Fixing bytea json conversion error (update to hibernate 6, spring 3)

src/main/java/org/commonwl/view/workflow/QueuedWorkflowRepositoryImpl.java

@@ -3,19 +3,21 @@
 import io.hypersistence.utils.hibernate.type.json.JsonType;
 import jakarta.persistence.EntityManager;
 import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.PersistenceContextType;
 import org.commonwl.view.git.GitDetails;
 import org.hibernate.query.Query;
+import org.springframework.transaction.annotation.Transactional;
 
 public class QueuedWorkflowRepositoryImpl implements QueuedWorkflowRepositoryCustom {
 
-  // Tested this query directly, and it works! Problem is elsewhere!
   private static final String QUERY_FIND_BY_RETRIEVED_FROM =
       "SELECT q.* FROM queued_workflow q WHERE q.temp_representation -> 'retrievedFrom' = :retrievedFrom";
 
   private static final String QUERY_DELETE_BY_RETRIEVED_FROM =
       "DELETE FROM queued_workflow q WHERE q.temp_representation -> 'retrievedFrom' = :retrievedFrom";
 
-  @PersistenceContext EntityManager entityManager;
+  @PersistenceContext(type = PersistenceContextType.EXTENDED)
+  EntityManager entityManager;
 
   @Override
   public QueuedWorkflow findByRetrievedFrom(GitDetails retrievedFrom) {
@@ -27,22 +29,30 @@ public QueuedWorkflow findByRetrievedFrom(GitDetails retrievedFrom) {
     //      out of ideas, so started testing everything found online):
     //      Use `new JsonType(GitDetails.class)`. That finally solved it.
     //      Ref: https://github.com/common-workflow-language/cwlviewer/pull/568
-    return (QueuedWorkflow)
+    final Query<?> query =
         entityManager
             .createNativeQuery(QUERY_FIND_BY_RETRIEVED_FROM, QueuedWorkflow.class)
-            .unwrap(Query.class)
-            .setParameter("retrievedFrom", retrievedFrom, new JsonType(GitDetails.class))
-            .stream()
-            .findFirst()
-            .orElse(null);
+            .unwrap(Query.class);
+
+    if (query == null) {
+      return null;
+    }
+
+    query.setParameter("retrievedFrom", retrievedFrom, new JsonType(GitDetails.class));
+    return (QueuedWorkflow) query.uniqueResult();
   }
 
+  @Transactional
   @Override
   public void deleteByTempRepresentation_RetrievedFrom(GitDetails retrievedFrom) {
-    entityManager
-        .createNativeQuery(QUERY_DELETE_BY_RETRIEVED_FROM, QueuedWorkflow.class)
-        .unwrap(Query.class)
-        .setParameter("retrievedFrom", retrievedFrom, new JsonType(GitDetails.class))
-        .executeUpdate();
+    final Query<?> query =
+        entityManager
+            .createNativeQuery(QUERY_DELETE_BY_RETRIEVED_FROM, QueuedWorkflow.class)
+            .unwrap(Query.class);
+
+    if (query != null) {
+      query.setParameter("retrievedFrom", retrievedFrom, new JsonType(GitDetails.class));
+      query.executeUpdate();
+    }
   }
 }

src/main/java/org/commonwl/view/workflow/WorkflowRepository.java

@@ -20,11 +20,10 @@
 package org.commonwl.view.workflow;
 
 import java.util.List;
-import org.commonwl.view.git.GitDetails;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
+import org.springframework.data.jpa.repository.JpaRepository;
 import org.springframework.data.jpa.repository.Query;
-import org.springframework.data.repository.CrudRepository;
 import org.springframework.stereotype.Repository;
 
 /**
@@ -34,15 +33,8 @@
  * href="https://docs.spring.io/spring-data/jpa/docs/current/reference/html/">...</a>
  */
 @Repository
-public interface WorkflowRepository extends CrudRepository<Workflow, String> {
-
-  /**
-   * Finds a workflow model in the database based on where it was retrieved from
-   *
-   * @param retrievedFrom Details of where the workflow is from
-   * @return The workflow model
-   */
-  Workflow findByRetrievedFrom(GitDetails retrievedFrom);
+public interface WorkflowRepository
+    extends JpaRepository<Workflow, String>, WorkflowRepositoryCustom {
 
