Upgrade to Java 21

.github/workflows/run-tests.yml

@@ -9,25 +9,13 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        mongodb-version: [4.0.18]
-        java-version: [1.8]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Setup Java JDK
-        uses: actions/[email protected]
-        # The Java version to make available on the path. Takes a whole or semver Java version, or 1.x syntax (e.g. 1.8 => Java 8.x). Early access versions can be specified in the form of e.g. 14-ea, 14.0.0-ea, or 14.0.0-ea.28
+        uses: actions/setup-java@v4
         with:
-          java-version: ${{ matrix.java-version }}
-      - name: Install and Start MongoDB
-        run: |
-          wget http://fastdl.mongodb.org/linux/mongodb-linux-x86_64-${{ matrix.mongodb-version }}.tgz
-          tar xfz mongodb-linux-x86_64-${{ matrix.mongodb-version }}.tgz
-          export PATH=`pwd`/mongodb-linux-x86_64-${{ matrix.mongodb-version }}/bin:$PATH
-          mkdir -p data/db
-          mongod --dbpath=data/db &
-          mongod --version
+          java-version: '21'
+          distribution: 'temurin'
       - name: Run Maven tests
         run: mvn test

pom.xml

@@ -17,8 +17,8 @@
     </modules>
 
     <properties>
-        <java.version>1.8</java.version>
-        <spring.boot.version>2.1.0.RELEASE</spring.boot.version>
+        <java.version>21</java.version>
+        <spring.boot.version>3.4.1</spring.boot.version>
     </properties>
 
     <dependencyManagement>
@@ -38,20 +38,27 @@
                 </exclusions>
             </dependency>
             <dependency>
-                <groupId>com.lordofthejars</groupId>
-                <artifactId>nosqlunit-mongodb</artifactId>
+                <groupId>jakarta.validation</groupId>
+                <artifactId>jakarta.validation-api</artifactId>
+                <version>3.0.2</version>
+            </dependency>
+            <dependency>
+                <groupId>org.testcontainers</groupId>
+                <artifactId>testcontainers</artifactId>
+                <version>1.19.3</version>
                 <scope>test</scope>
-                <version>0.14.0</version>
             </dependency>
             <dependency>
-                <groupId>javax.validation</groupId>
-                <artifactId>validation-api</artifactId>
-                <version>1.1.0.Final</version>
+                <groupId>org.testcontainers</groupId>
+                <artifactId>mongodb</artifactId>
+                <version>1.19.3</version>
+                <scope>test</scope>
             </dependency>
             <dependency>
-                <groupId>com.fasterxml.jackson.core</groupId>
-                <artifactId>jackson-annotations</artifactId>
-                <version>2.9.9</version>
+                <groupId>org.testcontainers</groupId>
+                <artifactId>junit-jupiter</artifactId>
+                <version>1.19.3</version>
+                <scope>test</scope>
             </dependency>
             <dependency>
                 <groupId>io.swagger</groupId>
@@ -121,10 +128,9 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.2</version>
+                <version>3.12.1</version>
                 <configuration>
-                    <source>${java.version}</source>
-                    <target>${java.version}</target>
+                    <release>${java.version}</release>
                     <showDeprecation>true</showDeprecation>
                     <showWarnings>true</showWarnings>
                     <encoding>UTF-8</encoding>

variation-commons-batch/pom.xml

@@ -31,8 +31,13 @@
             <artifactId>spring-boot-starter-data-jpa</artifactId>
         </dependency>
         <dependency>
-            <groupId>com.lordofthejars</groupId>
-            <artifactId>nosqlunit-mongodb</artifactId>
+            <groupId>org.testcontainers</groupId>
+            <artifactId>mongodb</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.testcontainers</groupId>
+            <artifactId>junit-jupiter</artifactId>
             <scope>test</scope>
         </dependency>
     </dependencies>

variation-commons-batch/src/main/java/uk/ac/ebi/eva/commons/batch/configuration/SpringBoot1CompatibilityConfiguration.java

