Migrate common module to Junit5

pipelines/batch/src/main/java/com/google/fhir/analytics/FhirEtl.java

@@ -514,8 +514,12 @@ static List<Pipeline> setupAndBuildPipelines(
   }
 
   public static void main(String[] args)
-      throws IOException, SQLException, ViewDefinitionException, ProfileException,
-          ExecutionException, InterruptedException {
+      throws IOException,
+          SQLException,
+          ViewDefinitionException,
+          ProfileException,
+          ExecutionException,
+          InterruptedException {
 
     AvroConversionUtil.initializeAvroConverters();
 

pipelines/batch/src/test/java/com/google/fhir/analytics/ConvertResourceFnTest.java

@@ -71,8 +71,12 @@ public void setup() throws SQLException, ProfileException {
 
   @Test
   public void testProcessPatientResource_withoutForcedId()
-      throws IOException, java.text.ParseException, SQLException, PropertyVetoException,
-          ViewApplicationException, ProfileException {
+      throws IOException,
+          java.text.ParseException,
+          SQLException,
+          PropertyVetoException,
+          ViewApplicationException,
+          ProfileException {
     String[] args = {"--outputParquetPath=SOME_PATH"};
     setUp(args);
     String patientResourceStr =
@@ -96,8 +100,12 @@ public void testProcessPatientResource_withoutForcedId()
 
   @Test
   public void testProcessPatientResource_withForcedId()
-      throws IOException, java.text.ParseException, SQLException, PropertyVetoException,
-          ViewApplicationException, ProfileException {
+      throws IOException,
+          java.text.ParseException,
+          SQLException,
+          PropertyVetoException,
+          ViewApplicationException,
+          ProfileException {
     String[] args = {"--outputParquetPath=SOME_PATH"};
     setUp(args);
     String patientResourceStr =
@@ -127,8 +135,12 @@ public void testProcessPatientResource_withForcedId()
 
   @Test
   public void testProcessDeletedPatientResourceFullMode()
-      throws SQLException, IOException, ParseException, PropertyVetoException,
-          ViewApplicationException, ProfileException {
+      throws SQLException,
+          IOException,
+          ParseException,
+          PropertyVetoException,
+          ViewApplicationException,
+          ProfileException {
     String[] args = {"--outputParquetPath=SOME_PATH", "--since="};
     setUp(args);
     // Deleted Patient resource
@@ -142,8 +154,12 @@ public void testProcessDeletedPatientResourceFullMode()
 
   @Test
   public void testProcessDeletedPatientResourceIncrementalMode()
-      throws SQLException, IOException, ParseException, PropertyVetoException,
-          ViewApplicationException, ProfileException {
+      throws SQLException,
+          IOException,
+          ParseException,
+          PropertyVetoException,
+          ViewApplicationException,
+          ProfileException {
     String[] args = {"--outputParquetPath=SOME_PATH", "--since=NON-EMPTY"};
     setUp(args);
     // Deleted Patient resource
@@ -170,8 +186,12 @@ public void testProcessDeletedPatientResourceIncrementalMode()
 
   @Test
   public void testResourceMetaTags()
-      throws IOException, java.text.ParseException, SQLException, PropertyVetoException,
-          ViewApplicationException, ProfileException {
+      throws IOException,
+          java.text.ParseException,
+          SQLException,
+          PropertyVetoException,
+          ViewApplicationException,
+          ProfileException {
     String[] args = {"--outputParquetPath=SOME_PATH", "--since="};
     setUp(args);
     String patientResourceStr =

pipelines/common/pom.xml

@@ -251,6 +251,19 @@
       <artifactId>beam-sdks-java-io-google-cloud-platform</artifactId>
       <version>${beam.version}</version>
     </dependency>
+    <dependency>
+      <groupId>org.junit.jupiter</groupId>
+      <artifactId>junit-jupiter-api</artifactId>
+      <version>5.11.0</version>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.mockito</groupId>
+      <artifactId>mockito-junit-jupiter</artifactId>
+      <version>5.13.0</version>
+      <scope>test</scope>
+    </dependency>
   </dependencies>
 
+
 </project>

pipelines/common/src/test/java/com/google/fhir/analytics/AvroConversionUtilTest.java

