Fixing issues, resolving column naming conflicts between old and new entity classes

dmp-backend/core/src/main/java/eu/eudat/data/DescriptionTemplateEntity.java

@@ -23,16 +23,16 @@ public class DescriptionTemplateEntity implements DataEntity<DescriptionTemplate
     private UUID id;
     public static final String _id = "id";
 
-    @Column(name = "\"label\"", length = DescriptionTemplateEntity._labelLength, nullable = false)
+    @Column(name = "label", length = DescriptionTemplateEntity._labelLength, nullable = false)
     private String label;
     public static final String _label = "label";
     public static final int _labelLength = 250;
 
-    @Column(name = "\"definition\"", nullable = false)
+    @Column(name = "definition", nullable = false)
     private String definition;
     public static final String _definition = "definition";
 
-    @Column(name = "\"status\"", nullable = false)
+    @Column(name = "status", nullable = false)
     @Convert(converter = DescriptionTemplateStatusConverter.class)
     private DescriptionTemplateStatus status;
     public static final String _status = "status";
@@ -43,23 +43,23 @@ public class DescriptionTemplateEntity implements DataEntity<DescriptionTemplate
     public static final String _isActive = "isActive";
 
 
-    @Column(name = "\"created_at\"", nullable = false)
+    @Column(name = "created_at", nullable = false)
     private Instant createdAt = null;
     public static final String _createdAt = "createdAt";
 
-    @Column(name = "\"updated_at\"", nullable = false)
+    @Column(name = "updated_at", nullable = false)
     private Instant updatedAt;
     public static final String _updatedAt = "updatedAt";
 
-    @Column(name = "\"description\"", nullable = false)
+    @Column(name = "description", nullable = false)
     private String description;
     public static final String _description = "description";
 
-    @Column(name = "\"group_id\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
+    @Column(name = "group_id", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
     private UUID groupId;
     public static final String _groupId = "groupId";
 
-    @Column(name = "\"version\"", nullable = false)
+    @Column(name = "version", nullable = false)
     private Short version;
     public static final String _version = "version";
 
@@ -68,11 +68,11 @@ public class DescriptionTemplateEntity implements DataEntity<DescriptionTemplate
     private DescriptionTemplateVersionStatus versionStatus;
     public static final String _versionStatus = "versionStatus";
     
-    @Column(name = "\"language\"", nullable = false)
+    @Column(name = "language", nullable = false)
     private String language;
     public static final String _language = "language";
 
-    @Column(name = "\"type\"", nullable = false)
+    @Column(name = "type", nullable = false)
     private UUID typeId;
     public static final String _typeId = "typeId";
 

dmp-backend/core/src/main/java/eu/eudat/data/DmpBlueprintEntity.java

@@ -19,17 +19,17 @@ public class DmpBlueprintEntity {
     private UUID id;
     public static final String _id = "id";
 
-    @Column(name = "\"label\"", length = DmpBlueprintEntity._labelLength, nullable = false)
+    @Column(name = "label", length = DmpBlueprintEntity._labelLength, nullable = false)
     private String label;
     public static final String _label = "label";
     public static final int _labelLength = 250;
 
-    @Column(name = "\"definition\"", nullable = true)
+    @Column(name = "definition", nullable = true)
     private String definition;
     public static final String _definition = "definition";
 
 
-    @Column(name = "\"status\"", nullable = false)
+    @Column(name = "status", nullable = false)
     @Convert(converter = DmpBlueprintStatusConverter.class)
     private DmpBlueprintStatus status;
     public static final String _status = "status";
@@ -40,11 +40,11 @@ public class DmpBlueprintEntity {
     public static final String _isActive = "isActive";
 
 
-    @Column(name = "\"created_at\"", nullable = false)
+    @Column(name = "created_at", nullable = false)
     private Instant createdAt = null;
     public static final String _createdAt = "createdAt";
 
