Refactored persistence integration tests not to require Glassfish

dataverse-persistence/pom.xml

@@ -62,6 +62,13 @@
             <artifactId>javax.json</artifactId>
             <scope>test</scope>
         </dependency>
+
+   <!--    <dependency>
+            <groupId>org.eclipse.persistence</groupId>
+            <artifactId>org.eclipse.persistence.jpa</artifactId>
+            <version>2.6.1</version>
+            <scope>test</scope>
+        </dependency>-->
     </dependencies>
 
     <build>

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/datafile/FileMetadataRepository.java

@@ -3,6 +3,8 @@
 import edu.harvard.iq.dataverse.persistence.JpaRepository;
 
 import javax.ejb.Stateless;
+import javax.persistence.EntityManager;
+
 import java.util.Collection;
 import java.util.List;
 
@@ -14,6 +16,12 @@ public class FileMetadataRepository extends JpaRepository<Long, FileMetadata> {
     public FileMetadataRepository() {
         super(FileMetadata.class);
     }
+
+    public FileMetadataRepository(final EntityManager em) {
+
+        super(FileMetadata.class);
+        super.em = em;
+    }
 
     // -------------------- LOGIC --------------------
 

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/datafile/license/LicenseRepository.java

@@ -4,20 +4,22 @@
 
 import javax.ejb.Stateless;
 import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
 import java.util.List;
 import java.util.Optional;
 
 @Stateless
 public class LicenseRepository extends JpaRepository<Long, License> {
 
-    @PersistenceContext(unitName = "VDCNet-ejbPU")
-    private EntityManager em;
-
 
     public LicenseRepository() {
         super(License.class);
     }
+
+    public LicenseRepository(final EntityManager em) {
+
+        super(License.class);
+        super.em = em;
+    }
 
     //-------------------- LOGIC --------------------
 

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/dataset/DatasetCitationsCountRepository.java

@@ -3,6 +3,7 @@
 import edu.harvard.iq.dataverse.persistence.JpaRepository;
 
 import javax.ejb.Stateless;
+import javax.persistence.EntityManager;
 
 import java.util.Optional;
 
@@ -14,6 +15,12 @@ public class DatasetCitationsCountRepository extends JpaRepository<Long, Dataset
     public DatasetCitationsCountRepository() {
         super(DatasetCitationsCount.class);
     }
+
+    public DatasetCitationsCountRepository(final EntityManager em) {
+
+        super(DatasetCitationsCount.class);
+        super.em = em;
+    }
 
     // -------------------- LOGIC --------------------
 

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/dataset/DatasetRepository.java

@@ -3,6 +3,8 @@
 import edu.harvard.iq.dataverse.persistence.JpaRepository;
 
 import javax.ejb.Singleton;
+import javax.persistence.EntityManager;
+
 import java.util.List;
 
 @Singleton
@@ -13,6 +15,12 @@ public class DatasetRepository extends JpaRepository<Long, Dataset> {
     public DatasetRepository() {
         super(Dataset.class);
     }
+
+    public DatasetRepository(final EntityManager em) {
+
+        super(Dataset.class);
+        super.em = em;
+    }
 
     // -------------------- LOGIC --------------------
 

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/dataverse/DataverseFeaturedDataverseRepository.java

@@ -1,20 +1,26 @@
 package edu.harvard.iq.dataverse.persistence.dataverse;
 
-import edu.harvard.iq.dataverse.persistence.JpaRepository;
+import java.util.List;
 
 import javax.ejb.Stateless;
-import java.util.List;
-import java.util.logging.Logger;
+import javax.persistence.EntityManager;
+
+import edu.harvard.iq.dataverse.persistence.JpaRepository;
 
 @Stateless
 public class DataverseFeaturedDataverseRepository extends JpaRepository<Long, DataverseFeaturedDataverse> {
-    private static final Logger logger = Logger.getLogger(DataverseFeaturedDataverseRepository.class.getCanonicalName());
 
