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Merge branch 'dmp-refactoring' of https://code-repo.d4science.org/MaDgiK-CITE/argos into dmp-refactoring

This commit is contained in:
Diamantis Tziotzios 2023-11-23 15:06:16 +02:00
parent c779bd00f0 9433beaaa6
commit 3dbfc18fd6
18 changed files with 829 additions and 165 deletions
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1
dmp-backend/core/src/main/java/eu/eudat/data/DescriptionEntity.java
View File

@ -64,7 +64,6 @@ public class DescriptionEntity implements DataEntity<DescriptionEntity, UUID> {
public static final String _isActive = "isActive";
@Column(name = "\"finalized_at\"")
@Convert(converter = DateToUTCConverter.class)
private Instant finalizedAt;
public static final String _finalizedAt = "finalizedAt";

3
dmp-backend/core/src/main/java/eu/eudat/data/DmpEntity.java
View File

@ -6,6 +6,7 @@ import eu.eudat.commons.enums.DmpVersionStatus;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.data.converters.enums.DmpAccessTypeConverter;
import eu.eudat.data.converters.enums.DmpStatusConverter;
import eu.eudat.data.converters.enums.DmpVersionStatusConverter;
import eu.eudat.data.converters.enums.IsActiveConverter;
import eu.eudat.data.old.queryableentity.DataEntity;
import jakarta.persistence.*;
@ -35,7 +36,7 @@ public class DmpEntity implements DataEntity<DmpEntity, UUID> {
public static final String _version = "version";
@Column(name = "version_status", nullable = false)
@Convert(converter = DmpStatusConverter.class)
@Convert(converter = DmpVersionStatusConverter.class)
private DmpVersionStatus versionStatus;
public static final String _versionStatus = "versionStatus";

70
dmp-db-scema/updates/00.01.010_Align_DescriptionTemplate_table.sql
View File

@ -1,51 +1,61 @@
ALTER TABLE public."DescriptionTemplate" RENAME "ID" TO id;
DO $$DECLARE
this_version CONSTANT varchar := '00.01.010';
BEGIN
PERFORM * FROM "DBVersion" WHERE version = this_version;
IF FOUND THEN RETURN; END IF;
ALTER TABLE public."DescriptionTemplate" RENAME "ID" TO id;
ALTER TABLE public."DescriptionTemplate" RENAME "Label" TO label;
ALTER TABLE public."DescriptionTemplate" RENAME "Label" TO label;
ALTER TABLE public."DescriptionTemplate" RENAME "Definition" TO definition;
ALTER TABLE public."DescriptionTemplate" RENAME "Definition" TO definition;
ALTER TABLE public."DescriptionTemplate" RENAME "Status" TO status;
ALTER TABLE public."DescriptionTemplate" RENAME "Status" TO status;
ALTER TABLE public."DescriptionTemplate" RENAME "Created" TO created_at;
ALTER TABLE public."DescriptionTemplate" RENAME "Created" TO created_at;
ALTER TABLE public."DescriptionTemplate" RENAME "Modified" TO updated_at;
ALTER TABLE public."DescriptionTemplate" RENAME "Modified" TO updated_at;
ALTER TABLE public."DescriptionTemplate" RENAME "Description" TO description;
ALTER TABLE public."DescriptionTemplate" RENAME "Description" TO description;
ALTER TABLE public."DescriptionTemplate" RENAME "GroupId" TO group_id;
ALTER TABLE public."DescriptionTemplate" RENAME "GroupId" TO group_id;
ALTER TABLE public."DescriptionTemplate" RENAME "Version" TO version;
ALTER TABLE public."DescriptionTemplate" RENAME "Version" TO version;
ALTER TABLE public."DescriptionTemplate" RENAME "Language" TO "language";
ALTER TABLE public."DescriptionTemplate" RENAME "Language" TO "language";
ALTER TABLE public."DescriptionTemplate" RENAME "Type" TO "type";
ALTER TABLE public."DescriptionTemplate" RENAME "Type" TO "type";
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN created_at TYPE timestamp without time zone ;
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN created_at TYPE timestamp without time zone ;
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN updated_at TYPE timestamp without time zone ;
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN updated_at TYPE timestamp without time zone ;
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN group_id DROP DEFAULT;
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN group_id DROP DEFAULT;
ALTER TABLE public."DescriptionTemplate" ADD COLUMN is_active smallint;
ALTER TABLE public."DescriptionTemplate" ADD COLUMN is_active smallint;
UPDATE public."DescriptionTemplate" SET is_active = 1;
UPDATE public."DescriptionTemplate" SET is_active = 1;
UPDATE public."DescriptionTemplate" SET is_active = 0 where status = 99;
UPDATE public."DescriptionTemplate" SET status = 0 where is_active = 0;
UPDATE public."DescriptionTemplate" SET is_active = 0 where status = 99;
UPDATE public."DescriptionTemplate" SET status = 0 where is_active = 0;
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN is_active SET NOT NULL;
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN is_active SET NOT NULL;
ALTER TABLE public."DescriptionTemplate" ADD COLUMN version_status smallint;
ALTER TABLE public."DescriptionTemplate" ADD COLUMN version_status smallint;
UPDATE public."DescriptionTemplate" SET version_status = 1;
UPDATE public."DescriptionTemplate" SET version_status = 1;
UPDATE public."DescriptionTemplate" SET version_status = 0 where id in (
select dt.id from public."DescriptionTemplate" as dt
where dt.version =
(
select Max(f.version)
from public."DescriptionTemplate" as f where f.group_id=dt.group_id
)
);
UPDATE public."DescriptionTemplate" SET version_status = 0 where id in (
select dt.id from public."DescriptionTemplate" as dt
where dt.version =
(
select Max(f.version)
from public."DescriptionTemplate" as f where f.group_id=dt.group_id
)
);
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN version_status SET NOT NULL;
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN version_status SET NOT NULL;
INSERT INTO public."DBVersion" VALUES ('DMPDB', '00.01.010', '2023-11-02 12:00:00.000000+02', now(), 'Aling DescriptionTemplate table.');
END$$;

2
dmp-db-scema/updates/00.01.012_Add_Dmp_description_template_table.sql
View File

@ -9,7 +9,7 @@ CREATE TABLE IF NOT EXISTS public."DmpDescriptionTemplate"
"id" uuid NOT NULL,
"dmp" uuid NOT NULL,
"description_template" uuid NOT NULL,
"data" text COLLATE pg_catalog."default" NOT NULL,
"section_id" uuid NOT NULL,
"created_at" timestamp without time zone NOT NULL DEFAULT now(),
"updated_at" timestamp without time zone NOT NULL DEFAULT now(),
"is_active" smallint NOT NULL DEFAULT 1,

23
dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/DataRepositoryMigrationService.java
View File

