#813 - more javax => jakarta. hibernate/postgres related changes

avni-server-api/build.gradle

@@ -41,31 +41,38 @@ repositories { mavenCentral() }
 
 configurations {
     dev
+    all*.exclude group: 'org.slf4j', module: 'slf4j-reload4j'
     all*.exclude group: 'org.slf4j', module: 'slf4j-simple'
 }
 
 dependencies {
-    implementation group: 'org.apache.tomcat', name: 'tomcat-jdbc', version: '8.5.46'
+    implementation group: 'org.apache.tomcat', name: 'tomcat-jdbc'
     implementation("org.springframework.boot:spring-boot-starter-web:${springBootVersion}")
     implementation "org.springframework.boot:spring-boot-starter-data-jpa:${springBootVersion}"
     testImplementation "org.springframework.boot:spring-boot-starter-test:${springBootVersion}"
     implementation "org.springframework.boot:spring-boot-starter-data-rest:${springBootVersion}"
     implementation("org.springframework.boot:spring-boot-starter-security:${springBootVersion}")
     testImplementation "com.github.tomakehurst:wiremock-jre8-standalone:2.34.0"
-    implementation "org.postgresql:postgresql:9.4-1200-jdbc41"
+    implementation "org.postgresql:postgresql"
     implementation 'org.springframework.boot:spring-boot-starter-batch'
     testImplementation 'org.springframework.batch:spring-batch-test'
-    implementation "joda-time:joda-time:2.9.4"
-    implementation group: 'org.jadira.usertype', name: 'usertype.core', version: '6.0.1.GA'
-    implementation "org.flywaydb:flyway-core:4.0.3"
-    implementation "org.flywaydb.flyway-test-extensions:flyway-spring-test:4.0"
-    implementation "com.zaxxer:HikariCP:2.5.1"
+    implementation "joda-time:joda-time"
+    runtimeOnly("javax.transaction:jta:1.1")
+//    implementation(group: 'org.jadira.usertype', name: 'usertype.core', version: '7.0.0.CR1') {
+//        exclude(group: 'org.hibernate', module: 'hibernate-core')
+//    }
+    implementation "org.flywaydb:flyway-core:10.20.1"
+    runtimeOnly("org.flywaydb:flyway-database-postgresql:10.20.1")
+    implementation "org.flywaydb.flyway-test-extensions:flyway-spring6-test:10.0.0"
+    implementation "com.zaxxer:HikariCP"
     implementation "org.apache.poi:poi:3.16-beta2"
     implementation "org.apache.poi:poi-ooxml:3.16-beta2"
-    implementation 'org.apache.httpcomponents:httpclient:4.5.9'
+    implementation 'org.apache.httpcomponents:httpclient'
     implementation 'com.auth0:jwks-rsa:0.3.0'
     implementation 'com.auth0:java-jwt:3.3.0'
-    implementation group: 'org.hibernate', name: 'hibernate-search-orm', version: '5.9.2.Final'
+    implementation(group: 'org.hibernate', name: 'hibernate-search-orm', version: '5.9.2.Final') {
+        exclude(group: 'org.hibernate', module: 'hibernate-core')
+    }
     implementation 'com.bugsnag:bugsnag:3.+'
     implementation 'com.amazonaws:aws-java-sdk-s3'
     implementation 'com.amazonaws:aws-java-sdk-cognitoidp'
@@ -74,12 +81,14 @@ dependencies {
     implementation 'org.springframework.boot:spring-boot-starter-cache'
     implementation 'org.keycloak:keycloak-spring-boot-starter:21.0.2'
     implementation 'org.keycloak:keycloak-admin-client:21.0.2'
-    implementation 'com.fasterxml.jackson.core:jackson-databind:2.12.6'
-    implementation 'com.fasterxml.jackson.core:jackson-core:2.12.6'
-    implementation 'com.fasterxml.jackson.core:jackson-annotations:2.12.6'
-    implementation 'com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider:2.12.6'
-    implementation 'com.fasterxml.jackson.datatype:jackson-datatype-joda:2.12.6'
-    implementation 'org.hibernate:hibernate-ehcache:5.6.15.Final'
+    implementation 'com.fasterxml.jackson.core:jackson-databind:2.15.4'
+    implementation 'com.fasterxml.jackson.core:jackson-core:2.15.4'
+    implementation 'com.fasterxml.jackson.core:jackson-annotations:2.15.4'
+    implementation 'com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider:2.15.2'
+    implementation 'com.fasterxml.jackson.datatype:jackson-datatype-joda:2.15.4'
+    implementation('org.hibernate:hibernate-ehcache:5.6.15.Final') {
+        exclude(group: 'org.hibernate', module: 'hibernate-core')
+    }
     implementation 'javax.cache:cache-api:1.1.1'
     dev "org.springframework.boot:spring-boot-devtools:${springBootVersion}"
     testImplementation "org.mockito:mockito-core:2.23.4"

