WIP: Try out higher version (3.5.5) and Java 17 compile on starter compared to master

README.md

@@ -225,7 +225,7 @@ You will also need to add an additional dependency to your maven pom:
 #### TextIndexer @Indexable annotations
 The legacy TextIndexer can use reflection to automatically index entities using the `@Indexable` annotation on an entity's
 fields and/or public getters. By default, if a field is public it will be indexed.  If a field
-is not public, then the field must be annotated with either `@Indexable` or `@javax.persistance.Id`
+is not public, then the field must be annotated with either `@Indexable` or `@jakarta.persistance.Id`
 for it to be indexed.  If the entity has any superclasses, any inherited fields that meet
 these indexing criteria are also indexed.
 

gsrs-controlled-vocabulary-api/pom.xml

@@ -43,8 +43,8 @@
     </scm>
 
     <properties>
-        <maven.compiler.source>8</maven.compiler.source>
-        <maven.compiler.target>8</maven.compiler.target>
+        <maven.compiler.source>17</maven.compiler.source>
+        <maven.compiler.target>17</maven.compiler.target>
     </properties>
 
     <dependencies>
@@ -69,7 +69,6 @@
         <dependency>
             <groupId>org.junit.jupiter</groupId>
             <artifactId>junit-jupiter</artifactId>
-            <version>5.8.2</version>            
             <scope>test</scope>
         </dependency>
 

gsrs-controlled-vocabulary-api/src/main/java/gsrs/cv/api/GsrsVocabularyTermDTO.java

@@ -8,7 +8,7 @@
 import lombok.NoArgsConstructor;
 import lombok.experimental.SuperBuilder;
 
-import javax.persistence.Column;
+import jakarta.persistence.Column;
 import java.util.Date;
 
 @Data

gsrs-controlled-vocabulary/pom.xml

@@ -12,8 +12,8 @@
     <artifactId>gsrs-controlled-vocabulary</artifactId>
 
     <properties>
-        <maven.compiler.source>8</maven.compiler.source>
-        <maven.compiler.target>8</maven.compiler.target>
+        <maven.compiler.source>17</maven.compiler.source>
+        <maven.compiler.target>17</maven.compiler.target>
     </properties>
 
     <name>gsrs-controlled-vocabulary</name>

gsrs-controlled-vocabulary/src/main/java/gsrs/LoadCvOnStartup.java

@@ -19,7 +19,7 @@
 import org.springframework.core.io.Resource;
 import org.springframework.stereotype.Component;
 
-import javax.persistence.EntityManagerFactory;
+import jakarta.persistence.EntityManagerFactory;
 import java.io.InputStream;
 import java.util.Arrays;
 import java.util.List;

gsrs-controlled-vocabulary/src/main/java/gsrs/cv/CvController.java

@@ -16,8 +16,8 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.hateoas.server.ExposesResourceFor;
 
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
 import java.util.Map;
 import java.util.Optional;
 import java.util.stream.Stream;

gsrs-controlled-vocabulary/src/main/java/ix/ginas/models/v1/CodeSystemControlledVocabulary.java

@@ -3,9 +3,9 @@
 import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
 import ix.ginas.models.serialization.CodeSystemVocabularyTermListDeserializer;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.Inheritance;
+import jakarta.persistence.DiscriminatorValue;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Inheritance;
 import java.util.ArrayList;
 import java.util.List;
 

gsrs-controlled-vocabulary/src/main/java/ix/ginas/models/v1/CodeSystemVocabularyTerm.java

@@ -2,9 +2,9 @@
 
 import ix.core.SingleParent;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.Inheritance;
+import jakarta.persistence.DiscriminatorValue;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Inheritance;
 
 /**
  * Created by peryeata on 2/17/16.

gsrs-controlled-vocabulary/src/main/java/ix/ginas/models/v1/ControlledVocabulary.java

@@ -13,7 +13,7 @@
 import lombok.Getter;
 import lombok.Setter;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.ArrayList;
 import java.util.List;
 

gsrs-controlled-vocabulary/src/main/java/ix/ginas/models/v1/FragmentControlledVocabulary.java

@@ -3,9 +3,9 @@
 import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
 import ix.ginas.models.serialization.FragmentVocabularyTermListDeserializer;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.Inheritance;
+import jakarta.persistence.DiscriminatorValue;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Inheritance;
 import java.util.ArrayList;
 import java.util.List;
 

gsrs-controlled-vocabulary/src/main/java/ix/ginas/models/v1/FragmentVocabularyTerm.java

@@ -2,9 +2,9 @@
 
 import ix.core.SingleParent;
 
-import javax.persistence.DiscriminatorValue;
-import javax.persistence.Entity;
-import javax.persistence.Inheritance;
+import jakarta.persistence.DiscriminatorValue;
+import jakarta.persistence.Entity;
+import jakarta.persistence.Inheritance;
 