@ -1,8 +1,13 @@
package eu.old.eudat.migration;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.enums.ReferenceFieldDataType;
import eu.eudat.commons.enums.ReferenceSourceType;
import eu.eudat.commons.enums.ReferenceType;
import eu.eudat.commons.types.reference.DefinitionEntity;
import eu.eudat.commons.types.reference.FieldEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.ReferenceEntity;
import eu.old.eudat.data.dao.entities.DataRepositoryDao;
import eu.old.eudat.data.entities.DataRepository;
@ -23,9 +28,13 @@ public class DataRepositoryMigrationService {
private static final String InternalReferenceSource = "dmp";
private final DatabaseRepository databaseRepository;
private final EntityManager entityManager;
public DataRepositoryMigrationService(DatabaseRepository databaseRepository, EntityManager entityManager) {
private final ConventionService conventionService;
private final XmlHandlingService xmlHandlingService;
public DataRepositoryMigrationService(DatabaseRepository databaseRepository, EntityManager entityManager, ConventionService conventionService, XmlHandlingService xmlHandlingService) {
this.databaseRepository = databaseRepository;
this.entityManager = entityManager;
this.conventionService = conventionService;
this.xmlHandlingService = xmlHandlingService;
}
public void migrate(){
@ -49,6 +58,8 @@ public class DataRepositoryMigrationService {
String[] referenceParts = item.getReference().split(":", 2);
boolean isInternal = referenceParts[0].equals(InternalReferenceSource);
ReferenceEntity data = new ReferenceEntity();
data.setId(item.getId());
@ -61,6 +72,16 @@ public class DataRepositoryMigrationService {
data.setReference(referenceParts[1]);
data.setSource(isInternal? "Internal" : referenceParts[0]);
data.setSourceType(isInternal? ReferenceSourceType.Internal : ReferenceSourceType.External);
if (!this.conventionService.isNullOrEmpty(item.getUri())){
DefinitionEntity definitionEntity = new DefinitionEntity();
FieldEntity fieldEntity = new FieldEntity();
fieldEntity.setCode("uri");
fieldEntity.setDataType(ReferenceFieldDataType.Text);
fieldEntity.setValue(item.getUri());
definitionEntity.setFields(List.of(fieldEntity));
data.setDefinition(this.xmlHandlingService.toXmlSafe(definitionEntity));
}
this.entityManager.persist(data);
}
this.entityManager.flush();

99
dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/DatasetMigrationService.java Normal file
View File

@ -0,0 +1,99 @@
package eu.old.eudat.migration;
import com.fasterxml.jackson.core.JsonProcessingException;
import eu.eudat.commons.JsonHandlingService;
import eu.eudat.commons.enums.*;
import eu.eudat.data.DescriptionEntity;
import eu.old.eudat.data.entities.Dataset;
import eu.old.eudat.logic.services.operations.DatabaseRepository;
import eu.old.eudat.models.data.datasetwizard.DatasetWizardModel;
import eu.old.eudat.queryable.QueryableList;
import jakarta.persistence.EntityManager;
import org.springframework.stereotype.Service;
import java.util.ArrayList;
import java.util.List;
@Service
public class DatasetMigrationService {
private final DatabaseRepository databaseRepository;
private final JsonHandlingService jsonHandlingService;
private final EntityManager entityManager;
public DatasetMigrationService(DatabaseRepository databaseRepository, JsonHandlingService jsonHandlingService, EntityManager entityManager) {
this.databaseRepository = databaseRepository;
this.jsonHandlingService = jsonHandlingService;
this.entityManager = entityManager;
}
public QueryableList<Dataset> datasetQueryableList() {
return databaseRepository.getDatasetDao().asQueryable();
}
public List<DatasetWizardModel> getDatasets(Integer skip, Integer take) {
List<Dataset> datasets = datasetQueryableList()
.orderBy((builder, root) -> builder.desc(root.get("created")))
.skip(skip)
.take(take)
.toList();
return datasets.stream().map(x -> {
DatasetWizardModel dataset = new DatasetWizardModel();
dataset.fromDataModel(x);
return dataset;
}).toList();
}
public List<DatasetMigrationCollectedInfo> collectDatasetsInfo() throws JsonProcessingException {
List<DatasetMigrationCollectedInfo> collectedInfoList = new ArrayList<>();
List<DatasetWizardModel> datasets = getDatasets(0, Integer.MAX_VALUE);
for (DatasetWizardModel datasetWizardModel : datasets) {
DatasetMigrationCollectedInfo datasetMigrationCollectedInfo = new DatasetMigrationCollectedInfo();
//Collect basic dataset information
DescriptionEntity descriptionEntity = new DescriptionEntity();
descriptionEntity.setId(datasetWizardModel.getId());
descriptionEntity.setDescription(datasetWizardModel.getDescription());
descriptionEntity.setCreatedById(datasetWizardModel.getCreatedBy());
descriptionEntity.setDmpId(datasetWizardModel.getDmp().getId());
descriptionEntity.setLabel(datasetWizardModel.getLabel());
if (datasetWizardModel.getCreated() != null)
descriptionEntity.setCreatedAt(datasetWizardModel.getCreated().toInstant());
if (datasetWizardModel.getModified() != null)
descriptionEntity.setUpdatedAt(datasetWizardModel.getModified().toInstant());
if (datasetWizardModel.getFinalized() != null)
descriptionEntity.setFinalizedAt(datasetWizardModel.getFinalized().toInstant());
if (datasetWizardModel.getStatus() == 99) {
descriptionEntity.setIsActive(IsActive.Inactive);
descriptionEntity.setStatus(DescriptionStatus.Canceled);
} else {
descriptionEntity.setIsActive(IsActive.Active);
descriptionEntity.setStatus(DescriptionStatus.of(datasetWizardModel.getStatus()));
}
// descriptionEntity.setDmpDescriptionTemplateId(); //TODO MIGRATE DMPDESCRIPTIONTEMPLATES
datasetMigrationCollectedInfo.descriptionEntity = descriptionEntity;
collectedInfoList.add(datasetMigrationCollectedInfo);
}
return collectedInfoList;
}
public String migrate() throws JsonProcessingException {
for (DatasetMigrationCollectedInfo collectedInfo : collectDatasetsInfo()) {
this.entityManager.persist(collectedInfo.descriptionEntity);
}
this.entityManager.flush();
return "Migrated dmps";
}
public static class DatasetMigrationCollectedInfo {
public DescriptionEntity descriptionEntity;
}
}

214
dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/DmpDatasetProfileMigrationService.java Normal file
View File