   /**
    * Finds a workflow model in the database based on a commit ID and path

src/main/java/org/commonwl/view/workflow/WorkflowRepositoryCustom.java

@@ -0,0 +1,32 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 org.commonwl.view.workflow;
+
+import org.commonwl.view.git.GitDetails;
+
+public interface WorkflowRepositoryCustom {
+
+  /**
+   * Finds a workflow model in the database based on where it was retrieved from
+   *
+   * @param retrievedFrom Details of where the workflow is from
+   * @return The workflow model
+   */
+  Workflow findByRetrievedFrom(GitDetails retrievedFrom);
+}

src/main/java/org/commonwl/view/workflow/WorkflowRepositoryImpl.java

@@ -0,0 +1,51 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 org.commonwl.view.workflow;
+
+import io.hypersistence.utils.hibernate.type.json.JsonType;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.persistence.PersistenceContextType;
+import org.commonwl.view.git.GitDetails;
+import org.hibernate.query.Query;
+
+public class WorkflowRepositoryImpl implements WorkflowRepositoryCustom {
+
+  private static final String QUERY_FIND_BY_RETRIEVED_FROM =
+      "SELECT w.* FROM workflow w WHERE w.retrieved_from = :retrievedFrom";
+
+  @PersistenceContext(type = PersistenceContextType.EXTENDED)
+  EntityManager entityManager;
+
+  @Override
+  public Workflow findByRetrievedFrom(GitDetails retrievedFrom) {
+    final Query<?> query =
+        entityManager
+            .createNativeQuery(QUERY_FIND_BY_RETRIEVED_FROM, Workflow.class)
+            .unwrap(Query.class);
+
+    if (query == null) {
+      return null;
+    }
+
+    query.setParameter("retrievedFrom", retrievedFrom, new JsonType(GitDetails.class));
+    return (Workflow) query.uniqueResult();
+  }
+}

src/test/java/org/commonwl/view/workflow/PostgreSQLContextInitializer.java

@@ -17,7 +17,7 @@ public class PostgreSQLContextInitializer
   @Override
   public void initialize(ConfigurableApplicationContext applicationContext) {
     PostgreSQLContainer<?> postgreSQLContainer =
-        new PostgreSQLContainer<>("postgres:9.6.12")
+        new PostgreSQLContainer<>("postgres:17.4")
             .withDatabaseName("cwlviewer")
             .withUsername("sa")
             .withPassword("sa");

src/test/java/org/commonwl/view/workflow/QueuedWorkflowRepositoryTest.java

@@ -12,17 +12,18 @@
 import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest;
 import org.springframework.test.context.ContextConfiguration;
 import org.springframework.test.context.TestPropertySource;
+import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
 
 @TestPropertySource(locations = "classpath:it-application.properties")
 @DataJpaTest(showSql = true)
+@Transactional(propagation = Propagation.NOT_SUPPORTED)
 @ContextConfiguration(initializers = PostgreSQLContextInitializer.class)
 @AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE)
 public class QueuedWorkflowRepositoryTest {
 
   @Autowired QueuedWorkflowRepository repository;
 
-  @Transactional
   @Test
   public void deleteQueuedWorkflowByRetrievedFromTest() {
 

src/test/java/org/commonwl/view/workflow/WorkflowRepositoryTest.java

@@ -0,0 +1,78 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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 org.commonwl.view.workflow;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
+import static org.junit.jupiter.api.Assertions.assertNull;
+
+import java.util.List;
+import org.commonwl.view.git.GitDetails;
+import org.junit.jupiter.api.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.autoconfigure.jdbc.AutoConfigureTestDatabase;
+import org.springframework.boot.test.autoconfigure.orm.jpa.DataJpaTest;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.TestPropertySource;
+import org.springframework.transaction.annotation.Propagation;
+import org.springframework.transaction.annotation.Transactional;
+
+@TestPropertySource(locations = "classpath:it-application.properties")
+@DataJpaTest(showSql = true)
+@Transactional(propagation = Propagation.NOT_SUPPORTED)
+@ContextConfiguration(initializers = PostgreSQLContextInitializer.class)
+@AutoConfigureTestDatabase(replace = AutoConfigureTestDatabase.Replace.NONE)
+public class WorkflowRepositoryTest {
+
+  @Autowired WorkflowRepository repository;
+
+  @Test
+  public void deletedWorkflowByRetrievedFromTest() {
+
+    assertNotNull(repository);
+
+    // create stub workflow
+    GitDetails gitDetails =
+        new GitDetails("https://github.com/common-workflow-language/cwlviewer/", "main", "/");
+    gitDetails.setPackedId("test_packedId");
+
+    Workflow workflow = new Workflow();
+    workflow.setRetrievedFrom(gitDetails);
+
+    // save workflow
+    repository.saveAndFlush(workflow);
+
+    List<Workflow> all = repository.findAll();
+    assertNotNull(all);
+    assertEquals(1, all.size());
+
+    // retrieve saved workflow by git details
+    Workflow retrievedWorkflowAfterSave =
+        repository.findByRetrievedFrom(workflow.getRetrievedFrom());
+    assertNotNull(retrievedWorkflowAfterSave);
+
+    // delete saved workflow by git details
+    repository.delete(workflow);
+
+    // retrieve deleted workflow by workflow git details
+    Workflow retrievedWorkflowAfterDelete =
+        repository.findByRetrievedFrom(workflow.getRetrievedFrom());
+    assertNull(retrievedWorkflowAfterDelete);
+  }
+}