-    @Column(name = "\"updated_at\"", nullable = false)
+    @Column(name = "updated_at", nullable = false)
     private Instant updatedAt;
     public static final String _updatedAt = "updatedAt";
 

dmp-backend/core/src/main/java/eu/eudat/data/UserRoleEntity.java

@@ -18,12 +18,12 @@ public class UserRoleEntity implements DataEntity<UserRoleEntity, UUID> {
 	private UUID id;
 	public static final String _id = "id";
 
-	@Column(name = "\"role\"", length = UserRoleEntity._roleLength, nullable = false)
+	@Column(name = "role", length = UserRoleEntity._roleLength, nullable = false)
 	private String role;
 	public static final String _role = "role";
 	public static final int _roleLength = 512;
 
-	@Column(name = "\"user\"", nullable = false)
+	@Column(name = "user", nullable = false)
 	private UUID userId;
 	public static final String _userId = "userId";
 

dmp-migration-tool/data/src/main/java/eu/old/eudat/data/entities/DMPProfile.java

@@ -47,7 +47,7 @@ public class DMPProfile implements DataEntity<DMPProfile, UUID> {
     @Id
     @GeneratedValue
     @GenericGenerator(name = "uuid2", strategy = "uuid2")
-    @Column(name = "\"id\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
+    @Column(name = "id", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
     private UUID id;
 
 
@@ -55,22 +55,22 @@ public class DMPProfile implements DataEntity<DMPProfile, UUID> {
     private Set<DMP> dmps;
 
 
-    @Column(name = "\"label\"")
+    @Column(name = "label")
     private String label;
 
-    @Column(name = "\"definition\"", columnDefinition = "xml", nullable = true)
+    @Column(name = "definition", columnDefinition = "xml", nullable = true)
     private String definition;
 
 
-    @Column(name = "\"status\"", nullable = false)
+    @Column(name = "status", nullable = false)
     private int status;
 
 
-    @Column(name = "\"created_at\"")
+    @Column(name = "created_at")
     @Convert(converter = DateToUTCConverter.class)
     private Date created = null;
 
-    @Column(name = "\"updated_at\"")
+    @Column(name = "updated_at")
     @Convert(converter = DateToUTCConverter.class)
     private Date modified = new Date();
 

dmp-migration-tool/data/src/main/java/eu/old/eudat/data/entities/DescriptionTemplate.java

@@ -45,46 +45,46 @@ public class DescriptionTemplate implements DataEntity<DescriptionTemplate,UUID>
     @Id
     @GeneratedValue
     @GenericGenerator(name = "uuid2", strategy = "uuid2")
-    @Column(name = "\"id\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
+    @Column(name = "id", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
     private UUID id;
 
-    @Column(name = "\"label\"", nullable = false)
+    @Column(name = "label", nullable = false)
     private String label;
 
     @OneToMany(fetch = FetchType.LAZY, mappedBy = "profile")
     private Set<Dataset> dataset;
 
-    @Column(name = "\"definition\"", columnDefinition = "xml", nullable = false)
+    @Column(name = "definition", columnDefinition = "xml", nullable = false)
     private String definition;
 
-    @Column(name = "\"status\"", nullable = false)
+    @Column(name = "status", nullable = false)
     private Short status;
 
-    @Column(name = "\"created_at\"")
+    @Column(name = "created_at")
     @Convert(converter = DateToUTCConverter.class)
     private Date created;
 
-    @Column(name = "\"updated_at\"")
+    @Column(name = "updated_at")
     @Convert(converter = DateToUTCConverter.class)
     private Date modified = new Date();
 
-    @Column(name = "\"description\"")
+    @Column(name = "description")
     private String description;
 
-    @Column(name = "\"group_id\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
+    @Column(name = "group_id", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
     private UUID groupId;
 
-    @Column(name = "\"version\"", nullable = false)
+    @Column(name = "version", nullable = false)
     private Short version;
 
     @OneToMany(fetch = FetchType.LAZY)
     private Set<DMP> dmps;
 