@ -0,0 +1,214 @@
package eu.old.eudat.migration;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.core.JsonProcessingException;
import eu.eudat.commons.JsonHandlingService;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.enums.ReferenceFieldDataType;
import eu.eudat.commons.enums.ReferenceSourceType;
import eu.eudat.commons.enums.ReferenceType;
import eu.eudat.commons.types.reference.FieldEntity;
import eu.eudat.data.DescriptionTemplateEntity;
import eu.eudat.data.DmpBlueprintEntity;
import eu.eudat.data.DmpDescriptionTemplateEntity;
import eu.eudat.data.ReferenceEntity;
import eu.eudat.model.DmpBlueprint;
import eu.eudat.query.DescriptionTemplateQuery;
import eu.eudat.query.DmpBlueprintQuery;
import eu.old.eudat.data.dao.entities.DmpDatasetProfileDao;
import eu.old.eudat.data.dao.entities.ResearcherDao;
import eu.old.eudat.data.entities.DMPDatasetProfile;
import eu.old.eudat.data.entities.Researcher;
import eu.old.eudat.logic.services.operations.DatabaseRepository;
import eu.old.eudat.queryable.QueryableList;
import gr.cite.tools.data.query.QueryFactory;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.logging.LoggerService;
import jakarta.persistence.EntityManager;
import jakarta.xml.bind.JAXBException;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service;
import org.xml.sax.SAXException;
import eu.eudat.commons.types.dmpblueprint.DefinitionEntity;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
import java.time.Instant;
import java.util.*;
@Service
public class DmpDatasetProfileMigrationService {
private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(DmpDatasetProfileMigrationService.class));
private final DatabaseRepository databaseRepository;
private final JsonHandlingService jsonHandlingService;
private final QueryFactory queryFactory;
private final XmlHandlingService xmlHandlingService;
private static final int PageSize = 500;
private static final boolean TestMode = false;
private final EntityManager entityManager;
public DmpDatasetProfileMigrationService(DatabaseRepository databaseRepository, JsonHandlingService jsonHandlingService, QueryFactory queryFactory, XmlHandlingService xmlHandlingService, EntityManager entityManager) {
this.databaseRepository = databaseRepository;
this.jsonHandlingService = jsonHandlingService;
this.queryFactory = queryFactory;
this.xmlHandlingService = xmlHandlingService;
this.entityManager = entityManager;
}
public void migrate() throws IOException, JAXBException, ParserConfigurationException, InstantiationException, IllegalAccessException, SAXException {
DmpDatasetProfileDao dmpDatasetProfileDao = databaseRepository.getDmpDatasetProfileDao();
long total = dmpDatasetProfileDao.asQueryable().count();
logger.debug("Migrate DmpDatasetProfile Total : " + total);
int page = 0;
List<DMPDatasetProfile> items;
do {
items = dmpDatasetProfileDao.asQueryable().orderBy((builder, root) -> builder.asc(root.get("ID"))).skip(page * PageSize).take(PageSize).toList();
if (items != null && !items.isEmpty()) {
logger.debug("Migrate DmpDatasetProfile " + page * PageSize + " of " + total);
List<DmpBlueprintEntity> dmpBlueprints = this.queryFactory.query(DmpBlueprintQuery.class).ids(items.stream().map(x-> x.getDmp().getProfile().getId()).distinct().toList()).collect();
Map<UUID, DefinitionEntity> dmpBlueprintsMap = new HashMap<>();
for (DmpBlueprintEntity dmpBlueprint : dmpBlueprints) {
DefinitionEntity definitionEntity = this.xmlHandlingService.fromXml(DefinitionEntity.class, dmpBlueprint.getDefinition());
dmpBlueprintsMap.put(dmpBlueprint.getId(), definitionEntity);
}
for (DMPDatasetProfile item : items) {
entityManager.detach(item);
DmpDatasetProfileData profileData = jsonHandlingService.fromJson(DmpDatasetProfileData.class, item.getData());
if (profileData == null || profileData.dmpSectionIndex == null || profileData.dmpSectionIndex.isEmpty()){
logger.error("Migrate DmpDatasetProfile " + item.getId() + " failed no section info ");
throw new MyApplicationException();
}
DefinitionEntity definition = dmpBlueprintsMap.getOrDefault(item.getDmp().getProfile().getId(), null);
if (definition == null){
logger.error("Migrate DmpDatasetProfile " + item.getId() + " failed blueprint definition not found for blueprint " + item.getDmp().getProfile().getId());
}
for (int sectionIndex: profileData.dmpSectionIndex) {
if (definition == null || definition.getSections() == null || definition.getSections().size() < sectionIndex) {
logger.error("Migrate DmpDatasetProfile " + item.getId() + " can nto found section id for section " + sectionIndex);
throw new MyApplicationException();
}
UUID sectionId = definition.getSections().get(sectionIndex).getId();
if (sectionId == null) {
logger.error("Migrate DmpDatasetProfile " + item.getId() + " can nto found section id for section " + sectionIndex);
throw new MyApplicationException();
}
DmpDescriptionTemplateEntity data = new DmpDescriptionTemplateEntity();
data.setId(UUID.randomUUID());
data.setDescriptionTemplateId(item.getDatasetprofile().getId());
data.setDmpId(item.getDmp().getId());
data.setCreatedAt(Instant.now());
data.setUpdatedAt(Instant.now());
data.setSectionId(sectionId);
data.setIsActive(IsActive.Active);
this.entityManager.persist(data);
}
}
this.entityManager.flush();
page++;
}
} while (items != null && !items.isEmpty() && !TestMode);
}
//
// public QueryableList<DMPDatasetProfile> dmpDatasetProfileQueryableList() {
// return databaseRepository.getDmpDatasetProfileDao().asQueryable();
// }
//
// public List<DMPDatasetProfile> getDatasets(Integer skip, Integer take) {
// return dmpDatasetProfileQueryableList()
//// .orderBy((builder, root) -> builder.desc(root.get("created")))
// .skip(skip)
// .take(take)
// .toList();
// }
//
// public List<DmpDatasetProfileMigrationCollectedInfo> collectDatasetsInfo() throws Exception {
// List<DmpDatasetProfileMigrationCollectedInfo> collectedInfoList = new ArrayList<>();
// List<DMPDatasetProfile> items = getDatasets(0, 4);
//
// List<DmpBlueprintEntity> dmpBlueprints = this.queryFactory.query(DmpBlueprintQuery.class).ids(items.stream().map(x-> x.getDmp().getProfile().getId()).distinct().toList()).collect();
// Map<UUID, DefinitionEntity> dmpBlueprintsMap = new HashMap<>();
// for (DmpBlueprintEntity dmpBlueprint : dmpBlueprints) {
// DefinitionEntity definitionEntity = this.xmlHandlingService.fromXml(DefinitionEntity.class, dmpBlueprint.getDefinition());
// dmpBlueprintsMap.put(dmpBlueprint.getId(), definitionEntity);
// }
//
// for (DMPDatasetProfile item : items) {
// this.entityManager.detach(item);
//
// DmpDatasetProfileMigrationCollectedInfo dmpDatasetProfileMigrationCollectedInfo = new DmpDatasetProfileMigrationCollectedInfo();
//
// DmpDatasetProfileData profileData = jsonHandlingService.fromJson(DmpDatasetProfileData.class, item.getData());
//
// if (profileData == null || profileData.dmpSectionIndex == null || profileData.dmpSectionIndex.isEmpty()){
// throw new Exception();
// }
// DefinitionEntity definition = dmpBlueprintsMap.getOrDefault(item.getDmp().getProfile().getId(), null);
// if (definition == null){
// throw new Exception();
// }
//
// for (int sectionIndex: profileData.dmpSectionIndex) {
// if ( definition.getSections().size() < sectionIndex) {
// throw new Exception();
// }
// UUID sectionId = definition.getSections().get(sectionIndex).getId();
//
// DmpDescriptionTemplateEntity data = new DmpDescriptionTemplateEntity();
// data.setDescriptionTemplateId(item.getDatasetprofile().getId());
// data.setDmpId(item.getDmp().getId());
// data.setCreatedAt(Instant.now());
// data.setUpdatedAt(Instant.now());
// data.setSectionId(sectionId); //TODO
// data.setIsActive(IsActive.Active);
// }
//
//
//
// dmpDatasetProfileMigrationCollectedInfo.dmpDescriptionTemplateEntity = data;
//
// collectedInfoList.add(dmpDatasetProfileMigrationCollectedInfo);
// }
// return collectedInfoList;
// }
//
// public String migrate() throws JsonProcessingException {
// for (DmpDatasetProfileMigrationCollectedInfo collectedInfo : collectDatasetsInfo()) {
//// this.entityManager.persist(collectedInfo.dmpDescriptionTemplateEntity);
// }
// this.entityManager.flush();
// return "Migrated dmps";
// }
//
// public static class DmpDatasetProfileMigrationCollectedInfo {
//
// public DmpDescriptionTemplateEntity dmpDescriptionTemplateEntity;
//
// }
//
@JsonIgnoreProperties({"validationErrorModel"})
public static class DmpDatasetProfileData {
private List<Integer> dmpSectionIndex;
public List<Integer> getDmpSectionIndex() {
return dmpSectionIndex;
}
public void setDmpSectionIndex(List<Integer> dmpSectionIndex) {
this.dmpSectionIndex = dmpSectionIndex;
}
}
}