     // -------------------- CONSTRUCTORS --------------------
 
     public DataverseFeaturedDataverseRepository() {
         super(DataverseFeaturedDataverse.class);
     }
+
+    public DataverseFeaturedDataverseRepository(final EntityManager em) {
+
+        super(DataverseFeaturedDataverse.class);
+        super.em = em;
+    }
 
     // -------------------- LOGIC --------------------
 

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/dataverse/DataverseRepository.java

@@ -3,6 +3,8 @@
 import edu.harvard.iq.dataverse.persistence.JpaRepository;
 
 import javax.ejb.Singleton;
+import javax.persistence.EntityManager;
+
 import java.util.List;
 
 @Singleton
@@ -13,6 +15,12 @@ public class DataverseRepository extends JpaRepository<Long, Dataverse> {
     public DataverseRepository() {
         super(Dataverse.class);
     }
+
+    public DataverseRepository(final EntityManager em) {
+
+        super(Dataverse.class);
+        super.em = em;
+    }
 
     // -------------------- LOGIC --------------------
 

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/group/MailDomainGroupRepository.java

@@ -3,6 +3,8 @@
 import edu.harvard.iq.dataverse.persistence.JpaRepository;
 
 import javax.ejb.Singleton;
+import javax.persistence.EntityManager;
+
 import java.util.Optional;
 
 @Singleton
@@ -13,6 +15,12 @@ public class MailDomainGroupRepository extends JpaRepository<Long, MailDomainGro
     public MailDomainGroupRepository() {
         super(MailDomainGroup.class);
     }
+
+    public MailDomainGroupRepository(final EntityManager em) {
+
+        super(MailDomainGroup.class);
+        super.em = em;
+    }
 
     // -------------------- LOGIC --------------------
 

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/harvest/OAIRecordRepository.java

@@ -3,6 +3,7 @@
 import edu.harvard.iq.dataverse.persistence.JpaRepository;
 
 import javax.ejb.Stateless;
+import javax.persistence.EntityManager;
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
 import javax.persistence.criteria.Predicate;
@@ -19,6 +20,12 @@ public class OAIRecordRepository extends JpaRepository<Long, OAIRecord> {
     public OAIRecordRepository() {
         super(OAIRecord.class);
     }
+
+    public OAIRecordRepository(final EntityManager em) {
+
+        super(OAIRecord.class);
+        super.em = em;
+    }
 
     // -------------------- LOGIC --------------------
 

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/harvest/OAISet.java

@@ -74,6 +74,12 @@ public class OAISet implements Serializable, JpaEntity<Long> {
 
     public OAISet() {
     }
+
+    public OAISet(final String name, final String specName) {
+
+        this.name = name;
+        this.spec = specName;
+    }
 
     // -------------------- GETTERS --------------------
 

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/harvest/OAISetRepository.java

@@ -3,6 +3,7 @@
 import edu.harvard.iq.dataverse.persistence.JpaRepository;
 
 import javax.ejb.Stateless;
+import javax.persistence.EntityManager;
 
 import java.util.List;
 import java.util.Optional;
@@ -15,6 +16,12 @@ public class OAISetRepository extends JpaRepository<Long, OAISet> {
     public OAISetRepository() {
         super(OAISet.class);
     }
+    public OAISetRepository(final EntityManager em) {
+
+        super(OAISet.class);
+        super.em = em;
+    }
+
 
     // -------------------- LOGIC --------------------
 

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/ror/RorDataRepository.java

@@ -3,6 +3,7 @@
 import edu.harvard.iq.dataverse.persistence.JpaRepository;
 
 import javax.ejb.Singleton;
+import javax.persistence.EntityManager;
 import javax.persistence.Query;
 
 @Singleton
@@ -13,6 +14,12 @@ public class RorDataRepository extends JpaRepository<Long, RorData> {
     public RorDataRepository() {
         super(RorData.class);
     }
+
+    public RorDataRepository(final EntityManager em) {
+
+        super(RorData.class);
+        super.em = em;
+    }
 
     // -------------------- LOGIC --------------------
 

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/user/AuthenticatedUserRepository.java