avni-server-api/src/main/java/org/avni/messaging/domain/ManualMessage.java

@@ -5,9 +5,7 @@
 import org.avni.server.framework.hibernate.NextTriggerDetailsUserType;
 import org.hibernate.annotations.Type;
 
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.Table;
+import jakarta.persistence.*;
 
 @Entity
 @Table(name = "manual_message")

avni-server-api/src/main/java/org/avni/messaging/domain/MessageReceiver.java

@@ -2,7 +2,7 @@
 
 import org.avni.server.domain.OrganisationAwareEntity;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import jakarta.validation.constraints.NotNull;
 
 @Entity

avni-server-api/src/main/java/org/avni/messaging/domain/MessageRequest.java

@@ -3,7 +3,7 @@
 import org.avni.server.domain.OrganisationAwareEntity;
 import org.joda.time.DateTime;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import jakarta.validation.constraints.NotNull;
 
 @Entity

avni-server-api/src/main/java/org/avni/messaging/domain/MessageRule.java

@@ -2,7 +2,7 @@
 
 import org.avni.server.domain.OrganisationAwareEntity;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import jakarta.validation.constraints.NotNull;
 
 @Entity

avni-server-api/src/main/java/org/avni/server/application/DecisionConcept.java

@@ -2,7 +2,7 @@
 
 import org.avni.server.domain.Concept;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import jakarta.validation.constraints.NotNull;
 
 @Entity

avni-server-api/src/main/java/org/avni/server/application/Form.java

@@ -8,7 +8,7 @@
 import org.avni.server.framework.hibernate.DeclarativeRuleUserType;
 import org.hibernate.annotations.Type;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import jakarta.validation.constraints.NotNull;
 import java.util.*;
 import java.util.stream.Collectors;

avni-server-api/src/main/java/org/avni/server/application/FormElement.java

@@ -11,7 +11,7 @@
 import org.avni.server.web.validation.ValidationException;
 import org.springframework.util.StringUtils;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import jakarta.validation.constraints.NotNull;
 import java.util.ArrayList;
 import java.util.HashSet;

avni-server-api/src/main/java/org/avni/server/application/FormElementGroup.java

@@ -6,7 +6,7 @@
 import org.hibernate.annotations.BatchSize;
 import org.hibernate.annotations.Type;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import jakarta.validation.constraints.NotNull;
 import java.util.HashSet;
 import java.util.List;

avni-server-api/src/main/java/org/avni/server/application/FormMapping.java

@@ -10,7 +10,7 @@
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.data.rest.core.config.Projection;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 @Entity
 @Table(name = "form_mapping")

avni-server-api/src/main/java/org/avni/server/application/Format.java

@@ -1,7 +1,6 @@
 package org.avni.server.application;
 
-import javax.persistence.Column;
-import javax.persistence.Embeddable;
+import jakarta.persistence.*;
 
 @Embeddable
 public class Format {

avni-server-api/src/main/java/org/avni/server/application/NonApplicableFormElement.java