283
dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/DmpMigrationService.java
View File

@ -9,30 +9,43 @@ import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.types.dmp.DmpBlueprintValueEntity;
import eu.eudat.commons.types.dmp.DmpContactEntity;
import eu.eudat.commons.types.dmp.DmpPropertiesEntity;
import eu.eudat.commons.types.dmpblueprint.DefinitionEntity;
import eu.eudat.data.DmpBlueprintEntity;
import eu.eudat.data.DmpDescriptionTemplateEntity;
import eu.eudat.data.DmpEntity;
import eu.eudat.query.DmpBlueprintQuery;
import eu.old.eudat.data.dao.entities.DMPDao;
import eu.old.eudat.data.dao.entities.DmpDatasetProfileDao;
import eu.old.eudat.data.entities.DMP;
import eu.old.eudat.data.entities.DMPDatasetProfile;
import eu.old.eudat.logic.services.operations.DatabaseRepository;
import eu.old.eudat.models.data.dmp.DataManagementPlan;
import eu.old.eudat.publicapi.migration.MigrationController;
import eu.old.eudat.queryable.QueryableList;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.logging.LoggerService;
import jakarta.persistence.EntityManager;
import jakarta.xml.bind.JAXBException;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.PathVariable;
import org.xml.sax.SAXException;
import java.util.ArrayList;
import java.util.List;
import java.util.UUID;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
import java.time.Instant;
import java.util.*;
@Service
public class DmpMigrationService {
private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(DmpMigrationService.class));
private final DatabaseRepository databaseRepository;
private final JsonHandlingService jsonHandlingService;
private final EntityManager entityManager;
private static final int PageSize = 500;
private static final boolean TestMode = false;
public DmpMigrationService(DatabaseRepository databaseRepository, JsonHandlingService jsonHandlingService, EntityManager entityManager) {
this.databaseRepository = databaseRepository;
@ -40,99 +53,189 @@ public class DmpMigrationService {
this.entityManager = entityManager;
}
public QueryableList<DMP> dmpQueryableList() {
return databaseRepository.getDmpDao().asQueryable();
}
public void migrate() throws JsonProcessingException {
DMPDao dmpDao = databaseRepository.getDmpDao();
long total = dmpDao.asQueryable().count();
logger.debug("Migrate Dmp Total : " + total);
int page = 0;
public List<DataManagementPlan> getDmps(@PathVariable("skip") Integer skip, @PathVariable("take") Integer take) {
List<DMP> dmps = dmpQueryableList()
.orderBy((builder, root) -> builder.desc(root.get("created")))
.skip(skip)
.take(take)
.toList();
List<DMP> items;
do {
items = dmpDao.asQueryable().orderBy((builder, root) -> builder.asc(root.get("created"))).orderBy((builder, root) -> builder.asc(root.get("ID"))).skip(page * PageSize).take(PageSize).toList();
if (items != null && !items.isEmpty()) {
logger.debug("Migrate Dmp " + page * PageSize + " of " + total);
return dmps.stream().map(x -> {
DataManagementPlan dmp = new DataManagementPlan();
dmp.fromDataModel(x);
return dmp;
}).toList();
}
for (DMP item : items) {
//entityManager.detach(item);
DataManagementPlan model = new DataManagementPlan();
model.fromDataModel(item);
public List<DmpMigrationCollectedInfo> collectDmpsInfo() throws JsonProcessingException {
List<DmpMigrationCollectedInfo> collectedInfoList = new ArrayList<>();
List<DataManagementPlan> dmps = getDmps(0, 4);
for (DataManagementPlan dataManagementPlan : dmps) {
DmpMigrationCollectedInfo dmpMigrationCollectedInfo = new DmpMigrationCollectedInfo();
DmpPropertiesEntity dmpProperties = new DmpPropertiesEntity();
dmpProperties.setDmpBlueprintValues(new ArrayList<>());
dmpProperties.setContacts(new ArrayList<>());
DmpPropertiesEntity dmpProperties = new DmpPropertiesEntity();
dmpProperties.setDmpBlueprintValues(new ArrayList<>());
dmpProperties.setContacts(new ArrayList<>());
DmpEntity data = new DmpEntity();
data.setId(model.getId());
data.setLabel(model.getLabel());
data.setDescription(model.getDescription());
if (model.getCreator() != null)
data.setCreatorId(model.getCreator().getId());
data.setGroupId(model.getGroupId());
data.setVersion((short) model.getVersion());
data.setVersionStatus(DmpVersionStatus.of((short) model.getVersionStatus()));
if (model.getCreated() != null)
data.setCreatedAt(model.getCreated().toInstant());
if (model.getModified() != null)
data.setUpdatedAt(model.getModified().toInstant());
if (model.getFinalized() != null)
data.setFinalizedAt(model.getFinalized().toInstant());
data.setBlueprintId(model.getProfile().getId());
if (model.getExtraProperties() != null) {
if (model.getExtraProperties().containsKey("language") && model.getExtraProperties().get("language") != null)
data.setLanguage((String) model.getExtraProperties().get("language"));
if (model.getExtraProperties().containsKey("visible") && model.getExtraProperties().get("visible") != null)
data.setAccessType((boolean) model.getExtraProperties().get("visible") ? DmpAccessType.Public : DmpAccessType.Restricted);
if (model.getExtraProperties().containsKey("contact") && model.getExtraProperties().get("contact") != null) {
DmpContactEntity contactEntity = new DmpContactEntity();
contactEntity.setUserId((String) model.getExtraProperties().get("contact"));
dmpProperties.getContacts().add(contactEntity);
}
}
if (model.getProperties() != null) {
model.getProperties().forEach((key,val) -> {
DmpBlueprintValueEntity valueEntity = new DmpBlueprintValueEntity();
valueEntity.setFieldId(key);
valueEntity.setValue((String) val);
dmpProperties.getDmpBlueprintValues().add(valueEntity);
});
}
if (model.getStatus() == 99) {
data.setIsActive(IsActive.Inactive);
data.setStatus(DmpStatus.Draft);
} else {
data.setIsActive(IsActive.Active);
data.setStatus(DmpStatus.of((short) model.getStatus()));
}
data.setProperties(jsonHandlingService.toJson(dmpProperties));
//Collect basic dmp information
DmpEntity dmpEntity = new DmpEntity();
dmpEntity.setId(UUID.randomUUID());
dmpEntity.setLabel(dataManagementPlan.getLabel());
dmpEntity.setDescription(dataManagementPlan.getDescription());
if (dataManagementPlan.getCreator() != null)
dmpEntity.setCreatorId(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.setBlueprintId(dataManagementPlan.getProfile().getId());