@@ -1,65 +1,40 @@
 package uk.ac.ebi.eva.commons.batch.configuration;
 
-import org.springframework.batch.core.configuration.annotation.BatchConfigurer;
-import org.springframework.batch.core.configuration.annotation.DefaultBatchConfigurer;
-import org.springframework.batch.core.explore.JobExplorer;
-import org.springframework.batch.core.explore.support.JobExplorerFactoryBean;
-import org.springframework.batch.core.repository.JobRepository;
-import org.springframework.batch.core.repository.support.JobRepositoryFactoryBean;
+import org.springframework.batch.core.configuration.support.DefaultBatchConfiguration;
+import org.springframework.batch.core.repository.ExecutionContextSerializer;
+import org.springframework.batch.core.repository.dao.Jackson2ExecutionContextStringSerializer;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.vendor.HibernateJpaDialect;
 import org.springframework.transaction.PlatformTransactionManager;
 
-
-import javax.persistence.EntityManagerFactory;
+import jakarta.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
 
-public class SpringBoot1CompatibilityConfiguration {
+/**
+ * Spring Batch configuration for JPA/Hibernate compatibility.
+ *
+ * Updated for Spring Batch 5.x which removes BatchConfigurer and DefaultBatchConfigurer.
+ * Extend this class and override getDataSource() to provide your DataSource.
+ */
+public abstract class SpringBoot1CompatibilityConfiguration extends DefaultBatchConfiguration {
+
+    private final EntityManagerFactory entityManagerFactory;
+
+    protected SpringBoot1CompatibilityConfiguration(EntityManagerFactory entityManagerFactory) {
+        this.entityManagerFactory = entityManagerFactory;
+    }
 
-    // Due to the bug here: https://github.com/spring-projects/spring-batch/issues/1289#issue-538711146
-    // BatchConfigurer seems to override the transaction manager that is already present in the ExecutionContext
-    // This leads to issues like https://github.com/spring-projects/spring-batch/issues/961#issue-538704176
-    // Therefore, we have to "re-assert" to Spring Boot that we intend to use
-    // a JPA Transaction manager by putting back in the ExecutionContext
-    private static JpaTransactionManager getTransactionManager(DataSource dataSource, EntityManagerFactory entityManagerFactory) {
+    @Override
+    public PlatformTransactionManager getTransactionManager() {
         final JpaTransactionManager jpaTransactionManager = new JpaTransactionManager();
-        jpaTransactionManager.setDataSource(dataSource);
+        jpaTransactionManager.setDataSource(getDataSource());
         jpaTransactionManager.setJpaDialect(new HibernateJpaDialect());
         jpaTransactionManager.setEntityManagerFactory(entityManagerFactory);
         return jpaTransactionManager;
     }
 
-    public static BatchConfigurer getSpringBoot1CompatibleBatchConfigurer(DataSource dataSource,
-                                                                          EntityManagerFactory entityManagerFactory)
-            throws Exception {
-        final JpaTransactionManager transactionManager = getTransactionManager(dataSource, entityManagerFactory);
-        final SpringBoot1CompatibleSerializer serializer = new SpringBoot1CompatibleSerializer();
-        return new DefaultBatchConfigurer(dataSource) {
-
-            @Override
-            protected JobRepository createJobRepository() throws Exception {
-
-                JobRepositoryFactoryBean factory = new JobRepositoryFactoryBean();
-                factory.setDataSource(dataSource);
-                factory.setTransactionManager(transactionManager);
-                factory.setSerializer(serializer);
-                factory.afterPropertiesSet();
-                return factory.getObject();
-            }
-
-            @Override
-            protected JobExplorer createJobExplorer() throws Exception {
-                JobExplorerFactoryBean jobExplorerFactoryBean = new JobExplorerFactoryBean();
-                jobExplorerFactoryBean.setSerializer(serializer);
-                jobExplorerFactoryBean.setDataSource(dataSource);
-                jobExplorerFactoryBean.afterPropertiesSet();
-                return jobExplorerFactoryBean.getObject();
-            }
-
-            @Override
-            public PlatformTransactionManager getTransactionManager() {
-                return transactionManager;
-            }
-        };
+    @Override
+    protected ExecutionContextSerializer getExecutionContextSerializer() {
+        return new Jackson2ExecutionContextStringSerializer();
     }
 }