-    @Column(name = "\"language\"", nullable = false)
+    @Column(name = "language", nullable = false)
     private String language;
 
     @OneToOne(fetch = FetchType.EAGER)
-    @JoinColumn(name = "\"type\"", nullable = false)
+    @JoinColumn(name = "type", nullable = false)
     private DescriptionTemplateType type;
 
     @OneToMany(mappedBy = "descriptionTemplate", fetch = FetchType.LAZY)

dmp-migration-tool/data/src/main/java/eu/old/eudat/data/entities/DescriptionTemplateType.java

@@ -40,13 +40,13 @@ public class DescriptionTemplateType implements DataEntity<DescriptionTemplateTy
     @Id
     @GeneratedValue
     @GenericGenerator(name = "uuid2", strategy = "uuid2")
-    @Column(name = "\"id\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
+    @Column(name = "id", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
     private UUID id;
 
-    @Column(name = "\"name\"", nullable = false)
+    @Column(name = "name", nullable = false)
     private String name;
 
-    @Column(name = "\"status\"", nullable = false)
+    @Column(name = "status", nullable = false)
     private Short status;
 
     public UUID getId() {

dmp-migration-tool/data/src/main/java/eu/old/eudat/data/entities/EntityDoi.java

@@ -19,29 +19,29 @@ public class EntityDoi implements DataEntity<EntityDoi, UUID> {
     }
 
     @Id
-    @Column(name = "\"id\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
+    @Column(name = "id", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
     private UUID id;
 
     @Enumerated(EnumType.STRING)
-    @Column(name = "\"entity_type\"", nullable = false)
+    @Column(name = "entity_type", nullable = false)
     private EntityType entityType;
 
-    @Column(name = "\"repository_id\"", nullable = false)
+    @Column(name = "repository_id", nullable = false)
     private String repositoryId;
 
-    @Column(name = "\"doi\"", nullable = false)
+    @Column(name = "doi", nullable = false)
     private String doi;
 
-    @Column(name = "\"created_at\"", nullable = false)
+    @Column(name = "created_at", nullable = false)
     @Convert(converter = DateToUTCConverter.class)
     private Date createdAt;
 
-    @Column(name = "\"updated_at\"", nullable = false)
+    @Column(name = "updated_at", nullable = false)
     @Convert(converter = DateToUTCConverter.class)
     private Date updatedAt;
 
     @ManyToOne(fetch = FetchType.LAZY)
-    @JoinColumn(name = "\"entity_id\"", nullable = false)
+    @JoinColumn(name = "entity_id", nullable = false)
     private DMP entityId;
 
     public UUID getId() {

dmp-migration-tool/data/src/main/java/eu/old/eudat/data/entities/UserRole.java

@@ -16,14 +16,14 @@ public class UserRole implements DataEntity<UserRole, UUID> {
 	@Id
 	@GeneratedValue
 	@GenericGenerator(name = "uuid2", strategy = "uuid2")
-	@Column(name = "\"id\"", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
+	@Column(name = "id", updatable = false, nullable = false, columnDefinition = "BINARY(16)")
 	private UUID id;
 
-	@Column(name = "\"role\"", nullable = false)
+	@Column(name = "role", nullable = false)
 	private int role;
 
 	@ManyToOne(fetch = FetchType.EAGER)
-	@JoinColumn(name = "\"user\"", nullable = false)
+	@JoinColumn(name = "user", nullable = false)
 	private UserInfo userInfo;
 
 	public UUID getId() {

dmp-migration-tool/web/pom.xml

@@ -42,6 +42,10 @@
             <version>1.0.4</version>
         </dependency>
 
+        <dependency>
+            <groupId>com.fasterxml.jackson.datatype</groupId>
+            <artifactId>jackson-datatype-jsr310</artifactId>
+        </dependency>
 