if (dataManagementPlan.getExtraProperties() != null) {
if (dataManagementPlan.getExtraProperties().containsKey("language") && dataManagementPlan.getExtraProperties().get("language") != null)
dmpEntity.setLanguage((String) dataManagementPlan.getExtraProperties().get("language"));
if (dataManagementPlan.getExtraProperties().containsKey("visible") && dataManagementPlan.getExtraProperties().get("visible") != null)
dmpEntity.setAccessType((boolean) dataManagementPlan.getExtraProperties().get("visible") ? DmpAccessType.Public : DmpAccessType.Restricted);
if (dataManagementPlan.getExtraProperties().containsKey("contact") && dataManagementPlan.getExtraProperties().get("contact") != null) {
DmpContactEntity contactEntity = new DmpContactEntity();
contactEntity.setUserId((String) dataManagementPlan.getExtraProperties().get("contact"));
dmpProperties.getContacts().add(contactEntity);
if (data.getAccessType() == null) {
logger.warn("AccessType not found set to default for dmp " + item.getId());
data.setAccessType(DmpAccessType.Restricted); //TODO
}
if (data.getLanguage() == null) {
logger.warn("Language not found set to default for dmp " + item.getId());
data.setLanguage(""); //TODO
}
if (data.getCreatorId() == null){
logger.warn("Migration skipped creator not found " + item.getId());
continue;
}
this.entityManager.persist(data);
this.entityManager.flush();
}
}
if (dataManagementPlan.getProperties() != null) {
dataManagementPlan.getProperties().forEach((key,val) -> {
DmpBlueprintValueEntity valueEntity = new DmpBlueprintValueEntity();
valueEntity.setFieldId(key);
valueEntity.setValue((String) val);
dmpProperties.getDmpBlueprintValues().add(valueEntity);
});
}
if (dataManagementPlan.getStatus() == 99) {
dmpEntity.setIsActive(IsActive.Inactive);
} else {
dmpEntity.setIsActive(IsActive.Active);
dmpEntity.setStatus(DmpStatus.of((short) dataManagementPlan.getStatus()));
}
dmpEntity.setProperties(jsonHandlingService.toJson(dmpProperties));
dmpMigrationCollectedInfo.dmpEntity = dmpEntity;
//Collect dmp Organization info
collectedInfoList.add(dmpMigrationCollectedInfo);
}
return collectedInfoList;
page++;
}
} while (items != null && !items.isEmpty() && !TestMode);
}
@Transactional
public String migrate() throws JsonProcessingException {
for (DmpMigrationCollectedInfo collectedInfo : collectDmpsInfo()) {
this.entityManager.persist(collectedInfo.dmpEntity);
}
this.entityManager.flush();
return "Migrated dmps";
}
// public QueryableList<DMP> dmpQueryableList() {
// return databaseRepository.getDmpDao().asQueryable();
// }
//
// public List<DataManagementPlan> getDmps(Integer skip, Integer take) {
// List<DMP> dmps = dmpQueryableList()
// .orderBy((builder, root) -> builder.desc(root.get("created")))
// .skip(skip)
// .take(take)
// .toList();
//
// return dmps.stream().map(x -> {
// DataManagementPlan dmp = new DataManagementPlan();
// dmp.fromDataModel(x);
// return dmp;
// }).toList();
// }
public static class DmpMigrationCollectedInfo {
public DmpEntity dmpEntity;
}
// public List<DmpMigrationCollectedInfo> collectDmpsInfo() throws JsonProcessingException {
// List<DmpMigrationCollectedInfo> collectedInfoList = new ArrayList<>();
// List<DataManagementPlan> dmps = getDmps(0, Integer.MAX_VALUE);
// for (DataManagementPlan dataManagementPlan : dmps) {
// DmpMigrationCollectedInfo dmpMigrationCollectedInfo = new DmpMigrationCollectedInfo();
//
// DmpPropertiesEntity dmpProperties = new DmpPropertiesEntity();
// dmpProperties.setDmpBlueprintValues(new ArrayList<>());
// dmpProperties.setContacts(new ArrayList<>());
//
// //Collect basic dmp information
// DmpEntity dmpEntity = new DmpEntity();
// dmpEntity.setId(dataManagementPlan.getId());
// dmpEntity.setLabel(dataManagementPlan.getLabel());
// dmpEntity.setDescription(dataManagementPlan.getDescription());
// if (dataManagementPlan.getCreator() != null)
// dmpEntity.setCreatorId(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.setBlueprintId(dataManagementPlan.getProfile().getId());
// if (dataManagementPlan.getExtraProperties() != null) {
// if (dataManagementPlan.getExtraProperties().containsKey("language") && dataManagementPlan.getExtraProperties().get("language") != null)
// dmpEntity.setLanguage((String) dataManagementPlan.getExtraProperties().get("language"));
// if (dataManagementPlan.getExtraProperties().containsKey("visible") && dataManagementPlan.getExtraProperties().get("visible") != null)
// dmpEntity.setAccessType((boolean) dataManagementPlan.getExtraProperties().get("visible") ? DmpAccessType.Public : DmpAccessType.Restricted);
// if (dataManagementPlan.getExtraProperties().containsKey("contact") && dataManagementPlan.getExtraProperties().get("contact") != null) {
// DmpContactEntity contactEntity = new DmpContactEntity();
// contactEntity.setUserId((String) dataManagementPlan.getExtraProperties().get("contact"));
// dmpProperties.getContacts().add(contactEntity);
// }
// }
// if (dataManagementPlan.getProperties() != null) {
// dataManagementPlan.getProperties().forEach((key,val) -> {
// DmpBlueprintValueEntity valueEntity = new DmpBlueprintValueEntity();
// valueEntity.setFieldId(key);
// valueEntity.setValue((String) val);
// dmpProperties.getDmpBlueprintValues().add(valueEntity);
// });
// }
// if (dataManagementPlan.getStatus() == 99) {
// dmpEntity.setIsActive(IsActive.Inactive);
// dmpEntity.setStatus(DmpStatus.Draft);
// } else {
// dmpEntity.setIsActive(IsActive.Active);
// dmpEntity.setStatus(DmpStatus.of((short) dataManagementPlan.getStatus()));
// }
// dmpEntity.setProperties(jsonHandlingService.toJson(dmpProperties));
// dmpMigrationCollectedInfo.dmpEntity = dmpEntity;
//
// //Collect dmp Organization info
//
// collectedInfoList.add(dmpMigrationCollectedInfo);
// }
// return collectedInfoList;
// }
//
// public String migrate() throws JsonProcessingException {
// for (DmpMigrationCollectedInfo collectedInfo : collectDmpsInfo()) {
// this.entityManager.persist(collectedInfo.dmpEntity);
// }
// this.entityManager.flush();
// return "Migrated dmps";
// }
//
// public static class DmpMigrationCollectedInfo {
//
// public DmpEntity dmpEntity;
//
// }
}

