chore: upgrade to spring 6 (#18314)

* chore: upgrade spring 6 * replace httpclient with httpclient5 * fix: setReadTimeOut is removed * fix use jakarta adapter for ActiveMQ lib * fix HttpStatusCode * upgrade spring-security to 6.3.1 * upgrade jakarta-persistence-api 3.2.0 * replace hibernate-types with hypersistence-utils * Fix CommonsMultipartFile * fix micrometer-hibernate * exclude hibernate-core dependency * fix jasperreport jakarta * upgrade tomcat-embed-core to 10.1.28 * upgrade jetty to 12.0.12 * minor fix * Add DhisPersistenceUnitManager and DhisPersistenceUnitInfo * fix programruleaction.notificationtemplateid type in database * fix spring security conflicts * fix prometheus conflicts * remove redundant class * merge from master * merge from master * merge from master * remove redundant hibernate config * fix HttpUtils * fix maven dependency issues * fix maven dependency issues * fix BulkSmsGatewayTest * merge from master * fix TrackedEntityAttributeStoreTest * revert javax package fix * fix cors config for spring security 6 * merge from master * merge from master * clear cache * fix setUseTrailingSlashMatch issue * merge from master * fix CustomRequestMappingHandlerMapping * fix ContentNegotiationManager in test * fix: hibernate configs * fix messageSender test * merge from masterwq * fix HibernateApiTrackedEntityAuditStorewq * fix messageSender in test config * merge from master * merge from master * fix dataSource bean config * replace @EnableMethodSecurity * fix messageSender bean wiring * fix flyway migration * fix emailMessageSender wiring * fix emailMessageSender in test * fix DataApprovalControllerTest * fix MessageSender bean autowire issue * fix merge conflicts * fix code formats * fix maven dependency issue * fix merge conflicts * fix maven dependency * fix tracker tests * fix NodeService bean injection * code format * code format * Disable test testDeleteWithException * fix test * revert debug log * fix: fix ecache issue with DataDimensionTypeUserType * fix jakarta in TrailingSlashInterceptor * fix: remove usage of requires_new * Change tomcat version * fix test * fix: revert remove usage of requires_new, except for jobs * fix HttpStatusCode * fix deps * fix job update status * code format * fix systemSettings api content-type * code format * code format * code format * chore: Fix file resource multipart upload test * chore: fix formatting * fix: wrong charset in content-type headers * fix: remove merge artifacts * fix: merge artifacts * fix: fake message sender refactorings * code format * fix sonarcloud issue * fix sonarcloud issue * chore: adjust sms related * fix: adjust sms test * fix: adjust sms test * add jobSchedulerService.createThenExecute method * code format * remove entityManager.getReference in HibernateIdentifiableObjectStore * fix sonar issues * fix merge conflicts * code format * fix DhisCorsFilter * remove interface FakeMessageSender * fix DhisCorsProcessor * revert build.sh * temp amend jenkins dev file for pipeline test * update docker build image to use tomcat 10 to test pipeline * update root pom to tomcat 10 to test pipeline * update jenkins dev to tomcat 10 to test pipeline * uncomment code in jenkins dev file after testing * format --------- Co-authored-by: Morrten Svanaes <[email protected]> Co-authored-by: Enrico <[email protected]> Co-authored-by: David Mackessy <[email protected]> Co-authored-by: Jan Bernitt <[email protected]>
dhis2 · Oct 3, 2024 · 2097f7e · 2097f7e
1 parent 942cd60
commit 2097f7e
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diff --git a/dhis-2/build-docker-image.sh b/dhis-2/build-docker-image.sh
@@ -215,7 +215,7 @@ jdk_version="$(
   echo "$stable_versions_json" |
   jq -r --argjson major "$major" '.versions[] | select(.version == $major) .jdk'
 )"
-BASE_IMAGE="${BASE_IMAGE:-"tomcat:9.0-jre$jdk_version"}"
+BASE_IMAGE="${BASE_IMAGE:-"tomcat:10.0-jre$jdk_version"}"
 