variation-commons-batch/src/main/java/uk/ac/ebi/eva/commons/batch/configuration/SpringBoot1CompatibleSerializer.java

@@ -1,49 +1,29 @@
 package uk.ac.ebi.eva.commons.batch.configuration;
 
-import java.io.BufferedInputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.util.Map;
-import com.fasterxml.jackson.core.JsonProcessingException;
+
 import org.springframework.batch.core.repository.ExecutionContextSerializer;
 import org.springframework.batch.core.repository.dao.Jackson2ExecutionContextStringSerializer;
-import org.springframework.batch.core.repository.dao.XStreamExecutionContextStringSerializer;
-
 
 /**
- * ExecutionContext serialization/deserialization from Job repository changed in mechanism
- * from XStream to Jackson in Spring Boot 2 (which includes the Spring Batch 4 library)
- * - see https://docs.spring.io/spring-batch/docs/4.0.4.RELEASE/reference/html/whatsnew.html#whatsNewSerialization
- *
- * This class enables reading ExecutionContext entries written by Spring Boot 1.5 (Spring Batch 3)
- * as well as Spring Boot 2.1 (Spring Batch 4) and write entries in Spring Boot 2 (Spring Batch 4) format
+ * ExecutionContext serializer using Jackson.
  *
- * Adapted from https://stackoverflow.com/a/55375553
+ * Note: XStreamExecutionContextStringSerializer has been removed in Spring Batch 5.x.
+ * This class now only supports Jackson-based serialization format.
+ * Legacy XStream-serialized data will need to be migrated separately if still present.
  */
 public class SpringBoot1CompatibleSerializer implements ExecutionContextSerializer {
-    private final XStreamExecutionContextStringSerializer xStream = new XStreamExecutionContextStringSerializer();
     private final Jackson2ExecutionContextStringSerializer jackson = new Jackson2ExecutionContextStringSerializer();
 
-    public SpringBoot1CompatibleSerializer() throws Exception {
-        xStream.afterPropertiesSet();
+    public SpringBoot1CompatibleSerializer() {
     }
 
     @Override
     public Map<String, Object> deserialize(InputStream inputStream) throws IOException {
-        InputStream repeatableInputStream = ensureMarkSupported(inputStream);
-        repeatableInputStream.mark(Integer.MAX_VALUE);
-
-        try {
-            return jackson.deserialize(repeatableInputStream);
-        } catch (JsonProcessingException e) {
-            repeatableInputStream.reset();
-            return xStream.deserialize(repeatableInputStream);
-        }
-    }
-
-    private static InputStream ensureMarkSupported(InputStream in) {
-        return in.markSupported() ? in : new BufferedInputStream(in);
+        return jackson.deserialize(inputStream);
     }
 
     @Override

variation-commons-batch/src/main/java/uk/ac/ebi/eva/commons/batch/io/AggregatedVcfLineMapper.java

@@ -26,7 +26,7 @@
 import uk.ac.ebi.eva.commons.core.models.factories.VariantVcfFactory;
 import uk.ac.ebi.eva.commons.core.models.pipeline.Variant;
 
-import javax.annotation.Nullable;
+import jakarta.annotation.Nullable;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.util.List;

variation-commons-batch/src/main/java/uk/ac/ebi/eva/commons/batch/io/AggregatedVcfReader.java