1
dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/ExternalDatasetMigrationService.java
View File

@ -54,6 +54,7 @@ public class ExternalDatasetMigrationService {
ReferenceEntity data = new ReferenceEntity();
data.setId(item.getId());
data.setLabel(item.getLabel());
data.setAbbreviation(item.getAbbreviation());
data.setIsActive(IsActive.Active);
data.setType(ReferenceType.Datasets);
data.setCreatedAt(item.getCreated().toInstant());

2
dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/FunderMigrationService.java
View File

@ -54,7 +54,7 @@ public class FunderMigrationService {
ReferenceEntity data = new ReferenceEntity();
data.setId(item.getId());
data.setLabel(item.getLabel());
data.setIsActive(DMP.DMPStatus.fromInteger(item.getStatus()).equals(DMP.DMPStatus.DELETED) ? IsActive.Inactive : IsActive.Active);
data.setIsActive(IsActive.Active);
data.setType(ReferenceType.Funder);
data.setCreatedAt(item.getCreated().toInstant());
data.setUpdatedAt(item.getModified().toInstant());

47
dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/GrantMigrationService.java
View File

@ -1,11 +1,15 @@
package eu.old.eudat.migration;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.enums.ReferenceFieldDataType;
import eu.eudat.commons.enums.ReferenceSourceType;
import eu.eudat.commons.enums.ReferenceType;
import eu.eudat.commons.types.reference.DefinitionEntity;
import eu.eudat.commons.types.reference.FieldEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.ReferenceEntity;
import eu.old.eudat.data.dao.entities.GrantDao;
import eu.old.eudat.data.entities.DMP;
import eu.old.eudat.data.entities.Grant;
import eu.old.eudat.logic.services.operations.DatabaseRepository;
import gr.cite.tools.logging.LoggerService;
@ -13,6 +17,7 @@ import jakarta.persistence.EntityManager;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service;
import java.util.ArrayList;
import java.util.List;
import java.util.Locale;
@ -24,9 +29,13 @@ public class GrantMigrationService {
private static final String InternalReferenceSource = "dmp";
private final DatabaseRepository databaseRepository;
private final EntityManager entityManager;
public GrantMigrationService(DatabaseRepository databaseRepository, EntityManager entityManager) {
private final ConventionService conventionService;
private final XmlHandlingService xmlHandlingService;
public GrantMigrationService(DatabaseRepository databaseRepository, EntityManager entityManager, ConventionService conventionService, XmlHandlingService xmlHandlingService) {
this.databaseRepository = databaseRepository;
this.entityManager = entityManager;
this.conventionService = conventionService;
this.xmlHandlingService = xmlHandlingService;
}
public void migrate(){
@ -54,7 +63,8 @@ public class GrantMigrationService {
data.setId(item.getId());
data.setLabel(item.getLabel());
data.setDescription(item.getDescription());
data.setIsActive(DMP.DMPStatus.fromInteger(item.getStatus()).equals(DMP.DMPStatus.DELETED) ? IsActive.Inactive : IsActive.Active);
data.setAbbreviation(item.getAbbreviation());
data.setIsActive(IsActive.Active);
data.setType(ReferenceType.Grants);
data.setCreatedAt(item.getCreated().toInstant());
data.setUpdatedAt(item.getModified().toInstant());
@ -62,6 +72,37 @@ public class GrantMigrationService {
data.setReference(referenceParts[1]);
data.setSource(isInternal? "Internal" : referenceParts[0]);
data.setSourceType(isInternal ? ReferenceSourceType.Internal : ReferenceSourceType.External);
DefinitionEntity definitionEntity = new DefinitionEntity();
definitionEntity.setFields(new ArrayList<>());
if (!this.conventionService.isNullOrEmpty(item.getUri())){
FieldEntity fieldEntity = new FieldEntity();
fieldEntity.setCode("uri");
fieldEntity.setDataType(ReferenceFieldDataType.Text);
fieldEntity.setValue(item.getUri());
definitionEntity.getFields().add(fieldEntity);
}
if (item.getStartdate() != null){
FieldEntity fieldEntity = new FieldEntity();
fieldEntity.setCode("startDate");
fieldEntity.setDataType(ReferenceFieldDataType.Date);
fieldEntity.setValue(item.getStartdate().toInstant().toString());
definitionEntity.getFields().add(fieldEntity);
}
if (item.getEnddate() != null){
FieldEntity fieldEntity = new FieldEntity();
fieldEntity.setCode("endDate");
fieldEntity.setDataType(ReferenceFieldDataType.Date);
fieldEntity.setValue(item.getEnddate().toInstant().toString());
definitionEntity.getFields().add(fieldEntity);
}
if (!definitionEntity.getFields().isEmpty()){
data.setDefinition(this.xmlHandlingService.toXmlSafe(definitionEntity));
}
this.entityManager.persist(data);
}
this.entityManager.flush();

25
dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/OrganizationMigrationService.java
View File

@ -1,11 +1,15 @@
package eu.old.eudat.migration;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.enums.ReferenceFieldDataType;
import eu.eudat.commons.enums.ReferenceSourceType;
import eu.eudat.commons.enums.ReferenceType;
import eu.eudat.commons.types.reference.DefinitionEntity;
import eu.eudat.commons.types.reference.FieldEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.ReferenceEntity;
import eu.old.eudat.data.dao.entities.OrganisationDao;
import eu.old.eudat.data.entities.DMP;
import eu.old.eudat.data.entities.Organisation;
import eu.old.eudat.logic.services.operations.DatabaseRepository;
import gr.cite.tools.logging.LoggerService;
@ -13,7 +17,6 @@ import jakarta.persistence.EntityManager;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service;
import java.util.ArrayList;
import java.util.List;
import java.util.Locale;
@ -25,9 +28,13 @@ public class OrganizationMigrationService {
private static final String InternalReferenceSource = "Internal";
private final DatabaseRepository databaseRepository;
private final EntityManager entityManager;
public OrganizationMigrationService(DatabaseRepository databaseRepository, EntityManager entityManager) {
private final ConventionService conventionService;
private final XmlHandlingService xmlHandlingService;
public OrganizationMigrationService(DatabaseRepository databaseRepository, EntityManager entityManager, ConventionService conventionService, XmlHandlingService xmlHandlingService) {
this.databaseRepository = databaseRepository;
this.entityManager = entityManager;
this.conventionService = conventionService;
this.xmlHandlingService = xmlHandlingService;
}
public void migrate(){
@ -56,7 +63,8 @@ public class OrganizationMigrationService {
ReferenceEntity data = new ReferenceEntity();
data.setId(item.getId());
data.setLabel(item.getLabel());
data.setIsActive(DMP.DMPStatus.fromInteger(item.getStatus()).equals(DMP.DMPStatus.DELETED) ? IsActive.Inactive : IsActive.Active);
data.setAbbreviation(item.getAbbreviation());
data.setIsActive(IsActive.Active);
data.setType(ReferenceType.Organizations);
data.setCreatedAt(item.getCreated().toInstant());
data.setUpdatedAt(item.getModified().toInstant());
@ -64,6 +72,15 @@ public class OrganizationMigrationService {
data.setAbbreviation(item.getAbbreviation());
data.setSource(isInternal? "Internal" : referenceParts[0]);
data.setSourceType(isInternal? ReferenceSourceType.Internal : ReferenceSourceType.External);
if (!this.conventionService.isNullOrEmpty(item.getUri())){
DefinitionEntity definitionEntity = new DefinitionEntity();
FieldEntity fieldEntity = new FieldEntity();
fieldEntity.setCode("uri");
fieldEntity.setDataType(ReferenceFieldDataType.Text);
fieldEntity.setValue(item.getUri());
definitionEntity.setFields(List.of(fieldEntity));
data.setDefinition(this.xmlHandlingService.toXmlSafe(definitionEntity));
}
this.entityManager.persist(data);
}
this.entityManager.flush();

46
dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/ProjectMigrationService.java
View File