 build_main_image
 

diff --git a/dhis-2/build.sh b/dhis-2/build.sh
diff --git a/dhis-2/dhis-api/pom.xml b/dhis-2/dhis-api/pom.xml
@@ -49,6 +49,10 @@
       <groupId>com.fasterxml.jackson.core</groupId>
       <artifactId>jackson-databind</artifactId>
     </dependency>
+    <dependency>
+      <groupId>jakarta.xml.bind</groupId>
+      <artifactId>jakarta.xml.bind-api</artifactId>
+    </dependency>
     <dependency>
       <groupId>com.fasterxml.jackson.dataformat</groupId>
       <artifactId>jackson-dataformat-xml</artifactId>
@@ -117,18 +121,14 @@
       <groupId>org.geotools</groupId>
       <artifactId>gt-geojson</artifactId>
     </dependency>
-    <dependency>
-      <groupId>javax.xml.bind</groupId>
-      <artifactId>jaxb-api</artifactId>
-    </dependency>
     <dependency>
       <groupId>org.projectlombok</groupId>
       <artifactId>lombok</artifactId>
       <scope>provided</scope>
     </dependency>
     <dependency>
       <groupId>org.hibernate</groupId>
-      <artifactId>hibernate-core</artifactId>
+      <artifactId>hibernate-core-jakarta</artifactId>
     </dependency>
     <dependency>
       <groupId>com.google.code.findbugs</groupId>
@@ -139,8 +139,8 @@
       <artifactId>gt-opengis</artifactId>
     </dependency>
     <dependency>
-      <groupId>javax.persistence</groupId>
-      <artifactId>javax.persistence-api</artifactId>
+      <groupId>jakarta.persistence</groupId>
+      <artifactId>jakarta.persistence-api</artifactId>
     </dependency>
 
     <!-- SMPP -->
@@ -186,8 +186,8 @@
       <scope>test</scope>
     </dependency>
     <dependency>
-      <groupId>javax.servlet</groupId>
-      <artifactId>javax.servlet-api</artifactId>
+      <groupId>jakarta.servlet</groupId>
+      <artifactId>jakarta.servlet-api</artifactId>
     </dependency>
   </dependencies>
 </project>
diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/common/ObjectDeletionRequestedEvent.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/common/ObjectDeletionRequestedEvent.java
@@ -33,8 +33,9 @@
  * @author Lars Helge Overland
  */
 public class ObjectDeletionRequestedEvent extends ApplicationEvent {
+
   /** Should rollback the transaction if DeleteNotAllowedException is thrown */
-  private boolean shouldRollBack = true;
+  private boolean rollback = true;
 
   // -------------------------------------------------------------------------
   // Constructors
@@ -44,15 +45,16 @@ public ObjectDeletionRequestedEvent(Object source) {
     super(source);
   }
 
+  public ObjectDeletionRequestedEvent(Object source, boolean rollback) {
+    super(source);
+    this.rollback = rollback;
+  }
+
   // -------------------------------------------------------------------------
   // Getter && Setter
   // -------------------------------------------------------------------------
 
-  public boolean isShouldRollBack() {
-    return shouldRollBack;
-  }
-
-  public void setShouldRollBack(boolean shouldRollBack) {
-    this.shouldRollBack = shouldRollBack;
+  public boolean isRollback() {
+    return rollback;
   }
 }
diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/deletedobject/DeletedObject.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/deletedobject/DeletedObject.java
@@ -32,17 +32,17 @@
 import com.fasterxml.jackson.dataformat.xml.annotation.JacksonXmlRootElement;
 import com.google.common.base.MoreObjects;
 import com.google.common.base.Objects;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.GeneratedValue;
+import jakarta.persistence.Id;
+import jakarta.persistence.SequenceGenerator;
+import jakarta.persistence.Table;
+import jakarta.persistence.Temporal;
+import jakarta.persistence.TemporalType;
+import jakarta.persistence.UniqueConstraint;
 import java.io.Serializable;
 import java.util.Date;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.Id;
-import javax.persistence.SequenceGenerator;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
-import javax.persistence.UniqueConstraint;
 import org.apache.commons.lang3.StringUtils;
 import org.hisp.dhis.common.DxfNamespaces;
 import org.hisp.dhis.common.IdentifiableObject;