         <dependency>
             <groupId>org.springframework.boot</groupId>

dmp-migration-tool/web/src/main/java/eu/old/eudat/EuDatApplication.java

@@ -1,12 +1,22 @@
 package eu.old.eudat;
 
+import com.fasterxml.jackson.databind.DeserializationFeature;
+import com.fasterxml.jackson.databind.Module;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.module.SimpleModule;
+import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
+import eu.old.eudat.criteria.entities.Criteria;
+import eu.old.eudat.criteria.serialzier.CriteriaSerializer;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
 import org.springframework.boot.builder.SpringApplicationBuilder;
 import org.springframework.boot.web.servlet.support.SpringBootServletInitializer;
+import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.scheduling.annotation.EnableAsync;
 
+import java.util.ArrayList;
+
 @SpringBootApplication(scanBasePackages = {"eu.eudat" ,"eu.old.eudat", "eu.old.eudat.depositinterface", "gr.cite"})
 @Configuration
 @EnableAsync

dmp-migration-tool/web/src/main/java/eu/old/eudat/configurations/DevelDatabaseConfiguration.java

@@ -1,28 +1,38 @@
 package eu.old.eudat.configurations;
 
 
+import org.jetbrains.annotations.NotNull;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.context.properties.ConfigurationProperties;
 import org.springframework.boot.jdbc.DataSourceBuilder;
 import org.springframework.context.annotation.*;
 import org.springframework.core.env.Environment;
 import org.springframework.dao.annotation.PersistenceExceptionTranslationPostProcessor;
+import org.springframework.data.jpa.repository.config.EnableJpaRepositories;
 import org.springframework.jdbc.datasource.DriverManagerDataSource;
 import org.springframework.orm.jpa.JpaTransactionManager;
 import org.springframework.orm.jpa.JpaVendorAdapter;
 import org.springframework.orm.jpa.LocalContainerEntityManagerFactoryBean;
+import org.springframework.orm.jpa.persistenceunit.MutablePersistenceUnitInfo;
+import org.springframework.orm.jpa.persistenceunit.PersistenceUnitPostProcessor;
 import org.springframework.orm.jpa.vendor.HibernateJpaVendorAdapter;
 import org.springframework.transaction.PlatformTransactionManager;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
 import jakarta.persistence.EntityManagerFactory;
 import javax.sql.DataSource;
+import java.util.List;
 import java.util.Properties;
 
 @Configuration
 @EnableTransactionManagement
 @Profile("devel")
-@ComponentScan(basePackages = {"eu.old.eudat.data.entities"})
+@EnableJpaRepositories(
+        basePackages = {"eu.old.eudat.data.entities", "eu.eudat.data"},
+        excludeFilters = {
+                @ComponentScan.Filter(type = FilterType.REGEX, pattern = "eu\\.eudat\\.data\\.old\\..*"),
+        }
+)
 public class DevelDatabaseConfiguration {
 
     @Autowired
@@ -32,7 +42,11 @@ public class DevelDatabaseConfiguration {
     public LocalContainerEntityManagerFactoryBean entityManagerFactory() {
         LocalContainerEntityManagerFactoryBean em = new LocalContainerEntityManagerFactoryBean();
         em.setDataSource(dataSource());
-        em.setPackagesToScan(new String[]{"eu.old.eudat.data.entities"});
+        em.setPackagesToScan("eu.old.eudat.data.entities", "eu.eudat.data");
+        em.setPersistenceUnitPostProcessors(persistenceUnit -> {
+            List<String> managedClassNames = persistenceUnit.getManagedClassNames();
+            managedClassNames.removeIf(fullClassName -> fullClassName.startsWith("eu.eudat.data.old"));
+        });
         JpaVendorAdapter vendorAdapter = new HibernateJpaVendorAdapter();
         em.setJpaVendorAdapter(vendorAdapter);
         em.setJpaProperties(additionalProperties());

dmp-migration-tool/web/src/main/java/eu/old/eudat/configurations/JacksonConfiguration.java

