run test:vitest",
-    "update-snippets": "echo skipped"
+    "update-snippets": "dev-tool run update-snippets"
   },
   "sideEffects": false,
   "autoPublish": false,
@@ -62,7 +62,7 @@
     "@azure/abort-controller": "^2.1.2",
     "@azure/core-auth": "^1.9.0",
     "@azure/core-lro": "^2.7.2",
-    "@azure/core-rest-pipeline": "^1.18.0",
+    "@azure/core-rest-pipeline": "^1.19.0",
     "@azure/logger": "^1.1.4",
     "tslib": "^2.8.1"
   },
@@ -72,16 +72,16 @@
     "@azure-tools/test-utils-vitest": "^1.0.0",
     "@azure/dev-tool": "^1.0.0",
     "@azure/eslint-plugin-azure-sdk": "^3.0.0",
-    "@azure/identity": "^4.0.1",
+    "@azure/identity": "^4.7.0",
     "@types/node": "^18.0.0",
-    "@vitest/browser": "^3.0.3",
-    "@vitest/coverage-istanbul": "^3.0.3",
+    "@vitest/browser": "^3.0.6",
+    "@vitest/coverage-istanbul": "^3.0.6",
     "autorest": "latest",
     "dotenv": "^16.0.0",
     "eslint": "^9.9.0",
-    "playwright": "^1.49.0",
+    "playwright": "^1.50.1",
     "typescript": "~5.7.2",
-    "vitest": "^3.0.3"
+    "vitest": "^3.0.6"
   },
   "homepage": "https://github.com/Azure/azure-sdk-for-js/tree/main/sdk/healthinsights/health-insights-cancerprofiling-rest/README.md",
   "//metadata": {
@@ -94,7 +94,7 @@
   },
   "browser": "./dist/browser/index.js",
   "//sampleConfiguration": {
-    "productName": "HealthInsightsCancerprifiling",
+    "productName": "HealthInsightsCancerprofiling",
     "productSlugs": [
       "azure"
     ],
@@ -103,6 +103,7 @@
   },
   "type": "module",
   "tshy": {
+    "project": "./tsconfig.src.json",
     "exports": {
       "./package.json": "./package.json",
       ".": "./src/index.ts"
@@ -115,8 +116,7 @@
       "browser",
       "react-native"
     ],
-    "selfLink": false,
-    "project": "./tsconfig.src.json"
+    "selfLink": false
   },
   "exports": {
     "./package.json": "./package.json",
@@ -138,5 +138,6 @@
         "default": "./dist/commonjs/index.js"
       }
     }
-  }
+  },
+  "react-native": "./dist/react-native/index.js"
 }

sdk/healthinsights/health-insights-cancerprofiling-rest/samples/v1-beta/typescript/src/sample_infer_cancer_profiling.ts

@@ -10,17 +10,14 @@
 
 import {AzureKeyCredential} from "@azure/core-auth";
 
-import * as dotenv from "dotenv";
+import "dotenv/config";
 import CancerProfilingRestClient, {
     CreateJobParameters,
     getLongRunningPoller,
     isUnexpected,
     OncoPhenotypeData,
     OncoPhenotypeResultOutput
-} from "../src";
-
-dotenv.config();
-
+} from "../src/index.js";
 // You will need to set this environment variables or edit the following values
 const endpoint = process.env["HEALTH_INSIGHTS_ENDPOINT"] || "";
 const apiKey = process.env["HEALTH_INSIGHTS_API_KEY"] || "";
@@ -188,7 +185,7 @@ function createRequestBody(): CreateJobParameters {
     };
 
 }
-export async function main() {
+export async function main(): Promise<void> {
     const credential = new AzureKeyCredential(apiKey);
     const client = CancerProfilingRestClient(endpoint, credential);
     // Create body request for cancer profiling