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/fileresource/SimpleImageResource.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/fileresource/SimpleImageResource.java
@@ -28,10 +28,10 @@
 package org.hisp.dhis.fileresource;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
+import jakarta.xml.bind.annotation.XmlRootElement;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Objects;
-import javax.xml.bind.annotation.XmlRootElement;
 
 /** This is simple class to represent the list of possible static image resources. */
 @XmlRootElement

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/hibernate/HibernateProxyUtils.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/hibernate/HibernateProxyUtils.java
@@ -29,7 +29,6 @@
 
 import java.util.Objects;
 import org.hibernate.Hibernate;
-import org.hibernate.proxy.HibernateProxy;
 import org.hibernate.proxy.HibernateProxyHelper;
 
 /**
@@ -55,15 +54,4 @@ public static Class getRealClass(Object object) {
   public static <T> T unproxy(T proxy) {
     return (T) Hibernate.unproxy(proxy);
   }
-
-  public static <T> void initializeAndUnproxy(T entity) {
-    if (entity == null) {
-      return;
-    }
-
-    Hibernate.initialize(entity);
-    if (entity instanceof HibernateProxy) {
-      ((HibernateProxy) entity).getHibernateLazyInitializer().getImplementation();
-    }
-  }
 }
diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/message/MessageSender.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/message/MessageSender.java
@@ -27,8 +27,10 @@
  */
 package org.hisp.dhis.message;
 
+import java.util.List;
 import java.util.Set;
 import java.util.concurrent.Future;
+import org.hisp.dhis.outboundmessage.OutboundMessage;
 import org.hisp.dhis.outboundmessage.OutboundMessageBatch;
 import org.hisp.dhis.outboundmessage.OutboundMessageResponse;
 import org.hisp.dhis.outboundmessage.OutboundMessageResponseSummary;
@@ -39,6 +41,7 @@
  * @author Lars Helge Overland
  */
 public interface MessageSender {
+
   /**
    * Sends a message. The given message will be sent to the given set of users.
    *
@@ -71,4 +74,14 @@ ListenableFuture<OutboundMessageResponseSummary> sendMessageBatchAsync(
 
   /** To check if given service is configured and ready to use. */
   boolean isConfigured();
+
+  default List<OutboundMessage> getMessagesByEmail(String recipient) {
+    return List.of();
+  }
+
+  default void clearMessages() {}
+
+  default List<OutboundMessage> getAllMessages() {
+    return List.of();
+  }
 }
diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/scheduling/JobConfigurationService.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/scheduling/JobConfigurationService.java
@@ -32,6 +32,7 @@
 import java.util.Map;
 import javax.annotation.Nonnull;
 import org.hisp.dhis.feedback.ConflictException;
+import org.hisp.dhis.feedback.NotFoundException;
 import org.hisp.dhis.schema.Property;
 import org.hisp.dhis.user.UserDetails;
 import org.springframework.util.MimeType;
@@ -61,6 +62,13 @@ String create(JobConfiguration config, MimeType contentType, InputStream content
 
   void createDefaultJob(JobType type, UserDetails actingUser);
 
+  String createInTransaction(
+      JobConfiguration jobConfiguration, MimeType contentType, InputStream content)
+      throws ConflictException, NotFoundException;
+
+  String createInTransaction(JobConfiguration jobConfiguration)
+      throws ConflictException, NotFoundException;
+
   /**
    * Updates all {@link JobConfiguration}s that are not {@link JobConfiguration#isEnabled()} to
    * state {@link JobStatus#DISABLED} in case they are in state {@link JobStatus#SCHEDULED}.

