#813 - source compiling

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

@@ -8,13 +8,12 @@
 import org.springframework.data.jpa.repository.support.JpaEntityInformation;
 import org.springframework.data.jpa.repository.support.SimpleJpaRepository;
 
-import javax.persistence.EntityManager;
-import javax.persistence.TypedQuery;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.TypedQuery;
 import java.io.Serializable;
 import java.util.List;
 
 public class CustomJpaRepositoryImpl<T extends CHSEntity, ID extends Serializable> extends SimpleJpaRepository<T, ID> implements CustomCHSJpaRepository<T, ID> {
-
     public CustomJpaRepositoryImpl(JpaEntityInformation<T, ?> entityInformation, EntityManager entityManager) {
         super(entityInformation, entityManager);
     }
@@ -25,6 +24,11 @@ public Slice<T> findAllAsSlice(Specification<T> specification, Pageable pageable
         return pageable.isUnpaged() ? new SliceImpl<>(query.getResultList()) : readSlice(query, pageable, specification);
     }
 
+    @Override
+    public void deleteInBatch(Iterable<T> entities) {
+        entities.forEach(this::delete);
+    }
+
     private Slice<T> readSlice(TypedQuery<T> query, Pageable pageable, Specification<T> specification){
         if (pageable.isPaged()){
             query.setFirstResult((int) pageable.getOffset());
@@ -37,4 +41,4 @@ private Slice<T> readSlice(TypedQuery<T> query, Pageable pageable, Specification
         }
         return new SliceImpl<>(content, pageable, hasNextPage);
     }
-}
+}

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

@@ -6,8 +6,8 @@
 import org.avni.server.web.api.EncounterSearchRequest;
 import org.springframework.stereotype.Repository;
 
-import javax.persistence.EntityManager;
-import javax.persistence.Query;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.Query;
 import javax.transaction.Transactional;
 import java.math.BigInteger;
 import java.util.List;

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

@@ -6,7 +6,7 @@
 import org.springframework.data.domain.Slice;
 import org.springframework.stereotype.Repository;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import javax.transaction.Transactional;
 
 /**

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

@@ -5,7 +5,7 @@
 import org.springframework.data.domain.Slice;
 import org.springframework.stereotype.Repository;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import javax.transaction.Transactional;
 
 @Repository

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

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

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

@@ -11,9 +11,9 @@
 import org.springframework.stereotype.Repository;
 import org.springframework.util.StringUtils;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
-import javax.persistence.Query;
+import jakarta.persistence.Query;
 import javax.transaction.Transactional;
 import java.math.BigInteger;
 import java.util.List;

avni-server-api/src/main/java/org/avni/server/exporter/ExportBatchConfiguration.java

@@ -27,7 +27,7 @@
 import org.springframework.context.annotation.Configuration;
 import org.springframework.data.domain.Sort;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import java.util.*;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;

avni-server-api/src/main/java/org/avni/server/exporter/LongitudinalExportTaskletImpl.java

@@ -5,13 +5,14 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.batch.core.StepContribution;
 import org.springframework.batch.core.scope.context.ChunkContext;
+import org.springframework.batch.item.Chunk;
 import org.springframework.batch.item.ExecutionContext;
 import org.springframework.batch.item.file.FlatFileItemWriter;
 import org.springframework.batch.item.file.transform.DelimitedLineAggregator;
 import org.springframework.batch.repeat.RepeatStatus;
 import org.springframework.core.io.FileSystemResource;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Iterator;
@@ -86,7 +87,8 @@ private void createFileWriter(String uuid, ExecutionContext executionContext) {
 
     private void writeToFile(List<ExportItemRow> rows) throws Exception {
         if (rows.size() == 0) return;
-        writer.write(rows);
+
+        writer.write(Chunk.of(rows.toArray(new ExportItemRow[0])));
     }
 
     @Override

avni-server-api/src/main/java/org/avni/server/exporter/v2/LongitudinalExportV2TaskletImpl.java

@@ -6,13 +6,14 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.batch.core.StepContribution;
 import org.springframework.batch.core.scope.context.ChunkContext;
+import org.springframework.batch.item.Chunk;
 import org.springframework.batch.item.ExecutionContext;
 import org.springframework.batch.item.file.FlatFileItemWriter;
 import org.springframework.batch.item.file.transform.DelimitedLineAggregator;
 import org.springframework.batch.repeat.RepeatStatus;
 import org.springframework.core.io.FileSystemResource;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.Iterator;
@@ -92,7 +93,7 @@ private void createFileWriter(String uuid, ExecutionContext executionContext) {
 
     private void writeToFile(List<LongitudinalExportItemRow> rows) throws Exception {
         if (rows.isEmpty()) return;
-        writer.write(rows);
+        writer.write(Chunk.of(rows.toArray(new LongitudinalExportItemRow[0])));
     }
 