@@ -4,6 +4,7 @@ import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.Module;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.fasterxml.jackson.databind.module.SimpleModule;
+import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
 import eu.old.eudat.criteria.entities.Criteria;
 import eu.old.eudat.criteria.serialzier.CriteriaSerializer;
 import org.springframework.context.annotation.Bean;
@@ -20,6 +21,7 @@ public class JacksonConfiguration {
 		SimpleModule criteriaSerializerModule = new SimpleModule();
 		criteriaSerializerModule.addDeserializer(Criteria.class, new CriteriaSerializer());
 		modules.add(criteriaSerializerModule);
+		modules.add(new JavaTimeModule());
 
 		return new ObjectMapper()
 				.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false)

dmp-migration-tool/web/src/main/java/eu/old/eudat/models/data/dmp/DataManagementPlan.java

@@ -25,6 +25,7 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
     private UUID groupId;
     private Tuple<UUID, String> profile;
     private int version;
+    private int versionStatus;
     private int status;
     private boolean lockable;
     private String description;
@@ -38,6 +39,7 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
     private eu.old.eudat.models.data.userinfo.UserInfo creator;
     private Date modified;
     private Date created;
+    private Date finalized;
     private List<DynamicFieldWithValue> dynamicFields;
     private Map<String, Object> properties;
     private List<UserInfoListingModel> users;
@@ -89,6 +91,13 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
         this.version = version;
     }
 
+    public int getVersionStatus() {
+        return versionStatus;
+    }
+    public void setVersionStatus(int versionStatus) {
+        this.versionStatus = versionStatus;
+    }
+
     public List<Organisation> getOrganisations() {
         return organisations;
     }
@@ -145,6 +154,13 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
         this.created = created;
     }
 
+    public Date getFinalized() {
+        return finalized;
+    }
+    public void setFinalized(Date finalized) {
+        this.finalized = finalized;
+    }
+
     public String getDescription() {
         return description;
     }
@@ -293,6 +309,7 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
         }
         this.modified = entity.getModified();
         this.created = entity.getCreated();
+        this.finalized = entity.getFinalizedAt();
         this.description = entity.getDescription();
         this.status = entity.getStatus();
         this.associatedUsers = entity.getUsers() != null ? entity.getUsers().stream().map(item -> new UserListingModel().fromDataModel(item.getUser())).collect(Collectors.toList()) : new ArrayList<>();
@@ -405,6 +422,7 @@ public class DataManagementPlan implements DataModel<DMP, DataManagementPlan> {
         }
         this.modified = entity.getModified();
         this.created = entity.getCreated();
+        this.finalized = entity.getFinalizedAt();
         this.description = entity.getDescription();
         this.status = entity.getStatus();
         this.associatedUsers = entity.getUsers() != null ? entity.getUsers().stream().map(item -> new UserListingModel().fromDataModel(item.getUser())).collect(Collectors.toList()) : new ArrayList<>();

dmp-migration-tool/web/src/main/java/eu/old/eudat/publicapi/migration/MigrationController.java

@@ -1,12 +1,18 @@
 package eu.old.eudat.publicapi.migration;
 
 import eu.eudat.commons.enums.DmpAccessType;
+import eu.eudat.commons.enums.DmpStatus;
+import eu.eudat.commons.enums.DmpVersionStatus;
+import eu.eudat.commons.enums.IsActive;
 import eu.eudat.data.DmpEntity;
 import eu.old.eudat.data.dao.criteria.DataManagementPlanCriteria;
 import eu.old.eudat.data.entities.DMP;
 import eu.old.eudat.logic.services.operations.DatabaseRepository;
 import eu.old.eudat.models.data.dmp.DataManagementPlan;
 import io.swagger.annotations.Api;
+import jakarta.persistence.EntityManager;
+import jakarta.persistence.PersistenceContext;
+import org.springframework.transaction.annotation.Transactional;
 import org.springframework.web.bind.annotation.*;
 
 import java.util.ArrayList;
@@ -21,8 +27,12 @@ public class MigrationController {
 
     private final DatabaseRepository databaseRepository;
 