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/scheduling/JobConfigurationStore.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/scheduling/JobConfigurationStore.java
@@ -175,6 +175,8 @@ public interface JobConfigurationStore extends GenericDimensionalObjectStore<Job
    */
   boolean tryRevertNow(@Nonnull String jobId);
 
+  boolean executeNow(@Nonnull String jobId);
+
   /**
    * A successful update means the DB state flipped from {@link JobStatus#SCHEDULED} to {@link
    * JobStatus#RUNNING}.

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/scheduling/JobSchedulerService.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/scheduling/JobSchedulerService.java
@@ -27,15 +27,18 @@
  */
 package org.hisp.dhis.scheduling;
 
+import java.io.InputStream;
 import java.util.List;
 import java.util.Set;
 import javax.annotation.CheckForNull;
 import javax.annotation.Nonnull;
+import org.hisp.dhis.common.NonTransactional;
 import org.hisp.dhis.common.UID;
 import org.hisp.dhis.feedback.ConflictException;
 import org.hisp.dhis.feedback.ForbiddenException;
 import org.hisp.dhis.feedback.NotFoundException;
 import org.hisp.dhis.scheduling.JobProgress.Progress;
+import org.springframework.util.MimeType;
 
 /**
  * This is the external API (called by users via controller API) for the scheduling.
@@ -60,6 +63,22 @@ public interface JobSchedulerService {
    */
   void executeNow(@Nonnull String jobId) throws ConflictException, NotFoundException;
 
+  /**
+   * Executes a job configuration in a separate transaction.
+   *
+   * @param jobId the job id to execute
+   * @throws NotFoundException
+   * @throws ConflictException
+   */
+  void runInTransaction(String jobId) throws NotFoundException, ConflictException;
+
+  @NonTransactional
+  void createThenExecute(JobConfiguration config, MimeType contentType, InputStream content)
+      throws ConflictException, NotFoundException;
+
+  @NonTransactional
+  void createThenExecute(JobConfiguration config) throws ConflictException, NotFoundException;
+
   /**
    * Reverts the {@link JobStatus} of the job from {@link JobStatus#RUNNING} to the appropriate
    * status after a failed execution. For an ad-hoc job this is {@link JobStatus#DISABLED}, for a

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/security/AuthenticationSerializer.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/security/AuthenticationSerializer.java
@@ -27,7 +27,7 @@
  */
 package org.hisp.dhis.security;
 
-import javax.xml.bind.DatatypeConverter;
+import jakarta.xml.bind.DatatypeConverter;
 import org.apache.commons.lang3.SerializationUtils;
 import org.springframework.security.core.Authentication;
 

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/sms/config/SmsConfiguration.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/sms/config/SmsConfiguration.java
@@ -28,11 +28,11 @@
 package org.hisp.dhis.sms.config;
 
 import com.fasterxml.jackson.annotation.JsonProperty;
+import jakarta.xml.bind.annotation.XmlRootElement;
 import java.io.Serial;
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
-import javax.xml.bind.annotation.XmlRootElement;
 import lombok.Getter;
 import lombok.NoArgsConstructor;
 import lombok.Setter;

diff --git a/dhis-2/dhis-api/src/main/java/org/hisp/dhis/user/UserAccountService.java b/dhis-2/dhis-api/src/main/java/org/hisp/dhis/user/UserAccountService.java
@@ -27,8 +27,8 @@
  */
 package org.hisp.dhis.user;
 