     @Override

avni-server-api/src/main/java/org/avni/server/framework/postgres/CHSPostgreSQLDialect.java

@@ -0,0 +1,20 @@
+package org.avni.server.framework.postgres;
+
+import org.hibernate.dialect.PostgreSQL10Dialect;
+import org.hibernate.type.StandardBasicTypes;
+import org.hibernate.type.descriptor.jdbc.JdbcType;
+import org.hibernate.type.descriptor.jdbc.spi.JdbcTypeRegistry;
+
+import java.sql.Types;
+
+public class CHSPostgreSQLDialect extends PostgreSQL10Dialect {
+    private static final String JSONB = "jsonb";
+    private static final String JSON = "json";
+
+    public CHSPostgreSQLDialect() {
+        super();
+//        this.registerColumnTypes();
+//        this.registerColumnType(Types.JAVA_OBJECT, JSONB);
+//        this.registerColumnType(Types.JAVA_OBJECT, JSON);
+    }
+}

avni-server-api/src/main/java/org/avni/server/service/AddressLevelCache.java

@@ -8,7 +8,7 @@
 import org.springframework.cache.annotation.Cacheable;
 import org.springframework.stereotype.Component;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import javax.transaction.Transactional;
 import java.util.List;
 

avni-server-api/src/main/java/org/avni/server/service/CatchmentService.java

@@ -16,7 +16,7 @@
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import javax.transaction.Transactional;
 import java.util.ArrayList;
 import java.util.HashSet;

avni-server-api/src/main/java/org/avni/server/web/CatchmentController.java

@@ -79,7 +79,7 @@ public EntityModel<CatchmentContract> getById(@PathVariable Long id) {
         CatchmentContract catchmentContract = CatchmentContract.fromEntity(catchment);
         boolean fastSyncExists = s3Service.fileExists(String.format("MobileDbBackup-%s", catchment.getUuid()));
         catchmentContract.setFastSyncExists(fastSyncExists);
-        return new EntityModel<>(catchmentContract);
+        return EntityModel.of(catchmentContract);
     }
 
     @GetMapping(value = "catchment/search/findAllById")

avni-server-api/src/main/java/org/avni/server/web/ErrorInterceptors.java

@@ -16,6 +16,7 @@
 import org.springframework.data.rest.webmvc.ResourceNotFoundException;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpStatus;
+import org.springframework.http.HttpStatusCode;
 import org.springframework.http.ResponseEntity;
 import org.springframework.http.converter.HttpMessageConversionException;
 import org.springframework.web.bind.MethodArgumentNotValidException;
@@ -72,7 +73,7 @@ public ErrorInterceptors(@Value("${spring.servlet.multipart.max-file-size}") Str
     }
 
     @Override
-    protected ResponseEntity<Object> handleMethodArgumentNotValid(MethodArgumentNotValidException ex, HttpHeaders headers, HttpStatus status, WebRequest request) {
+    protected ResponseEntity<Object> handleMethodArgumentNotValid(MethodArgumentNotValidException ex, HttpHeaders headers, HttpStatusCode status, WebRequest request) {
         Map<String, Object> body = new HashMap<>();
         List<ApiError> errors = ex.getBindingResult()
                 .getFieldErrors()
@@ -121,8 +122,8 @@ public ResponseEntity unknownException(Exception e) {
     }
 
     @Override
-    protected ResponseEntity<Object> handleExceptionInternal(Exception ex, Object body, HttpHeaders headers, HttpStatus status, WebRequest request) {
+    protected ResponseEntity<Object> handleExceptionInternal(Exception ex, Object body, HttpHeaders headers, HttpStatusCode statusCode, WebRequest request) {
         bugsnagReporter.logAndReportToBugsnag(ex);
-        return super.handleExceptionInternal(ex, errorBodyBuilder.getErrorBody(body), headers, status, request);
+        return super.handleExceptionInternal(ex, errorBodyBuilder.getErrorBody(body), headers, statusCode, request);
     }
 }

avni-server-api/src/main/java/org/avni/server/web/FormController.java

@@ -52,6 +52,8 @@
 import java.util.stream.Collectors;
 
 import static java.lang.String.format;
+import static org.springframework.hateoas.server.mvc.WebMvcLinkBuilder.linkTo;
+import static org.springframework.hateoas.server.mvc.WebMvcLinkBuilder.methodOn;
 
 @RestController
 public class FormController implements RestControllerResourceProcessor<BasicFormDetails> {
@@ -103,9 +105,9 @@ public CollectionModel<EntityModel<BasicFormDetails>> getAllFormsWeb(
             @RequestParam(value = "includeVoided", required = false) boolean includeVoided,
             Pageable pageable) {
         Long organisationId = UserContextHolder.getUserContext().getOrganisation().getId();
-        Sort sortWithId = pageable.getSort().and(new Sort("id"));
+        Sort sortWithId = pageable.getSort().and(Sort.by("id"));
 