-    public MigrationController(DatabaseRepository databaseRepository) {
+    @PersistenceContext
+    private final EntityManager entityManager;
+
+    public MigrationController(DatabaseRepository databaseRepository, EntityManager entityManager) {
         this.databaseRepository = databaseRepository;
+        this.entityManager = entityManager;
     }
 
     @GetMapping("dmps/all/{skip}/{take}")
@@ -44,19 +54,59 @@ public class MigrationController {
         return results;
     }
 
-    @GetMapping("dmps/migrate")
+    @GetMapping("dmps/collectInfo")
-    public List<DmpEntity> migrateDmps() {
+    public List<DmpMigrationCollectedInfo> collectDmpsInfo() {
+        List<DmpMigrationCollectedInfo> collectedInfoList = new ArrayList<>();
         List<DataManagementPlan> dmps = getDmps(0, 4);
-        List<DmpEntity> migratedDmps = new ArrayList<>();
         for (DataManagementPlan dataManagementPlan : dmps) {
+            DmpMigrationCollectedInfo dmpMigrationCollectedInfo = new DmpMigrationCollectedInfo();
+
+            //Collect basic dmp information
             DmpEntity dmpEntity = new DmpEntity();
             dmpEntity.setId(UUID.randomUUID());
             dmpEntity.setLabel(dataManagementPlan.getLabel());
             dmpEntity.setDescription(dataManagementPlan.getDescription());
             dmpEntity.setAccessType(dataManagementPlan.getPublic() ? DmpAccessType.Public : DmpAccessType.Restricted);
-            migratedDmps.add(dmpEntity);
+            if (dataManagementPlan.getCreator() != null)
+                dmpEntity.setCreator(dataManagementPlan.getCreator().getId());
+            dmpEntity.setGroupId(dataManagementPlan.getGroupId());
+            dmpEntity.setVersion((short) dataManagementPlan.getVersion());
+            dmpEntity.setVersionStatus(DmpVersionStatus.of((short) dataManagementPlan.getVersionStatus()));
+            if (dataManagementPlan.getCreated() != null)
+                dmpEntity.setCreatedAt(dataManagementPlan.getCreated().toInstant());
+            if (dataManagementPlan.getModified() != null)
+                dmpEntity.setUpdatedAt(dataManagementPlan.getModified().toInstant());
+            if (dataManagementPlan.getFinalized() != null)
+                dmpEntity.setFinalizedAt(dataManagementPlan.getFinalized().toInstant());
+            dmpEntity.setBlueprint(dataManagementPlan.getProfile().getId());
+            if (dataManagementPlan.getExtraProperties().containsKey("language") && dataManagementPlan.getExtraProperties().get("language") != null)
+                dmpEntity.setLanguage((String) dataManagementPlan.getExtraProperties().get("language"));
+            if (dataManagementPlan.getStatus() == 99) {
+                dmpEntity.setIsActive(IsActive.Inactive);
+            } else {
+                dmpEntity.setIsActive(IsActive.Active);
+                dmpEntity.setStatus(DmpStatus.of((short) dataManagementPlan.getStatus()));
             }
-        return migratedDmps;
+            dmpMigrationCollectedInfo.dmpEntity = dmpEntity;
+            collectedInfoList.add(dmpMigrationCollectedInfo);
+        }
+        return collectedInfoList;
+    }
+
+    @GetMapping("dmps/migrate")
+    @Transactional
+    public String migrate() {
+        for (DmpMigrationCollectedInfo collectedInfo : collectDmpsInfo()) {
+            this.entityManager.persist(collectedInfo.dmpEntity);
+        }
+        this.entityManager.flush();
+        return "Migrated dmps";
+    }
+
+    public static class DmpMigrationCollectedInfo {
+
+        public DmpEntity dmpEntity;
+
     }
 
 }