@ -1,11 +1,15 @@
package eu.old.eudat.migration;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.enums.ReferenceFieldDataType;
import eu.eudat.commons.enums.ReferenceSourceType;
import eu.eudat.commons.enums.ReferenceType;
import eu.eudat.commons.types.reference.DefinitionEntity;
import eu.eudat.commons.types.reference.FieldEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.ReferenceEntity;
import eu.old.eudat.data.dao.entities.ProjectDao;
import eu.old.eudat.data.entities.DMP;
import eu.old.eudat.data.entities.Project;
import eu.old.eudat.logic.services.operations.DatabaseRepository;
import gr.cite.tools.logging.LoggerService;
@ -13,6 +17,7 @@ import jakarta.persistence.EntityManager;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service;
import java.util.ArrayList;
import java.util.List;
import java.util.Locale;
@ -24,9 +29,13 @@ public class ProjectMigrationService {
private static final String InternalReferenceSource = "dmp";
private final DatabaseRepository databaseRepository;
private final EntityManager entityManager;
public ProjectMigrationService(DatabaseRepository databaseRepository, EntityManager entityManager) {
private final ConventionService conventionService;
private final XmlHandlingService xmlHandlingService;
public ProjectMigrationService(DatabaseRepository databaseRepository, EntityManager entityManager, ConventionService conventionService, XmlHandlingService xmlHandlingService) {
this.databaseRepository = databaseRepository;
this.entityManager = entityManager;
this.conventionService = conventionService;
this.xmlHandlingService = xmlHandlingService;
}
public void migrate(){
@ -54,8 +63,9 @@ public class ProjectMigrationService {
ReferenceEntity data = new ReferenceEntity();
data.setId(item.getId());
data.setLabel(item.getLabel());
data.setAbbreviation(item.getAbbreviation());
data.setDescription(item.getDescription());
data.setIsActive(DMP.DMPStatus.fromInteger(item.getStatus()).equals(DMP.DMPStatus.DELETED) ? IsActive.Inactive : IsActive.Active);
data.setIsActive(IsActive.Active);
data.setType(ReferenceType.Project);
data.setCreatedAt(item.getCreated().toInstant());
data.setUpdatedAt(item.getModified().toInstant());
@ -63,6 +73,36 @@ public class ProjectMigrationService {
data.setReference(referenceParts[1]);
data.setSource(isInternal? "Internal" : referenceParts[0]);
data.setSourceType(Project.ProjectType.INTERNAL.getValue().equals(item.getType())? ReferenceSourceType.Internal : ReferenceSourceType.External);
DefinitionEntity definitionEntity = new DefinitionEntity();
definitionEntity.setFields(new ArrayList<>());
if (!this.conventionService.isNullOrEmpty(item.getUri())){
FieldEntity fieldEntity = new FieldEntity();
fieldEntity.setCode("uri");
fieldEntity.setDataType(ReferenceFieldDataType.Text);
fieldEntity.setValue(item.getUri());
definitionEntity.getFields().add(fieldEntity);
}
if (item.getStartdate() != null){
FieldEntity fieldEntity = new FieldEntity();
fieldEntity.setCode("startDate");
fieldEntity.setDataType(ReferenceFieldDataType.Date);
fieldEntity.setValue(item.getStartdate().toInstant().toString());
definitionEntity.getFields().add(fieldEntity);
}
if (item.getEnddate() != null){
FieldEntity fieldEntity = new FieldEntity();
fieldEntity.setCode("endDate");
fieldEntity.setDataType(ReferenceFieldDataType.Date);
fieldEntity.setValue(item.getEnddate().toInstant().toString());
definitionEntity.getFields().add(fieldEntity);
}
if (!definitionEntity.getFields().isEmpty()){
data.setDefinition(this.xmlHandlingService.toXmlSafe(definitionEntity));
}
this.entityManager.persist(data);
}
this.entityManager.flush();

24
dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/RegistryMigrationService.java
View File

@ -1,11 +1,15 @@
package eu.old.eudat.migration;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.enums.ReferenceFieldDataType;
import eu.eudat.commons.enums.ReferenceSourceType;
import eu.eudat.commons.enums.ReferenceType;
import eu.eudat.commons.types.reference.DefinitionEntity;
import eu.eudat.commons.types.reference.FieldEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.ReferenceEntity;
import eu.old.eudat.data.dao.entities.RegistryDao;
import eu.old.eudat.data.entities.DMP;
import eu.old.eudat.data.entities.Registry;
import eu.old.eudat.logic.services.operations.DatabaseRepository;
import gr.cite.tools.logging.LoggerService;
@ -24,9 +28,13 @@ public class RegistryMigrationService {
private static final String InternalReferenceSource = "dmp";
private final DatabaseRepository databaseRepository;
private final EntityManager entityManager;
public RegistryMigrationService(DatabaseRepository databaseRepository, EntityManager entityManager) {
private final ConventionService conventionService;
private final XmlHandlingService xmlHandlingService;
public RegistryMigrationService(DatabaseRepository databaseRepository, EntityManager entityManager, ConventionService conventionService, XmlHandlingService xmlHandlingService) {
this.databaseRepository = databaseRepository;
this.entityManager = entityManager;
this.conventionService = conventionService;
this.xmlHandlingService = xmlHandlingService;
}
public void migrate(){
@ -54,7 +62,8 @@ public class RegistryMigrationService {
ReferenceEntity data = new ReferenceEntity();
data.setId(item.getId());
data.setLabel(item.getLabel());
data.setIsActive(DMP.DMPStatus.fromInteger(item.getStatus()).equals(DMP.DMPStatus.DELETED) ? IsActive.Inactive : IsActive.Active);
data.setAbbreviation(item.getAbbreviation());
data.setIsActive(IsActive.Active);
data.setType(ReferenceType.Registries);
data.setCreatedAt(item.getCreated().toInstant());
data.setUpdatedAt(item.getModified().toInstant());
@ -62,6 +71,15 @@ public class RegistryMigrationService {
data.setReference(referenceParts[1]);
data.setSource(isInternal? "Internal" : referenceParts[0]);
data.setSourceType(isInternal? ReferenceSourceType.Internal : ReferenceSourceType.External);
if (!this.conventionService.isNullOrEmpty(item.getUri())){
DefinitionEntity definitionEntity = new DefinitionEntity();
FieldEntity fieldEntity = new FieldEntity();
fieldEntity.setCode("uri");
fieldEntity.setDataType(ReferenceFieldDataType.Text);
fieldEntity.setValue(item.getUri());
definitionEntity.setFields(List.of(fieldEntity));
data.setDefinition(this.xmlHandlingService.toXmlSafe(definitionEntity));
}
this.entityManager.persist(data);
}
this.entityManager.flush();

40
dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/ResearcherMigrationService.java
View File