 /**
  * Created by peryeata on 02/17/2016.

gsrs-controlled-vocabulary/src/main/java/ix/ginas/models/v1/VocabularyTerm.java

@@ -13,7 +13,7 @@
 import lombok.Getter;
 import lombok.Setter;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 
 /**
  * Created by sheilstk on 6/29/15.

gsrs-core-entities/src/main/java/gsrs/AbstractEntityProcessorFactory.java

@@ -7,7 +7,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
-import javax.annotation.PostConstruct;
+import jakarta.annotation.PostConstruct;
 import java.util.*;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.function.Consumer;

gsrs-core-entities/src/main/java/gsrs/AuditConfig.java

@@ -27,8 +27,8 @@
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.transaction.support.TransactionTemplate;
 
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
 
 import java.time.temporal.TemporalAccessor;
 import java.util.Collections;

gsrs-core-entities/src/main/java/gsrs/BackupEntityProcessorListener.java

@@ -1,8 +1,8 @@
 package gsrs;
 
-import javax.persistence.PostPersist;
-import javax.persistence.PostRemove;
-import javax.persistence.PostUpdate;
+import jakarta.persistence.PostPersist;
+import jakarta.persistence.PostRemove;
+import jakarta.persistence.PostUpdate;
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationEventPublisher;

gsrs-core-entities/src/main/java/gsrs/EntityPersistAdapter.java

@@ -6,7 +6,7 @@
 import java.util.Optional;
 import java.util.concurrent.ConcurrentHashMap;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationEventPublisher;

gsrs-core-entities/src/main/java/gsrs/GsrsEntityDirtinessStrategy.java

@@ -4,7 +4,7 @@
 import org.hibernate.Session;
 import org.hibernate.persister.entity.EntityPersister;
 
-import javax.persistence.Version;
+import jakarta.persistence.Version;
 import java.lang.reflect.Field;
 import java.util.*;
 import java.util.concurrent.ConcurrentHashMap;

gsrs-core-entities/src/main/java/gsrs/GsrsEntityProcessorListener.java

@@ -3,13 +3,13 @@
 import java.util.HashSet;
 import java.util.LinkedHashSet;
 
-import javax.persistence.PostLoad;
-import javax.persistence.PostPersist;
-import javax.persistence.PostRemove;
-import javax.persistence.PostUpdate;
-import javax.persistence.PrePersist;
-import javax.persistence.PreRemove;
-import javax.persistence.PreUpdate;
+import jakarta.persistence.PostLoad;
+import jakarta.persistence.PostPersist;
+import jakarta.persistence.PostRemove;
+import jakarta.persistence.PostUpdate;
+import jakarta.persistence.PrePersist;
+import jakarta.persistence.PreRemove;
+import jakarta.persistence.PreUpdate;
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationEventPublisher;

gsrs-core-entities/src/main/java/gsrs/OutsideTransactionUtil.java

@@ -2,9 +2,9 @@
 
 import org.springframework.stereotype.Component;
 
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.transaction.Transactional;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import jakarta.transaction.Transactional;
 import java.util.function.Consumer;
 @Component
 public class OutsideTransactionUtil {

gsrs-core-entities/src/main/java/gsrs/controller/GsrsControllerConfiguration.java

@@ -9,7 +9,7 @@
 import org.springframework.security.access.AccessDeniedException;
 import org.springframework.web.context.request.WebRequest;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.lang.reflect.InvocationTargetException;
 import java.util.Collections;
 import java.util.HashMap;

gsrs-core-entities/src/main/java/gsrs/controller/GsrsControllerUtil.java

@@ -14,7 +14,7 @@
 import org.springframework.web.servlet.HandlerMapping;
 import org.springframework.web.servlet.resource.ResourceUrlProvider;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 import java.net.URI;
 import java.util.*;
 import java.util.function.Consumer;

gsrs-core-entities/src/main/java/gsrs/controller/hateoas/HttpRequestHolder.java

@@ -8,7 +8,7 @@
 import java.util.Map;
 import java.util.Optional;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 
 import org.springframework.http.HttpEntity;
 import org.springframework.http.HttpHeaders;

gsrs-core-entities/src/main/java/gsrs/controller/hateoas/IxContext.java

@@ -2,7 +2,7 @@
 
 import java.net.URI;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Configuration;

gsrs-core-entities/src/main/java/gsrs/controller/hateoas/LoopbackWebRequestHelper.java

@@ -10,7 +10,7 @@
 import java.util.Set;
 import java.util.stream.Collectors;
 
-import javax.servlet.http.HttpServletRequest;
+import jakarta.servlet.http.HttpServletRequest;
 
 import lombok.extern.slf4j.Slf4j;
 import org.springframework.beans.factory.annotation.Autowired;

gsrs-core-entities/src/main/java/gsrs/indexer/IndexerEntityListener.java

@@ -1,8 +1,8 @@
 package gsrs.indexer;
 
