Add Healthcare API snippets. (#1612)

* Add Healthcare API DICOMweb search studies by tag

* Use client library.

* Fix FhirStoreTests failures

* Remove unnecessary .dcm file and variables.

* Fix DicomStoreTests failures

* Make bucket name in tests an environment variable.

* Make bucket name in tests an environment variable.

* Fix lint, make Storage bucket hard-coded again

Author: noerog

healthcare/v1beta1/src/main/java/snippets/healthcare/dicom/DicomWebSearchStudies.java

@@ -0,0 +1,82 @@
+/*
+ * Copyright 2019 Google LLC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package snippets.healthcare.dicom;
+
+// [START healthcare_dicomweb_search_studies]
+import com.google.api.client.googleapis.auth.oauth2.GoogleCredential;
+import com.google.api.client.http.HttpRequestInitializer;
+import com.google.api.client.http.HttpResponse;
+import com.google.api.client.http.javanet.NetHttpTransport;
+import com.google.api.client.json.JsonFactory;
+import com.google.api.client.json.jackson2.JacksonFactory;
+import com.google.api.services.healthcare.v1beta1.CloudHealthcare;
+import com.google.api.services.healthcare.v1beta1.CloudHealthcare.Projects.Locations.Datasets.DicomStores;
+import com.google.api.services.healthcare.v1beta1.CloudHealthcareScopes;
+import java.io.IOException;
+import java.util.Collections;
+
+public class DicomWebSearchStudies {
+  private static final JsonFactory JSON_FACTORY = new JacksonFactory();
+  private static final NetHttpTransport HTTP_TRANSPORT = new NetHttpTransport();
+
+  public static void dicomWebSearchStudies(String dicomStoreName) throws IOException {
+    // String dicomStoreName =
+    //    String.format(
+    //        DICOM_NAME, "your-project-id", "your-region-id", "your-dataset-id", "your-dicom-id");
+
+    // Initialize the client, which will be used to interact with the service.
+    CloudHealthcare client = createClient();
+
+    DicomStores.SearchForStudies request =
+        client
+            .projects()
+            .locations()
+            .datasets()
+            .dicomStores()
+            .searchForStudies(dicomStoreName, "studies")
+            // Refine your search by appending DICOM tags to the
+            // request in the form of query parameters. This sample
+            // searches for studies containing a patient's name.
+            .set("PatientName", "Sally Zhang");
+
+    // Execute the request and process the results.
+    HttpResponse response = request.executeUnparsed();
+    System.out.println("Studies found: \n" + response.toString());
+  }
+
+  private static CloudHealthcare createClient() throws IOException {
+    // Use Application Default Credentials (ADC) to authenticate the requests
+    // For more information see https://cloud.google.com/docs/authentication/production
+    GoogleCredential credential =
+        GoogleCredential.getApplicationDefault(HTTP_TRANSPORT, JSON_FACTORY)
+            .createScoped(Collections.singleton(CloudHealthcareScopes.CLOUD_PLATFORM));
+
+    // Create a HttpRequestInitializer, which will provide a baseline configuration to all requests.
+    HttpRequestInitializer requestInitializer =
+        request -> {
+          credential.initialize(request);
+          request.setConnectTimeout(60000); // 1 minute connect timeout
+          request.setReadTimeout(60000); // 1 minute read timeout
+        };
+
+    // Build the client for interacting with the service.
+    return new CloudHealthcare.Builder(HTTP_TRANSPORT, JSON_FACTORY, requestInitializer)
+        .setApplicationName("your-application-name")
+        .build();
+  }
+}
+// [END healthcare_dicomweb_search_studies]

healthcare/v1beta1/src/test/java/snippets/healthcare/DicomStoreTests.java

@@ -165,7 +165,7 @@ public void test_DicomStoreExport() throws IOException {
   @Test
   public void test_DicomStoreImport() throws IOException {
     String gcsPath =
-        String.format("gs://%s/%s", GCLOUD_BUCKET_NAME, "IM-0002-0001-JPEG-BASELINE.dcm");
+        String.format("gs://%s/%s/%s", GCLOUD_BUCKET_NAME, "healthcare-api", "000009.dcm");
     DicomStoreImport.dicomStoreImport(dicomStoreName, gcsPath);
 
     String output = bout.toString();

healthcare/v1beta1/src/test/java/snippets/healthcare/DicomWebTests.java

@@ -27,7 +27,6 @@
 import java.io.PrintStream;
 import java.net.URISyntaxException;
 import java.util.UUID;
-
 import org.junit.After;
 import org.junit.AfterClass;
 import org.junit.Before;
@@ -43,6 +42,7 @@
 import snippets.healthcare.dicom.DicomWebRetrieveRendered;
 import snippets.healthcare.dicom.DicomWebRetrieveStudy;
 import snippets.healthcare.dicom.DicomWebSearchForInstances;
+import snippets.healthcare.dicom.DicomWebSearchStudies;
 import snippets.healthcare.dicom.DicomWebStoreInstance;
 