-        PageRequest pageRequest = new PageRequest(pageable.getPageNumber(), pageable.getPageSize(), sortWithId);
+        PageRequest pageRequest = PageRequest.of(pageable.getPageNumber(), pageable.getPageSize(), sortWithId);
 
         Page<Form> forms = formRepository.findAll((root, query, builder) -> {
             Predicate predicate = builder.equal(root.get("organisationId"), organisationId);
@@ -388,11 +390,11 @@ private List<BasicFormDetails> getFormsByProgram(Program program, Pageable pagea
             Form form = fm.getForm();
             BasicFormDetails formDetail = new BasicFormDetails(form, program.getOperationalProgramName());
             formDetail.add(linkTo(methodOn(FormController.class).getForms(programId, pageable)).withSelfRel());
-            Link formLink = entityLinks.linkToSingleResource(Form.class, form.getId());
+            Link formLink = entityLinks.linkToItemResource(Form.class, form.getId());
             formDetail.add(formLink);
             formDetail.add(Link.of(formLink.getHref() + "/formElementGroups", "formElementGroups"));
-            formDetail.add(entityLinks.linkToSingleResource(User.class, form.getCreatedBy().getId()).withRel("createdBy"));
-            formDetail.add(entityLinks.linkToSingleResource(User.class, form.getLastModifiedBy().getId()).withRel("lastModifiedBy"));
+            formDetail.add(entityLinks.linkToItemResource(User.class, form.getCreatedBy().getId()).withRel("createdBy"));
+            formDetail.add(entityLinks.linkToItemResource(User.class, form.getLastModifiedBy().getId()).withRel("lastModifiedBy"));
             return formDetail;
         }).collect(Collectors.toList());
     }

avni-server-api/src/main/java/org/avni/server/web/IndividualController.java

@@ -48,6 +48,7 @@
 import java.util.stream.Collectors;
 
 import static org.avni.server.web.resourceProcessors.ResourceProcessor.addAuditFields;
+import static org.springframework.data.jpa.domain.Specification.where;
 
 @RestController
 public class IndividualController extends AbstractController<Individual> implements RestControllerResourceProcessor<Individual> {

avni-server-api/src/main/java/org/avni/server/web/SyncSubjectController.java

@@ -26,15 +26,15 @@ public SyncSubjectController(SubjectSyncResponseBuilderService subjectSyncRespon
 
     public EntityModel<HashMap<String, Object>> process(SyncSubjectResponse syncSubjectResponse) {
         HashMap<String, Object> result = new HashMap<>();
-        result.put("individual", new IndividualResourceProcessor().process(new EntityModel<>(syncSubjectResponse.getIndividual())));
-        result.put("programEnrolments", syncSubjectResponse.getProgramEnrolments().stream().map(programEnrolment -> new ProgramEnrolmentResourceProcessor().process(new EntityModel<>(programEnrolment))));
-        result.put("programEncounters", syncSubjectResponse.getProgramEncounters().stream().map(programEncounter1 -> new ProgramEncounterResourceProcessor().process(new EntityModel<>(programEncounter1))));
-        result.put("encounters", syncSubjectResponse.getEncounters().stream().map(encounter -> new EncounterResourceProcessor().process(new EntityModel<>(encounter))));
-        result.put("checklists", syncSubjectResponse.getChecklists().stream().map(checklist -> new ChecklistResourceProcessor().process(new EntityModel<>(checklist))));
-        result.put("checklistItems", syncSubjectResponse.getChecklistItems().stream().map(checklistItem -> new ChecklistItemResourceProcessor().process(new EntityModel<>(checklistItem))));
-        result.put("groupSubjects", syncSubjectResponse.getGroupSubjects().stream().map(groupSubject -> new GroupSubjectResourceProcessor().process(new EntityModel<>(groupSubject))));
-        result.put("individualRelationships", syncSubjectResponse.getIndividualRelationships().stream().map(individualRelationship -> new IndividualRelationshipResourceProcessor().process(new EntityModel<>(individualRelationship))));
-        return new EntityModel<>(result);
+        result.put("individual", new IndividualResourceProcessor().process(EntityModel.of(syncSubjectResponse.getIndividual())));
+        result.put("programEnrolments", syncSubjectResponse.getProgramEnrolments().stream().map(programEnrolment -> new ProgramEnrolmentResourceProcessor().process(EntityModel.of(programEnrolment))));
+        result.put("programEncounters", syncSubjectResponse.getProgramEncounters().stream().map(programEncounter1 -> new ProgramEncounterResourceProcessor().process(EntityModel.of(programEncounter1))));
+        result.put("encounters", syncSubjectResponse.getEncounters().stream().map(encounter -> new EncounterResourceProcessor().process(EntityModel.of(encounter))));
+        result.put("checklists", syncSubjectResponse.getChecklists().stream().map(checklist -> new ChecklistResourceProcessor().process(EntityModel.of(checklist))));
+        result.put("checklistItems", syncSubjectResponse.getChecklistItems().stream().map(checklistItem -> new ChecklistItemResourceProcessor().process(EntityModel.of(checklistItem))));
+        result.put("groupSubjects", syncSubjectResponse.getGroupSubjects().stream().map(groupSubject -> new GroupSubjectResourceProcessor().process(EntityModel.of(groupSubject))));
+        result.put("individualRelationships", syncSubjectResponse.getIndividualRelationships().stream().map(individualRelationship -> new IndividualRelationshipResourceProcessor().process(EntityModel.of(individualRelationship))));
+        return EntityModel.of(result);
     }
 