@@ -45,19 +45,19 @@
 import org.hl7.fhir.r4.model.Observation;
 import org.hl7.fhir.r4.model.Patient;
 import org.hl7.fhir.r4.model.Resource;
-import org.junit.Before;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.mockito.junit.MockitoJUnitRunner;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.junit.jupiter.MockitoExtension;
 
-@RunWith(MockitoJUnitRunner.class)
+@ExtendWith(MockitoExtension.class)
 public class AvroConversionUtilTest {
   private String patientBundle;
   private String observationBundle;
   private String usCoreProfilesStructureDefinitionsPath;
   public static final String BASE_PATIENT = "http://hl7.org/fhir/StructureDefinition/Patient";
 
-  @Before
+  @BeforeEach
   public void setup()
       throws IOException, ClassNotFoundException, URISyntaxException, ProfileException {
     AvroConversionUtil.initializeAvroConverters();

pipelines/common/src/test/java/com/google/fhir/analytics/FetchUtilTest.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2023 Google LLC
+ * Copyright 2020-2024 Google LLC
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -26,14 +26,14 @@
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.impl.RestfulClientFactory;
 import org.hl7.fhir.r4.model.Patient;
-import org.junit.Before;
-import org.junit.Test;
-import org.junit.runner.RunWith;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
 import org.mockito.Answers;
 import org.mockito.Mock;
-import org.mockito.junit.MockitoJUnitRunner;
+import org.mockito.junit.jupiter.MockitoExtension;
 
-@RunWith(MockitoJUnitRunner.class)
+@ExtendWith(MockitoExtension.class)
 public class FetchUtilTest {
 
   private static final String SOURCE_FHIR_URL = "someurl";
@@ -49,7 +49,7 @@ public class FetchUtilTest {
 
   FetchUtil fetchUtil;
 
-  @Before
+  @BeforeEach
   public void setUp() throws Exception {
     fetchUtil =
         new FetchUtil(

pipelines/common/src/test/java/com/google/fhir/analytics/FhirStoreUtilTest.java

@@ -32,15 +32,15 @@
 import org.hamcrest.Matchers;
 import org.hl7.fhir.r4.model.Bundle;
 import org.hl7.fhir.r4.model.Patient;
-import org.junit.Before;
-import org.junit.Test;
-import org.junit.runner.RunWith;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
 import org.mockito.Answers;
 import org.mockito.ArgumentMatchers;
 import org.mockito.Mock;
-import org.mockito.junit.MockitoJUnitRunner;
+import org.mockito.junit.jupiter.MockitoExtension;
 
-@RunWith(MockitoJUnitRunner.class)
+@ExtendWith(MockitoExtension.class)
 public class FhirStoreUtilTest {
 
   @Mock(answer = Answers.RETURNS_DEEP_STUBS)
@@ -61,7 +61,7 @@ public class FhirStoreUtilTest {
 
   private Bundle patientResponseBundle;
 
-  @Before
+  @BeforeEach
   public void setup() throws IOException {
     IParser jsonParser = FhirContext.forR4().newJsonParser();
 
@@ -82,10 +82,13 @@ public void setup() throws IOException {
     patient = (Patient) patientBundle.getEntryFirstRep().getResource();
 
     when(clientFactory.newGenericClient(sinkUrl)).thenReturn(client);
-    when(client.update().resource(patient).withId(patient.getId()).encodedJson()).thenReturn(iexec);
-    when(client.transaction().withBundle(ArgumentMatchers.any(Bundle.class)).execute())
+    lenient()
+        .when(client.update().resource(patient).withId(patient.getId()).encodedJson())
+        .thenReturn(iexec);
+    lenient()
+        .when(client.transaction().withBundle(ArgumentMatchers.any(Bundle.class)).execute())
         .thenReturn(patientResponseBundle);
-    doReturn(outcome).when(iexec).execute();
+    lenient().doReturn(outcome).when(iexec).execute();
 
     fhirStoreUtil = FhirStoreUtil.createFhirStoreUtil(sinkUrl, clientFactory);
   }

pipelines/common/src/test/java/com/google/fhir/analytics/GZipUtilTest.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2020-2023 Google LLC
+ * Copyright 2020-2024 Google LLC
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -24,11 +24,11 @@
 import java.nio.charset.StandardCharsets;
 import java.util.zip.GZIPOutputStream;
 import org.apache.commons.io.IOUtils;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.mockito.junit.MockitoJUnitRunner;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.extension.ExtendWith;
+import org.mockito.junit.jupiter.MockitoExtension;
 