@@ -3,6 +3,7 @@
 import edu.harvard.iq.dataverse.persistence.JpaRepository;
 
 import javax.ejb.Stateless;
+import javax.persistence.EntityManager;
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
 import javax.persistence.criteria.Predicate;
@@ -17,6 +18,12 @@ public class AuthenticatedUserRepository extends JpaRepository<Long, Authenticat
     public AuthenticatedUserRepository() {
         super(AuthenticatedUser.class);
     }
+
+    public AuthenticatedUserRepository(final EntityManager em) {
+
+        super(AuthenticatedUser.class);
+        super.em = em;
+    }
 
     // -------------------- LOGIC --------------------
 

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/user/DataverseRoleRepository.java

@@ -3,6 +3,7 @@
 import edu.harvard.iq.dataverse.persistence.JpaRepository;
 
 import javax.ejb.Singleton;
+import javax.persistence.EntityManager;
 
 import java.util.List;
 import java.util.Optional;
@@ -15,6 +16,12 @@ public class DataverseRoleRepository extends JpaRepository<Long, DataverseRole>
     public DataverseRoleRepository() {
         super(DataverseRole.class);
     }
+
+    public DataverseRoleRepository(final EntityManager em) {
+
+        super(DataverseRole.class);
+        super.em = em;
+    }
 
     // -------------------- LOGIC --------------------
 

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/user/RoleAssignmentRepository.java

@@ -6,6 +6,7 @@
 import javax.ejb.Singleton;
 import javax.persistence.NoResultException;
 import javax.persistence.NonUniqueResultException;
+import javax.persistence.EntityManager;
 import javax.persistence.Query;
 
 import static java.util.stream.Collectors.joining;
@@ -21,6 +22,12 @@ public class RoleAssignmentRepository extends JpaRepository<Long, RoleAssignment
     public RoleAssignmentRepository() {
         super(RoleAssignment.class);
     }
+
+    public RoleAssignmentRepository(final EntityManager em) {
+
+        super(RoleAssignment.class);
+        super.em = em;
+    }
 
     // -------------------- LOGIC --------------------
 

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/user/UserNotificationRepository.java

@@ -7,7 +7,6 @@
 
 import javax.ejb.Stateless;
 import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
 import javax.persistence.criteria.Predicate;
@@ -23,14 +22,17 @@
 public class UserNotificationRepository extends JpaRepository<Long, UserNotification> {
     private final static int DELETE_BATCH_SIZE = 100;
 
-    @PersistenceContext(unitName = "VDCNet-ejbPU")
-    private EntityManager em;
-
     // -------------------- CONSTRUCTORS --------------------
 
     public UserNotificationRepository() {
         super(UserNotification.class);
     }
+
+    public UserNotificationRepository(final EntityManager em) {
+
+        super(UserNotification.class);
+        super.em = em;
+    }
 
     // -------------------- LOGIC --------------------
 
@@ -106,11 +108,13 @@ public Long getUnreadNotificationCountByUser(Long userId) {
     }
 
     public int updateEmailSent(long userNotificationId) {
-        return em.createQuery("UPDATE UserNotification notification SET notification.emailed = :emailSent" +
+        final int result =  em.createQuery("UPDATE UserNotification notification SET notification.emailed = :emailSent" +
                                       " WHERE notification.id = :userNotificationId")
                 .setParameter("emailSent", true)
                 .setParameter("userNotificationId", userNotificationId)
                 .executeUpdate();
+        em.clear();
+        return result;
     }
 
     public UserNotification findLastSubmitNotificationByObjectId(long datasetId) {

dataverse-persistence/src/main/java/edu/harvard/iq/dataverse/persistence/workflow/WorkflowExecutionRepository.java

@@ -3,6 +3,8 @@
 import edu.harvard.iq.dataverse.persistence.JpaRepository;
 
 import javax.ejb.Singleton;
+import javax.persistence.EntityManager;
+
 import java.util.Optional;
 
 @Singleton
@@ -14,6 +16,13 @@ public WorkflowExecutionRepository() {
         super(WorkflowExecution.class);
     }
 
+    public WorkflowExecutionRepository(final EntityManager em) {
+
+        super(WorkflowExecution.class);
+        super.em = em;
+    }
+
+
     // -------------------- LOGIC --------------------
 
     /**