+import jakarta.servlet.http.HttpServletRequest;
 import java.io.IOException;
-import javax.servlet.http.HttpServletRequest;
 import org.hisp.dhis.common.auth.RegistrationParams;
 import org.hisp.dhis.common.auth.UserInviteParams;
 import org.hisp.dhis.common.auth.UserRegistrationParams;

diff --git a/dhis-2/dhis-services/dhis-service-administration/pom.xml b/dhis-2/dhis-services/dhis-service-administration/pom.xml
@@ -101,8 +101,8 @@
       <scope>test</scope>
     </dependency>
     <dependency>
-      <groupId>javax.persistence</groupId>
-      <artifactId>javax.persistence-api</artifactId>
+      <groupId>jakarta.persistence</groupId>
+      <artifactId>jakarta.persistence-api</artifactId>
     </dependency>
     <dependency>
       <groupId>org.slf4j</groupId>

diff --git a/...tion/src/main/java/org/hisp/dhis/dataintegrity/hibernate/HibernateDataIntegrityStore.java b/...tion/src/main/java/org/hisp/dhis/dataintegrity/hibernate/HibernateDataIntegrityStore.java
@@ -29,10 +29,10 @@
 
 import static java.util.stream.Collectors.toUnmodifiableList;
 
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
 import java.util.Date;
 import java.util.List;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
 import lombok.RequiredArgsConstructor;
 import org.hisp.dhis.dataintegrity.DataIntegrityCheck;
 import org.hisp.dhis.dataintegrity.DataIntegrityDetails;

diff --git a/...administration/src/main/java/org/hisp/dhis/merge/dataelement/DataElementMergeService.java b/...administration/src/main/java/org/hisp/dhis/merge/dataelement/DataElementMergeService.java
@@ -28,12 +28,12 @@
 package org.hisp.dhis.merge.dataelement;
 
 import com.google.common.collect.ImmutableList;
+import jakarta.persistence.EntityManager;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 import javax.annotation.Nonnull;
 import javax.annotation.PostConstruct;
-import javax.persistence.EntityManager;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 import org.hisp.dhis.common.UID;

diff --git a/...on/src/main/java/org/hisp/dhis/merge/dataelement/handler/DataDataElementMergeHandler.java b/...on/src/main/java/org/hisp/dhis/merge/dataelement/handler/DataDataElementMergeHandler.java
@@ -27,6 +27,7 @@
  */
 package org.hisp.dhis.merge.dataelement.handler;
 
+import jakarta.persistence.EntityManager;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Comparator;
@@ -35,7 +36,6 @@
 import java.util.function.BiPredicate;
 import java.util.stream.Collectors;
 import javax.annotation.Nonnull;
-import javax.persistence.EntityManager;
 import lombok.RequiredArgsConstructor;
 import lombok.extern.slf4j.Slf4j;
 import org.hisp.dhis.dataelement.DataElement;

diff --git a/...nistration/src/main/java/org/hisp/dhis/merge/orgunit/handler/DataOrgUnitMergeHandler.java b/...nistration/src/main/java/org/hisp/dhis/merge/orgunit/handler/DataOrgUnitMergeHandler.java
@@ -29,7 +29,7 @@
 
 import static org.hisp.dhis.common.IdentifiableObjectUtils.getIdentifiers;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import lombok.RequiredArgsConstructor;
 import org.hisp.dhis.common.IdentifiableObjectUtils;
 import org.hisp.dhis.dataapproval.DataApprovalAuditService;

diff --git a/...tration/src/main/java/org/hisp/dhis/merge/orgunit/handler/TrackerOrgUnitMergeHandler.java b/...tration/src/main/java/org/hisp/dhis/merge/orgunit/handler/TrackerOrgUnitMergeHandler.java
@@ -27,7 +27,7 @@
  */
 package org.hisp.dhis.merge.orgunit.handler;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import lombok.RequiredArgsConstructor;
 import org.hisp.dhis.common.IdentifiableObjectUtils;
 import org.hisp.dhis.merge.orgunit.OrgUnitMergeRequest;