-@RunWith(MockitoJUnitRunner.class)
+@ExtendWith(MockitoExtension.class)
 public class GZipUtilTest {
 
   @Test

pipelines/common/src/test/java/com/google/fhir/analytics/GcsDwhFilesTest.java

@@ -50,10 +50,10 @@
 import org.apache.beam.sdk.options.PipelineOptionsFactory;
 import org.apache.beam.sdk.util.MimeTypes;
 import org.checkerframework.checker.nullness.qual.Nullable;
-import org.junit.After;
-import org.junit.Assert;
-import org.junit.Before;
-import org.junit.Test;
+import org.junit.jupiter.api.AfterEach;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
 import org.mockito.Mock;
 import org.mockito.Mockito;
 import org.mockito.MockitoAnnotations;
@@ -64,15 +64,15 @@ public class GcsDwhFilesTest {
   @Mock private GcsUtil mockGcsUtil;
   private AutoCloseable closeable;
 
-  @Before
+  @BeforeEach
   public void setUp() {
     closeable = MockitoAnnotations.openMocks(this);
     GcsOptions gcsOptions = PipelineOptionsFactory.as(GcsOptions.class);
     gcsOptions.setGcsUtil(mockGcsUtil);
     FileSystems.setDefaultPipelineOptions(gcsOptions);
   }
 
-  @After
+  @AfterEach
   public void closeService() throws Exception {
     closeable.close();
   }
@@ -176,7 +176,7 @@ public void writeTimestampFile_FileAlreadyExists_ThrowsError() throws IOExceptio
     Mockito.when(mockGcsUtil.getObjects(List.of(GcsPath.fromUri(gcsFileName)))).thenReturn(items);
 
     DwhFiles dwhFiles = new DwhFiles("gs://testbucket/testdirectory", FhirContext.forR4Cached());
-    Assert.assertThrows(
+    Assertions.assertThrows(
         FileAlreadyExistsException.class,
         () -> dwhFiles.writeTimestampFile(DwhFiles.TIMESTAMP_FILE_START));
   }
@@ -215,14 +215,14 @@ public void readTimestampFile() throws IOException {
     DwhFiles dwhFiles = new DwhFiles("gs://testbucket/testdirectory", FhirContext.forR4Cached());
     Instant actualInstant = dwhFiles.readTimestampFile(DwhFiles.TIMESTAMP_FILE_START);
 
-    Assert.assertEquals(currentInstant.getEpochSecond(), actualInstant.getEpochSecond());
+    Assertions.assertEquals(currentInstant.getEpochSecond(), actualInstant.getEpochSecond());
     Mockito.verify(mockGcsUtil, Mockito.times(1)).open(GcsPath.fromUri(gcsFileName));
   }
 
   @Test
   public void dwhRootPrefixForGCSPath_returnsFileSeparator() {
     String fileSeparator = DwhFiles.getFileSeparatorForDwhFiles("gs://testbucket/testdirectory");
-    Assert.assertEquals("/", fileSeparator);
+    Assertions.assertEquals("/", fileSeparator);
   }
 
   private void mockFileRead(String gcsFileName, Instant instant) throws IOException {

pipelines/common/src/test/java/com/google/fhir/analytics/LocalDwhFilesTest.java

@@ -38,21 +38,22 @@
 import org.apache.beam.sdk.io.fs.ResolveOptions.StandardResolveOptions;
 import org.apache.beam.sdk.io.fs.ResourceId;
 import org.apache.commons.lang3.SystemUtils;
-import org.junit.Assert;
 import org.junit.Assume;
-import org.junit.Test;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Assumptions;
+import org.junit.jupiter.api.Test;
 
 public class LocalDwhFilesTest {
   @Test
   public void getResourcePathTestNonWindows() {
-    Assume.assumeFalse(SystemUtils.IS_OS_WINDOWS);
+    Assumptions.assumeFalse(SystemUtils.IS_OS_WINDOWS);
     DwhFiles dwhFiles = new DwhFiles("/tmp", FhirContext.forR4Cached());
     assertThat(dwhFiles.getResourcePath("Patient").toString(), equalTo("/tmp/Patient/"));
   }
 