-import javax.persistence.PostPersist;
-import javax.persistence.PostRemove;
-import javax.persistence.PostUpdate;
+import jakarta.persistence.PostPersist;
+import jakarta.persistence.PostRemove;
+import jakarta.persistence.PostUpdate;
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationEventPublisher;

gsrs-core-entities/src/main/java/gsrs/model/AbstractGsrsEntity.java

@@ -1,7 +1,7 @@
 package gsrs.model;
 
-import javax.persistence.EntityListeners;
-import javax.persistence.MappedSuperclass;
+import jakarta.persistence.EntityListeners;
+import jakarta.persistence.MappedSuperclass;
 
 import org.springframework.data.jpa.domain.support.AuditingEntityListener;
 

gsrs-core-entities/src/main/java/gsrs/model/AbstractGsrsManualDirtyEntity.java

@@ -3,7 +3,7 @@
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import gsrs.GsrsManualDirtyMaker;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.*;
 import java.util.concurrent.ConcurrentHashMap;
 

gsrs-core-entities/src/main/java/gsrs/model/AbstractGsrsTablePerClassEntity.java

@@ -1,6 +1,6 @@
 package gsrs.model;
 
-import javax.persistence.EntityListeners;
+import jakarta.persistence.EntityListeners;
 
 import org.springframework.data.jpa.domain.support.AuditingEntityListener;
 

gsrs-core-entities/src/main/java/gsrs/model/AbstractNonAuditingGsrsEntity.java

@@ -9,10 +9,10 @@
 import ix.core.util.EntityUtils;
 import org.springframework.data.jpa.domain.support.AuditingEntityListener;
 
-import javax.persistence.EntityListeners;
-import javax.persistence.MappedSuperclass;
-import javax.persistence.PostLoad;
-import javax.persistence.Transient;
+import jakarta.persistence.EntityListeners;
+import jakarta.persistence.MappedSuperclass;
+import jakarta.persistence.PostLoad;
+import jakarta.persistence.Transient;
 
 /**
  * Base abstract class for Gsrs Entities should extend,

gsrs-core-entities/src/main/java/gsrs/repository/UserProfileRepository.java

@@ -31,7 +31,7 @@ public interface UserProfileRepository extends JpaRepository<UserProfile, Long>
      * @return the list of UserProfiles that might be admins.
      * @see #findAnAdminUsername()
      */
-    @Query("select up from UserProfile up where up.rolesJSON like '%Admin%'")
+    @Query("select up from UserProfile up where LOCATE('Admin', CAST(up.rolesJSON as string)) > 0")
     List<UserProfile> _findAllCandidateAdmins();
     /**
      * Get an admin name this will only return at most 1 admin username

gsrs-core-entities/src/main/java/gsrs/services/GroupServiceImpl.java

@@ -8,7 +8,7 @@
 import org.springframework.transaction.annotation.Transactional;
 import org.springframework.transaction.support.TransactionSynchronizationManager;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;

gsrs-core-entities/src/main/java/gsrs/services/PrincipalServiceImpl.java

@@ -5,7 +5,7 @@
 import java.util.Optional;
 import java.util.concurrent.ConcurrentHashMap;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;

gsrs-core-entities/src/main/java/gsrs/services/UserProfileService.java

@@ -18,8 +18,8 @@
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
 
 import java.util.*;
 import java.util.regex.Pattern;

gsrs-core-entities/src/main/java/ix/core/models/Acl.java

@@ -1,6 +1,6 @@
 package ix.core.models;
 
-import javax.persistence.*;
+import jakarta.persistence.*;
 import java.util.ArrayList;
 import java.util.List;
 

gsrs-core-entities/src/main/java/ix/core/models/BackupEntity.java

@@ -4,13 +4,13 @@
 import java.util.Objects;
 import java.util.Optional;
 
-import javax.persistence.Basic;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.Lob;
-import javax.persistence.SequenceGenerator;
-import javax.persistence.Table;
+import jakarta.persistence.Basic;
+import jakarta.persistence.Column;
+import jakarta.persistence.Entity;
+import jakarta.persistence.FetchType;
+import jakarta.persistence.Lob;
+import jakarta.persistence.SequenceGenerator;
+import jakarta.persistence.Table;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
 

gsrs-core-entities/src/main/java/ix/core/models/BaseModel.java

@@ -6,8 +6,8 @@
 import gsrs.model.AbstractGsrsManualDirtyEntity;
 import ix.core.util.EntityUtils.EntityWrapper;
 
-import javax.persistence.MappedSuperclass;
-import javax.persistence.Transient;
+import jakarta.persistence.MappedSuperclass;
+import jakarta.persistence.Transient;
 import java.util.*;
 import java.util.Map.Entry;