@@ -3,7 +3,7 @@
 import org.avni.server.domain.OrganisationAwareEntity;
 import org.hibernate.annotations.BatchSize;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 @Entity
 @Table(name = "non_applicable_form_element")

avni-server-api/src/main/java/org/avni/server/application/menu/MenuItem.java

@@ -2,7 +2,7 @@
 
 import org.avni.server.domain.OrganisationAwareEntity;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 @Entity
 @Table(name = "menu_item")

avni-server-api/src/main/java/org/avni/server/dao/EncounterSearchRepository.java

@@ -8,7 +8,7 @@
 
 import jakarta.persistence.EntityManager;
 import jakarta.persistence.Query;
-import javax.transaction.Transactional;
+import jakarta.transaction.Transactional;
 import java.math.BigInteger;
 import java.util.List;
 

avni-server-api/src/main/java/org/avni/server/dao/JobStatus.java

@@ -1,8 +1,6 @@
 package org.avni.server.dao;
 
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.Id;
+import jakarta.persistence.*;
 import java.util.Date;
 
 @Entity

avni-server-api/src/main/java/org/avni/server/dao/LocationMappingSyncRepository.java

@@ -7,7 +7,7 @@
 import org.springframework.stereotype.Repository;
 
 import jakarta.persistence.EntityManager;
-import javax.transaction.Transactional;
+import jakarta.transaction.Transactional;
 
 /**
  * LocationSyncRepository uses the postgres @> keyword for sync, which does not index well and creates poor plans.

avni-server-api/src/main/java/org/avni/server/dao/LocationSyncRepository.java

@@ -6,7 +6,7 @@
 import org.springframework.stereotype.Repository;
 
 import jakarta.persistence.EntityManager;
-import javax.transaction.Transactional;
+import jakarta.transaction.Transactional;
 
 @Repository
 public class LocationSyncRepository extends RoleSwitchableRepository implements SyncableRepository<AddressLevel> {

avni-server-api/src/main/java/org/avni/server/dao/RoleSwitchableRepository.java

@@ -2,9 +2,7 @@
 
 import org.avni.server.framework.security.UserContextHolder;
 
-import jakarta.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import jakarta.persistence.Query;
+import jakarta.persistence.*;
 
 public abstract class RoleSwitchableRepository {
     @PersistenceContext

avni-server-api/src/main/java/org/avni/server/dao/SubjectSearchRepository.java

@@ -4,18 +4,21 @@
 import org.avni.server.dao.search.SqlQuery;
 import org.avni.server.domain.SubjectType;
 import org.avni.server.web.request.webapp.search.SubjectSearchRequest;
-import org.hibernate.query.internal.NativeQueryImpl;
-import org.hibernate.transform.AliasToEntityMapResultTransformer;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.stereotype.Repository;
 import org.springframework.util.StringUtils;
 
 import jakarta.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+
+import jakarta.persistence.*;
+
 import jakarta.persistence.Query;
-import javax.transaction.Transactional;
+import jakarta.transaction.Transactional;
+
 import java.math.BigInteger;
+import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -32,6 +35,24 @@ public SubjectSearchRepository(EntityManager entityManager, SubjectTypeRepositor
         this.subjectTypeRepository = subjectTypeRepository;
     }
 
+    private List<Map<String, Object>> convertTuplesToMap(List<?> tuples) {
+        List<Map<String, Object>> result = new ArrayList<>();
+
+        tuples.forEach(object -> {
+            if (object instanceof Tuple single) {
+                Map<String, Object> tempMap = new HashMap<>();
+                for (TupleElement<?> key : single.getElements()) {
+                    tempMap.put(key.getAlias(), single.get(key));
+                }
+                result.add(tempMap);
+            } else {
+                throw new RuntimeException("Query should return instance of Tuple");
+            }
+        });
+
+        return result;
+    }
+
     @Transactional
     public List<Map<String, Object>> search(SubjectSearchRequest searchRequest, SearchBuilder searchBuilder) {
         SubjectType subjectType = StringUtils.isEmpty(searchRequest.getSubjectType()) ? null : subjectTypeRepository.findByUuid(searchRequest.getSubjectType());
@@ -41,12 +62,11 @@ public List<Map<String, Object>> search(SubjectSearchRequest searchRequest, Sear
             logger.debug("Executing query: " + query.getSql());
             logger.debug("Parameters: " + query.getParameters());
             Query sql = entityManager.createNativeQuery(query.getSql());
-            NativeQueryImpl nativeQuery = (NativeQueryImpl) sql;
-            nativeQuery.setResultTransformer(AliasToEntityMapResultTransformer.INSTANCE);
             query.getParameters().forEach((name, value) -> {
                 sql.setParameter(name, value);
             });
-            return sql.getResultList();
+            List resultList = sql.getResultList();
+            return convertTuplesToMap(resultList);
         } finally {
             setRoleBackToUser();
         }

avni-server-api/src/main/java/org/avni/server/dao/UserRepository.java

@@ -15,8 +15,7 @@
 import org.springframework.data.rest.core.annotation.RestResource;
 import org.springframework.stereotype.Repository;
 
