Fix tests

Author: tcezard

accession-commons-mongodb/src/test/java/uk/ac/ebi/ampt2d/commons/accession/CucumberSpringConfiguration.java

@@ -23,22 +23,21 @@
 import org.springframework.test.context.DynamicPropertyRegistry;
 import org.springframework.test.context.DynamicPropertySource;
 import org.testcontainers.containers.MongoDBContainer;
-import org.testcontainers.junit.jupiter.Container;
-import org.testcontainers.junit.jupiter.Testcontainers;
 import uk.ac.ebi.ampt2d.test.configuration.MongoDbCucumberTestConfiguration;
 
 @CucumberContextConfiguration
 @SpringBootTest(classes = {MongoDbCucumberTestConfiguration.class})
 @DirtiesContext
-@Testcontainers
 public class CucumberSpringConfiguration {
 
-    @Container
     static MongoDBContainer mongoDBContainer = new MongoDBContainer("mongo:6.0");
 
+    static {
+        mongoDBContainer.start();
+    }
+
     @DynamicPropertySource
     static void setProperties(DynamicPropertyRegistry registry) {
-        mongoDBContainer.start();
         registry.add("spring.data.mongodb.uri", mongoDBContainer::getReplicaSetUrl);
     }
 }

accession-commons-monotonic-generator-jpa/src/test/java/uk/ac/ebi/ampt2d/commons/accession/generators/monotonic/MonotonicAccessionRecoveryAgentTest.java

@@ -8,6 +8,8 @@
 import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.monotonic.entities.ContiguousIdBlock;
 import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.monotonic.repositories.ContiguousIdBlockRepository;
 import uk.ac.ebi.ampt2d.commons.accession.persistence.jpa.monotonic.service.ContiguousIdBlockService;
+
+import jakarta.persistence.EntityManager;
 import uk.ac.ebi.ampt2d.commons.accession.service.BasicSpringDataRepositoryMonotonicDatabaseService;
 import uk.ac.ebi.ampt2d.test.configuration.MonotonicAccessionGeneratorTestConfiguration;
 import uk.ac.ebi.ampt2d.test.configuration.TestMonotonicDatabaseServiceTestConfiguration;
@@ -37,6 +39,8 @@ public class MonotonicAccessionRecoveryAgentTest {
     private ContiguousIdBlockRepository repository;
     @Autowired
     private ContiguousIdBlockService service;
+    @Autowired
+    private EntityManager entityManager;
 
     @Test
     public void testRunRecovery() throws InterruptedException {
@@ -69,6 +73,9 @@ public void testRunRecovery() throws InterruptedException {
         MonotonicAccessionRecoveryAgent recoveryAgent = new MonotonicAccessionRecoveryAgent(service, monotonicDBService);
         recoveryAgent.runRecovery(TEST_CATEGORY, TEST_RECOVERY_AGENT_APP_INSTANCE_ID, recoverCutOffTime);
 
+        // Clear the persistence context to ensure we fetch fresh data from the database
+        entityManager.flush();
+        entityManager.clear();
 
         List<ContiguousIdBlock> blockList = StreamSupport.stream(repository.findAll().spliterator(), false)
                 .sorted(Comparator.comparing(ContiguousIdBlock::getFirstValue))