   @Test
   public void getResourcePathTestWindows() {
-    Assume.assumeTrue(SystemUtils.IS_OS_WINDOWS);
+    Assumptions.assumeTrue(SystemUtils.IS_OS_WINDOWS);
     DwhFiles dwhFiles = new DwhFiles("C:\\tmp", FhirContext.forR4Cached());
     assertThat(dwhFiles.getResourcePath("Patient").toString(), equalTo("C:\\tmp\\Patient\\"));
   }
@@ -76,7 +77,7 @@ public void getIncrementalRunPathTest() throws IOException {
 
   @Test
   public void newIncrementalRunPathTestNonWindows() throws IOException {
-    Assume.assumeFalse(SystemUtils.IS_OS_WINDOWS);
+    Assumptions.assumeFalse(SystemUtils.IS_OS_WINDOWS);
     DwhFiles instance = new DwhFiles("/tmp", FhirContext.forR4Cached());
     ResourceId incrementalRunPath = instance.newIncrementalRunPath();
     assertThat(
@@ -86,7 +87,7 @@ public void newIncrementalRunPathTestNonWindows() throws IOException {
 
   @Test
   public void newIncrementalRunPathTesWindows() throws IOException {
-    Assume.assumeTrue(SystemUtils.IS_OS_WINDOWS);
+    Assumptions.assumeTrue(SystemUtils.IS_OS_WINDOWS);
     DwhFiles instance = new DwhFiles("C:\\tmp", FhirContext.forR4Cached());
     ResourceId incrementalRunPath = instance.newIncrementalRunPath();
     assertThat(incrementalRunPath.toString(), equalTo("C:\\tmp\\incremental_run\\"));
@@ -197,7 +198,7 @@ public void writeTimestampFile_FileAlreadyExists_ThrowsError() throws IOExceptio
     createFile(timestampPath, Instant.now().toString().getBytes(StandardCharsets.UTF_8));
     DwhFiles dwhFiles = new DwhFiles(root.toString(), FhirContext.forR4Cached());
 
-    Assert.assertThrows(
+    Assertions.assertThrows(
         FileAlreadyExistsException.class,
         () -> dwhFiles.writeTimestampFile(DwhFiles.TIMESTAMP_FILE_START));
 
@@ -231,34 +232,34 @@ public void readTimestampFile() throws IOException {
 
     Instant actualInstant = dwhFiles.readTimestampFile(DwhFiles.TIMESTAMP_FILE_START);
 
-    Assert.assertEquals(currentInstant.getEpochSecond(), actualInstant.getEpochSecond());
+    Assertions.assertEquals(currentInstant.getEpochSecond(), actualInstant.getEpochSecond());
 
     Files.delete(timestampPath);
     Files.delete(root);
   }
 
   @Test
   public void passNonWindowsLocalPathDwhRootPrefix_returnsFileSeparator() {
-    Assume.assumeFalse(SystemUtils.IS_OS_WINDOWS);
+    Assumptions.assumeFalse(SystemUtils.IS_OS_WINDOWS);
     // Absolute Path
     String fs1 = DwhFiles.getFileSeparatorForDwhFiles("/rootDir/prefix");
-    Assert.assertEquals(File.separator, fs1);
+    Assertions.assertEquals(File.separator, fs1);
     // Relative Path
     String fs2 = DwhFiles.getFileSeparatorForDwhFiles("baseDir/prefix");
-    Assert.assertEquals(File.separator, fs2);
+    Assertions.assertEquals(File.separator, fs2);
   }
 
   @Test
   public void passWindowsLocalPathDwhRootPrefix_returnsFileSeparator() {
-    Assume.assumeTrue(SystemUtils.IS_OS_WINDOWS);
+    Assumptions.assumeTrue(SystemUtils.IS_OS_WINDOWS);
     // Absolute Path
     String fs1 = DwhFiles.getFileSeparatorForDwhFiles("C:\\prefix");
-    Assert.assertEquals(File.separator, fs1);
+    Assertions.assertEquals(File.separator, fs1);
     String fs2 = DwhFiles.getFileSeparatorForDwhFiles("C:\\rootDir\\prefix");
-    Assert.assertEquals(File.separator, fs2);
+    Assertions.assertEquals(File.separator, fs2);
     // Relative Path
     String fs3 = DwhFiles.getFileSeparatorForDwhFiles("baseDir\\prefix");
-    Assert.assertEquals(File.separator, fs3);
+    Assertions.assertEquals(File.separator, fs3);
   }
 
   private void createFile(Path path, byte[] bytes) throws IOException {