     @GetMapping("/subject/{uuid}/allEntities")

avni-server-api/src/main/resources/application.properties

@@ -30,9 +30,9 @@ spring.jpa.hibernate.ddl-auto=none
 spring.jpa.properties.jadira.usertype.databaseZone=jvm
 spring.jpa.properties.jadira.usertype.javaZone=jvm
 spring.jpa.properties.jadira.usertype.autoRegisterUserTypes=true
-spring.jpa.properties.hibernate.dialect=org.avni.server.framework.postgres.CHSPostgreSQL94Dialect
+spring.jpa.properties.hibernate.dialect=org.avni.server.framework.postgres.CHSPostgreSQLDialect
 spring.jpa.properties.hibernate.ejb.interceptor=org.avni.server.framework.hibernate.UpdateOrganisationHibernateInterceptor
-spring.jpa.database-platform=org.avni.server.framework.postgres.CHSPostgreSQL94Dialect
+spring.jpa.database-platform=org.avni.server.framework.postgres.CHSPostgreSQLDialect
 spring.jpa.hibernate.use-new-id-generator-mappings=true
 spring.jpa.properties.hibernate.temp.use_jdbc_metadata_defaults=false
 avni.custom.query.timeout=${AVNI_CUSTOM_QUERY_TIMEOUT:3}

avni-server-api/src/test/java/org/avni/server/common/AbstractControllerIntegrationTest.java

@@ -19,7 +19,7 @@
 import org.springframework.test.web.servlet.setup.MockMvcBuilders;
 import org.springframework.web.context.WebApplicationContext;
 
-import javax.persistence.EntityManager;
+import jakarta.persistence.EntityManager;
 import javax.persistence.PersistenceContext;
 import java.net.URL;
 import java.util.ArrayList;

avni-server-api/src/test/java/org/avni/server/service/AddressLevelServiceTest.java

@@ -16,8 +16,8 @@
 import org.powermock.core.classloader.annotations.PrepareForTest;
 import org.powermock.modules.junit4.PowerMockRunner;
 
-import javax.persistence.EntityManager;
-import javax.persistence.Query;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.Query;
 import java.util.Arrays;
 import java.util.Map;
 

avni-server-api/src/test/resources/application.properties

@@ -27,13 +27,13 @@ spring.jpa.hibernate.ddl-auto=none
 spring.jpa.properties.jadira.usertype.databaseZone=jvm
 spring.jpa.properties.jadira.usertype.javaZone=jvm
 spring.jpa.properties.jadira.usertype.autoRegisterUserTypes=true
-spring.jpa.properties.hibernate.dialect=org.avni.server.framework.postgres.CHSPostgreSQL94Dialect
+spring.jpa.properties.hibernate.dialect=org.avni.server.framework.postgres.CHSPostgreSQLDialect
 spring.jpa.properties.hibernate.ejb.interceptor=org.avni.server.framework.hibernate.UpdateOrganisationHibernateInterceptor
 spring.jpa.properties.hibernate.cache.use_second_level_cache=true
 spring.jpa.properties.hibernate.cache.use_query_cache=true
 spring.jpa.properties.hibernate.cache.region.factory_class=org.hibernate.cache.ehcache.EhCacheRegionFactory
 spring.cache.jcache.config=${AVNI_EHCACHE_FILE:classpath:ehcache.xml}
-spring.jpa.database-platform=org.avni.server.framework.postgres.CHSPostgreSQL94Dialect
+spring.jpa.database-platform=org.avni.server.framework.postgres.CHSPostgreSQLDialect
 spring.jpa.hibernate.use-new-id-generator-mappings=true
 spring.profiles.active=${OPENCHS_MODE:test}
 spring.jpa.properties.hibernate.temp.use_jdbc_metadata_defaults=false