 @RunWith(JUnit4.class)
@@ -57,8 +57,8 @@ public class DicomWebTests {
   private static String studyId = "2.25.330012077234033941963257891139480825153";
   private static String seriesId = "2.25.143186483950719304925806365081717734297";
   private static String instanceId = "2.25.195151962645072062560826889007364152748";
-  private static String dicomWebInstancePath = String.format(
-      "studies/%s/series/%s/instances/%s", studyId, seriesId, instanceId);
+  private static String dicomWebInstancePath =
+      String.format("studies/%s/series/%s/instances/%s", studyId, seriesId, instanceId);
   private static String dicomWebRenderedPath = dicomWebInstancePath + "/rendered";
 
   private static String instanceOutput = "instance.dcm";
@@ -85,11 +85,8 @@ public static void checkRequirements() {
   @BeforeClass
   public static void setUp() throws IOException {
     String datasetId = "dataset-" + UUID.randomUUID().toString().replaceAll("-", "_");
-    datasetName = String.format(
-        "projects/%s/locations/%s/datasets/%s",
-        PROJECT_ID,
-        REGION_ID,
-        datasetId);
+    datasetName =
+        String.format("projects/%s/locations/%s/datasets/%s", PROJECT_ID, REGION_ID, datasetId);
     DatasetCreate.datasetCreate(PROJECT_ID, REGION_ID, datasetId);
 
     String dicomStoreId = "dicom-" + UUID.randomUUID().toString().replaceAll("-", "_");
@@ -109,8 +106,7 @@ public void beforeTest() throws IOException, URISyntaxException {
     System.setOut(new PrintStream(bout));
 
     // Store before each test so it is always available.
-    DicomWebStoreInstance.dicomWebStoreInstance(
-        dicomStoreName, "src/test/resources/jpeg_text.dcm");
+    DicomWebStoreInstance.dicomWebStoreInstance(dicomStoreName, "src/test/resources/jpeg_text.dcm");
 
     bout = new ByteArrayOutputStream();
     System.setOut(new PrintStream(bout));
@@ -124,8 +120,7 @@ public void tearDown() {
 
   @Test
   public void test_DicomWebStoreInstance() throws Exception {
-    DicomWebStoreInstance.dicomWebStoreInstance(
-        dicomStoreName, "src/test/resources/jpeg_text.dcm");
+    DicomWebStoreInstance.dicomWebStoreInstance(dicomStoreName, "src/test/resources/jpeg_text.dcm");
 
     String output = bout.toString();
     assertThat(output, containsString("DICOM instance stored:"));
@@ -138,6 +133,13 @@ public void test_DicomWebSearchInstances() throws Exception {
     assertThat(output, containsString("Dicom store instances found:"));
   }
 
+  @Test
+  public void test_DicomWebSearchStudies() throws Exception {
+    DicomWebSearchStudies.dicomWebSearchStudies(dicomStoreName);
+    String output = bout.toString();
+    assertThat(output, containsString("Studies found:"));
+  }
+
   @Test
   public void test_DicomWebRetrieveStudy() throws Exception {
     DicomWebRetrieveStudy.dicomWebRetrieveStudy(dicomStoreName, studyId);
@@ -179,4 +181,3 @@ public void test_DicomWebDeleteStudy() throws IOException {
     assertThat(output, containsString("DICOM study deleted."));
   }
 }
-

healthcare/v1beta1/src/test/java/snippets/healthcare/FhirStoreTests.java

@@ -53,9 +53,6 @@ public class FhirStoreTests {
   private static final String GCLOUD_BUCKET_NAME = "java-docs-samples-testing";
   private static final String GCLOUD_PUBSUB_TOPIC = System.getenv("GCLOUD_PUBSUB_TOPIC");
 
-  private static String storageFileName = "IM-0002-0001-JPEG-BASELINE.dcm";
-  private static String gcsFileName = GCLOUD_BUCKET_NAME + "/" + storageFileName;
-
   private static String datasetName;
 
   private static String fhirStoreName;
@@ -177,7 +174,9 @@ public void test_FhirStoreExport() throws Exception {
 
   @Test
   public void test_FhirStoreImport() throws Exception {
-    FhirStoreImport.fhirStoreImport(fhirStoreName, "gs://" + gcsFileName);
+    FhirStoreImport.fhirStoreImport(
+        fhirStoreName,
+        "gs://" + GCLOUD_BUCKET_NAME + "/healthcare-api/Patient.json");
 
     String output = bout.toString();
     assertThat(output, containsString("FHIR store import complete:"));