-import javax.persistence.EntityNotFoundException;
-import jakarta.persistence.QueryHint;
+import jakarta.persistence.*;
 import java.util.List;
 import java.util.Optional;
 

avni-server-api/src/main/java/org/avni/server/domain/AbstractEncounter.java

@@ -8,7 +8,7 @@
 import org.hibernate.annotations.Type;
 import org.joda.time.DateTime;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import jakarta.validation.constraints.NotNull;
 import java.util.Objects;
 

avni-server-api/src/main/java/org/avni/server/domain/Account.java

@@ -3,7 +3,7 @@
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import org.hibernate.annotations.BatchSize;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.HashSet;
 import java.util.Set;
 

avni-server-api/src/main/java/org/avni/server/domain/AccountAdmin.java

@@ -3,7 +3,7 @@
 
 import org.hibernate.annotations.BatchSize;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 @Entity
 @Table(name = "account_admin")

avni-server-api/src/main/java/org/avni/server/domain/AddressLevel.java

@@ -12,7 +12,7 @@
 import org.avni.server.geo.Point;
 import org.springframework.data.rest.core.config.Projection;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import jakarta.validation.constraints.NotNull;
 import java.util.*;
 import java.util.stream.Collectors;

avni-server-api/src/main/java/org/avni/server/domain/AddressLevelType.java

@@ -6,7 +6,7 @@
 import org.avni.server.application.projections.BaseProjection;
 import org.springframework.data.rest.core.config.Projection;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import jakarta.validation.constraints.*;
 import jakarta.validation.constraints.NotNull;
 import java.util.HashSet;

avni-server-api/src/main/java/org/avni/server/domain/AnswerConceptMigration.java

@@ -4,7 +4,7 @@
 import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
 import org.hibernate.annotations.BatchSize;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 @Entity
 @Table(name = "answer_concept_migration")

avni-server-api/src/main/java/org/avni/server/domain/ApprovalStatus.java

@@ -3,7 +3,7 @@
 
 import org.hibernate.annotations.BatchSize;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import jakarta.validation.constraints.NotNull;
 import org.joda.time.DateTime;
 

avni-server-api/src/main/java/org/avni/server/domain/CHSBaseEntity.java

@@ -1,9 +1,10 @@
 package org.avni.server.domain;
 
 import jakarta.validation.constraints.NotNull;
-import org.hibernate.proxy.HibernateProxyHelper;
+import org.hibernate.proxy.HibernateProxy;
+import org.hibernate.proxy.LazyInitializer;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.UUID;
 
 @MappedSuperclass
@@ -59,7 +60,10 @@ public void assignUUIDIfRequired() {
     @Override
     public boolean equals(Object o) {
         if (this == o) return true;
-        if (o == null || HibernateProxyHelper.getClassWithoutInitializingProxy(this) != HibernateProxyHelper.getClassWithoutInitializingProxy(o)) return false;
+
+        LazyInitializer lazyInitializer1 = HibernateProxy.extractLazyInitializer(this);
+        LazyInitializer lazyInitializer2 = HibernateProxy.extractLazyInitializer(o);
+        if (o == null || lazyInitializer2 == null || lazyInitializer1 == null || lazyInitializer1.getImplementationClass() != lazyInitializer2.getImplementationClass()) return false;
 
         CHSBaseEntity that = (CHSBaseEntity) o;
 

avni-server-api/src/main/java/org/avni/server/domain/CHSEntity.java

@@ -11,7 +11,7 @@
 import org.springframework.data.annotation.LastModifiedDate;
 import org.springframework.data.jpa.domain.support.AuditingEntityListener;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.Date;
 
 @MappedSuperclass