Upgrade to java21

Author: tcezard

.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

accession-commons-core/pom.xml

@@ -21,6 +21,10 @@
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-data-jpa</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.springframework.boot</groupId>
+            <artifactId>spring-boot-starter-validation</artifactId>
+        </dependency>
     </dependencies>
 
     <build>
@@ -29,8 +33,9 @@
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
                 <configuration>
-                    <source>1.8</source>
-                    <target>1.8</target>
+                    <source>21</source>
+                    <target>21</target>
+                    <release>21</release>
                 </configuration>
             </plugin>
             <plugin>

accession-commons-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/hashing/SHA1HashingFunction.java

@@ -20,9 +20,9 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import javax.xml.bind.DatatypeConverter;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
+import java.util.HexFormat;
 import java.util.function.Function;
 
 /**
@@ -38,7 +38,7 @@ public String apply(String summary) {
     }
 
     private static String generateSha1FromBytes(byte[] nameBytes) {
-        return DatatypeConverter.printHexBinary(toSHA1(nameBytes));
+        return HexFormat.of().withUpperCase().formatHex(toSHA1(nameBytes));
     }
 
     private static byte[] toSHA1(byte[] bytes) {

accession-commons-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/rest/BasicRestControllerAdvice.java

@@ -41,8 +41,8 @@
 import uk.ac.ebi.ampt2d.commons.accession.rest.dto.ErrorMessage;
 import uk.ac.ebi.ampt2d.commons.accession.rest.validation.CollectionValidator;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.validation.ValidationException;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.validation.ValidationException;
 import java.net.URI;
 import java.util.stream.Collectors;
 

accession-commons-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/rest/controllers/BasicRestController.java

@@ -33,7 +33,7 @@
 import uk.ac.ebi.ampt2d.commons.accession.rest.dto.AccessionVersionsResponseDTO;
 import uk.ac.ebi.ampt2d.commons.accession.rest.dto.GetOrCreateAccessionResponseDTO;
 
-import javax.validation.Valid;
+import jakarta.validation.Valid;
 import java.util.List;
 import java.util.function.Function;
 import java.util.stream.Collectors;

accession-commons-core/src/main/java/uk/ac/ebi/ampt2d/commons/accession/rest/validation/CollectionValidator.java

@@ -21,8 +21,8 @@
 import org.springframework.validation.Validator;
 import org.springframework.validation.beanvalidation.LocalValidatorFactoryBean;
 
-import javax.validation.ConstraintViolation;
-import javax.validation.ValidationException;
+import jakarta.validation.ConstraintViolation;
+import jakarta.validation.ValidationException;
 import java.util.Collection;
 import java.util.Set;
 

accession-commons-core/src/test/java/uk/ac/ebi/ampt2d/commons/accession/core/exceptions/MissingUnsavedAccessionsExceptionTest.java

@@ -17,13 +17,13 @@
  */
 package uk.ac.ebi.ampt2d.commons.accession.core.exceptions;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import uk.ac.ebi.ampt2d.commons.accession.core.models.AccessionWrapper;
 
 import java.util.Arrays;
 import java.util.List;
 
-import static org.junit.Assert.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class MissingUnsavedAccessionsExceptionTest {
 

accession-commons-core/src/test/java/uk/ac/ebi/ampt2d/commons/accession/generators/SingleAccessionGeneratorTest.java

@@ -17,7 +17,7 @@
  */
 package uk.ac.ebi.ampt2d.commons.accession.generators;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import uk.ac.ebi.ampt2d.commons.accession.core.models.AccessionWrapper;
 import uk.ac.ebi.ampt2d.commons.accession.core.models.SaveResponse;
 import uk.ac.ebi.ampt2d.commons.accession.hashing.SHA1HashingFunction;
@@ -30,7 +30,7 @@
 import java.util.function.Function;
 import java.util.stream.Collectors;
 