@@ -17,7 +17,7 @@
 
 import uk.ac.ebi.eva.commons.core.models.Aggregation;
 
-import javax.annotation.Nullable;
+import jakarta.annotation.Nullable;
 import java.io.File;
 import java.io.IOException;
 

variation-commons-batch/src/main/java/uk/ac/ebi/eva/commons/batch/job/JobStatusManager.java

@@ -28,7 +28,7 @@
 import uk.ac.ebi.eva.commons.batch.exception.NoParametersHaveBeenPassedException;
 import uk.ac.ebi.eva.commons.batch.exception.NoPreviousJobExecutionException;
 
-import java.util.Date;
+import java.time.LocalDateTime;
 import java.util.Objects;
 
 /**
@@ -60,7 +60,7 @@ public static void markLastJobAsFailed(JobRepository jobRepository, String jobNa
             throw new NoPreviousJobExecutionException(jobName, jobParameters);
         }
 
-        Date currentTime = new Date();
+        LocalDateTime currentTime = LocalDateTime.now();
         lastJobExecution.setEndTime(currentTime);
         lastJobExecution.setStatus(BatchStatus.FAILED);
         lastJobExecution.setExitStatus(

variation-commons-batch/src/test/java/uk/ac/ebi/eva/commons/batch/io/AggregatedVcfReaderTest.java

@@ -15,9 +15,8 @@
  */
 package uk.ac.ebi.eva.commons.batch.io;
 
-import org.junit.Rule;
-import org.junit.Test;
-import org.junit.rules.TemporaryFolder;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
 import org.springframework.batch.item.ExecutionContext;
 import org.springframework.batch.test.MetaDataInstanceFactory;
 
@@ -30,12 +29,14 @@
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
+import java.nio.file.Path;
 import java.util.List;
 import java.util.zip.GZIPInputStream;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 /**
  * {@link AggregatedVcfReader}
@@ -54,17 +55,21 @@ public class AggregatedVcfReaderTest {
 
     private static final String INPUT_FILE_PATH_EVS = "/input-files/vcf/aggregated.evs.vcf.gz";
 
-    @Rule
-    public TemporaryFolder temporaryFolderRule = new TemporaryFolder();
+    @TempDir
+    Path temporaryFolder;
 
-    @Test(expected = IllegalArgumentException.class)
+    @Test
     public void shouldThrowOnInvalidAggregation() throws IOException {
-        new AggregatedVcfReader(FILE_ID, STUDY_ID, Aggregation.NONE, null, FileUtils.getResourceFile(INPUT_FILE_PATH));
+        assertThrows(IllegalArgumentException.class, () -> {
+            new AggregatedVcfReader(FILE_ID, STUDY_ID, Aggregation.NONE, null, FileUtils.getResourceFile(INPUT_FILE_PATH));
+        });
     }
 
-    @Test(expected = IllegalArgumentException.class)
+    @Test
     public void shouldThrowOnNullAggregation() throws IOException {
-        new AggregatedVcfReader(FILE_ID, STUDY_ID, null, null, FileUtils.getResourceFile(INPUT_FILE_PATH));
+        assertThrows(IllegalArgumentException.class, () -> {
+            new AggregatedVcfReader(FILE_ID, STUDY_ID, null, null, FileUtils.getResourceFile(INPUT_FILE_PATH));
+        });
     }
 
     @Test
@@ -104,7 +109,7 @@ public void testUncompressedVcf() throws Exception {
 
         // uncompress the input VCF into a temporal file
         File input = FileUtils.getResourceFile(INPUT_FILE_PATH);
-        File tempFile = temporaryFolderRule.newFile();
+        File tempFile = temporaryFolder.resolve("tempFile.vcf").toFile();
         CompressionHelper.uncompress(input.getAbsolutePath(), tempFile);
 
         AggregatedVcfReader vcfReader = new AggregatedVcfReader(FILE_ID, STUDY_ID, Aggregation.BASIC,