-import static org.junit.Assert.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertEquals;
 
 public class SingleAccessionGeneratorTest {
     private static String APPLICATION_INSTANCE_ID = "TEST_APPPLICATION_INSTANCE_ID";

accession-commons-core/src/test/java/uk/ac/ebi/ampt2d/commons/accession/hashing/SHA1HashingFunctionTest.java

@@ -17,11 +17,13 @@
  */
 package uk.ac.ebi.ampt2d.commons.accession.hashing;
 
-import org.junit.Assert;
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 
 import java.util.function.Function;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotEquals;
+
 public class SHA1HashingFunctionTest {
 
     @Test
@@ -32,8 +34,8 @@ public void testGenerateAccession() {
         String object1Accession = hashingFunction.apply(object1);
         String object2Accession = hashingFunction.apply(object2);
         String object3Accession = hashingFunction.apply(object2);
-        Assert.assertNotEquals(object1Accession, object2Accession);
-        Assert.assertEquals(object2Accession, object3Accession);
-        Assert.assertEquals(40, object1Accession.length());
+        assertNotEquals(object1Accession, object2Accession);
+        assertEquals(object2Accession, object3Accession);
+        assertEquals(40, object1Accession.length());
     }
-}
+}

accession-commons-core/src/test/java/uk/ac/ebi/ampt2d/commons/accession/utils/ExponentialBackOffTest.java

@@ -17,13 +17,14 @@
  */
 package uk.ac.ebi.ampt2d.commons.accession.utils;
 
-import org.junit.Test;
+import org.junit.jupiter.api.Test;
 import uk.ac.ebi.ampt2d.commons.accession.utils.exceptions.ExponentialBackOffMaxRetriesRuntimeException;
 
 import java.util.function.Supplier;
 
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
 public class ExponentialBackOffTest {
 
@@ -44,31 +45,39 @@ public String get() {
         }
     }
 
-    @Test(expected = ExponentialBackOffMaxRetriesRuntimeException.class)
+    @Test
     public void testRunnableDefaultTotalAttempts() {
         ExtendedRunnable runnable = new ExtendedRunnable();
-        ExponentialBackOff.execute((Runnable) runnable);
+        assertThrows(ExponentialBackOffMaxRetriesRuntimeException.class, () -> {
+            ExponentialBackOff.execute((Runnable) runnable);
+        });
         assertEquals(ExponentialBackOff.DEFAULT_TOTAL_ATTEMPTS, runnable.numRun);
     }
 
-    @Test(expected = ExponentialBackOffMaxRetriesRuntimeException.class)
+    @Test
     public void testFunctionDefaultTotalAttempts() {
         ExtendedRunnable runnable = new ExtendedRunnable();
-        ExponentialBackOff.execute((Supplier) runnable);
+        assertThrows(ExponentialBackOffMaxRetriesRuntimeException.class, () -> {
+            ExponentialBackOff.execute((Supplier) runnable);
+        });
         assertEquals(ExponentialBackOff.DEFAULT_TOTAL_ATTEMPTS, runnable.numRun);
     }
 
-    @Test(expected = ExponentialBackOffMaxRetriesRuntimeException.class)
+    @Test
     public void testRunnableTotalAttempts() {
         ExtendedRunnable runnable = new ExtendedRunnable();
-        ExponentialBackOff.execute((Runnable) runnable, 3, 1000);
+        assertThrows(ExponentialBackOffMaxRetriesRuntimeException.class, () -> {
+            ExponentialBackOff.execute((Runnable) runnable, 3, 1000);
+        });
         assertEquals(3, runnable.numRun);
     }
 
-    @Test(expected = ExponentialBackOffMaxRetriesRuntimeException.class)
+    @Test
     public void testFunctionTotalAttempts() {
         ExtendedRunnable runnable = new ExtendedRunnable();
-        ExponentialBackOff.execute((Supplier) runnable, 3, 1000);
+        assertThrows(ExponentialBackOffMaxRetriesRuntimeException.class, () -> {
+            ExponentialBackOff.execute((Supplier) runnable, 3, 1000);
+        });
         assertEquals(3, runnable.numRun);
     }