@ -1,13 +1,15 @@
package eu.old.eudat.migration;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.enums.ReferenceFieldDataType;
import eu.eudat.commons.enums.ReferenceSourceType;
import eu.eudat.commons.enums.ReferenceType;
import eu.eudat.commons.types.reference.DefinitionEntity;
import eu.eudat.commons.types.reference.FieldEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.ReferenceEntity;
import eu.old.eudat.data.dao.entities.OrganisationDao;
import eu.old.eudat.data.dao.entities.ResearcherDao;
import eu.old.eudat.data.entities.DMP;
import eu.old.eudat.data.entities.Organisation;
import eu.old.eudat.data.entities.Researcher;
import eu.old.eudat.logic.services.operations.DatabaseRepository;
import gr.cite.tools.logging.LoggerService;
@ -15,6 +17,7 @@ import jakarta.persistence.EntityManager;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service;
import java.util.ArrayList;
import java.util.List;
import java.util.Locale;
@ -26,9 +29,13 @@ public class ResearcherMigrationService {
private static final String InternalReferenceSource = "dmp";
private final DatabaseRepository databaseRepository;
private final EntityManager entityManager;
public ResearcherMigrationService(DatabaseRepository databaseRepository, EntityManager entityManager) {
private final ConventionService conventionService;
private final XmlHandlingService xmlHandlingService;
public ResearcherMigrationService(DatabaseRepository databaseRepository, EntityManager entityManager, ConventionService conventionService, XmlHandlingService xmlHandlingService) {
this.databaseRepository = databaseRepository;
this.entityManager = entityManager;
this.conventionService = conventionService;
this.xmlHandlingService = xmlHandlingService;
}
public void migrate(){
@ -56,7 +63,7 @@ public class ResearcherMigrationService {
ReferenceEntity data = new ReferenceEntity();
data.setId(item.getId());
data.setLabel(item.getLabel());
data.setIsActive(DMP.DMPStatus.fromInteger(item.getStatus()).equals(DMP.DMPStatus.DELETED) ? IsActive.Inactive : IsActive.Active);
data.setIsActive(IsActive.Active);
data.setType(ReferenceType.Researcher);
data.setCreatedAt(item.getCreated().toInstant());
data.setUpdatedAt(item.getModified().toInstant());
@ -64,6 +71,29 @@ public class ResearcherMigrationService {
data.setReference(referenceParts[1]);
data.setSource(isInternal? "Internal" : referenceParts[0]);
data.setSourceType(isInternal? ReferenceSourceType.Internal : ReferenceSourceType.External);
DefinitionEntity definitionEntity = new DefinitionEntity();
definitionEntity.setFields(new ArrayList<>());
if (!this.conventionService.isNullOrEmpty(item.getUri())){
FieldEntity fieldEntity = new FieldEntity();
fieldEntity.setCode("uri");
fieldEntity.setDataType(ReferenceFieldDataType.Text);
fieldEntity.setValue(item.getUri());
definitionEntity.getFields().add(fieldEntity);
}
if (!this.conventionService.isNullOrEmpty(item.getPrimaryEmail())){
FieldEntity fieldEntity = new FieldEntity();
fieldEntity.setCode("primaryEmail");
fieldEntity.setDataType(ReferenceFieldDataType.Text);
fieldEntity.setValue(item.getPrimaryEmail());
definitionEntity.getFields().add(fieldEntity);
}
if (!definitionEntity.getFields().isEmpty()){
data.setDefinition(this.xmlHandlingService.toXmlSafe(definitionEntity));
}
this.entityManager.persist(data);
}
this.entityManager.flush();

26
dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/ServiceMigrationService.java
View File

@ -1,11 +1,15 @@
package eu.old.eudat.migration;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.enums.ReferenceFieldDataType;
import eu.eudat.commons.enums.ReferenceSourceType;
import eu.eudat.commons.enums.ReferenceType;
import eu.eudat.commons.types.reference.DefinitionEntity;
import eu.eudat.commons.types.reference.FieldEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.ReferenceEntity;
import eu.old.eudat.data.dao.entities.ServiceDao;
import eu.old.eudat.data.entities.DMP;
import eu.old.eudat.logic.services.operations.DatabaseRepository;
import gr.cite.tools.logging.LoggerService;
import jakarta.persistence.EntityManager;
@ -23,9 +27,13 @@ public class ServiceMigrationService {
private static final String InternalReferenceSource = "dmp";
private final DatabaseRepository databaseRepository;
private final EntityManager entityManager;
public ServiceMigrationService(DatabaseRepository databaseRepository, EntityManager entityManager) {
private final ConventionService conventionService;
private final XmlHandlingService xmlHandlingService;
public ServiceMigrationService(DatabaseRepository databaseRepository, EntityManager entityManager, ConventionService conventionService, XmlHandlingService xmlHandlingService) {
this.databaseRepository = databaseRepository;
this.entityManager = entityManager;
this.conventionService = conventionService;
this.xmlHandlingService = xmlHandlingService;
}
public void migrate(){
@ -53,8 +61,8 @@ public class ServiceMigrationService {
ReferenceEntity data = new ReferenceEntity();
data.setId(item.getId());
data.setLabel(item.getLabel());
data.setDescription(item.getLabel());
data.setIsActive(DMP.DMPStatus.fromInteger(item.getStatus()).equals(DMP.DMPStatus.DELETED) ? IsActive.Inactive : IsActive.Active);
data.setAbbreviation(item.getAbbreviation());
data.setIsActive(IsActive.Active);
data.setType(ReferenceType.Services);
data.setCreatedAt(item.getCreated().toInstant());
data.setUpdatedAt(item.getModified().toInstant());
@ -62,6 +70,16 @@ public class ServiceMigrationService {
data.setReference(referenceParts[1]);
data.setSource(isInternal? "Internal" : referenceParts[0]);
data.setSourceType(isInternal? ReferenceSourceType.Internal : ReferenceSourceType.External);
if (!this.conventionService.isNullOrEmpty(item.getUri())){
DefinitionEntity definitionEntity = new DefinitionEntity();
FieldEntity fieldEntity = new FieldEntity();
fieldEntity.setCode("uri");
fieldEntity.setDataType(ReferenceFieldDataType.Text);
fieldEntity.setValue(item.getUri());
definitionEntity.setFields(List.of(fieldEntity));
data.setDefinition(this.xmlHandlingService.toXmlSafe(definitionEntity));
}
this.entityManager.persist(data);
}
this.entityManager.flush();

22
dmp-migration-tool/web/src/main/java/eu/old/eudat/models/data/datasetwizard/DatasetWizardModel.java
View File

@ -22,6 +22,7 @@ public class DatasetWizardModel implements DataModel<Dataset, DatasetWizardModel
private String description;
private short status;
private Date created;
private UUID createdBy;
private DataManagementPlan dmp;
private Integer dmpSectionIndex;
private PagedDatasetProfile datasetProfileDefinition;
@ -33,6 +34,7 @@ public class DatasetWizardModel implements DataModel<Dataset, DatasetWizardModel
private DatasetProfileOverviewModel profile;
private Boolean isProfileLatestVersion;
private Date modified;
private Date finalized;
public UUID getId() {
return id;
@ -83,6 +85,13 @@ public class DatasetWizardModel implements DataModel<Dataset, DatasetWizardModel
this.created = created;
}
public UUID getCreatedBy() {
return createdBy;
}
public void setCreatedBy(UUID createdBy) {
this.createdBy = createdBy;
}
public DataManagementPlan getDmp() {
return dmp;
}
@ -161,6 +170,13 @@ public class DatasetWizardModel implements DataModel<Dataset, DatasetWizardModel
this.modified = modified;
}
public Date getFinalized() {
return finalized;
}
public void setFinalized(Date finalized) {
this.finalized = finalized;
}
@Override
public DatasetWizardModel fromDataModel(Dataset entity) {
this.id = entity.getId();
@ -183,6 +199,7 @@ public class DatasetWizardModel implements DataModel<Dataset, DatasetWizardModel
}).collect(Collectors.toList()) : new ArrayList<>();
this.services = entity.getServices() != null ? entity.getServices().stream().map(item -> new eu.old.eudat.models.data.dataset.Service().fromDataModel(item.getService())).collect(Collectors.toList()) : new ArrayList<>();
this.created = entity.getCreated();
this.createdBy = entity.getCreator().getId();
this.dmp = new DataManagementPlan().fromDataModelNoDatasets(entity.getDmp());
this.dmpSectionIndex = entity.getDmpSectionIndex();
this.externalDatasets = entity.getDatasetExternalDatasets() != null ? entity.getDatasetExternalDatasets().stream().map(item -> {
@ -196,6 +213,7 @@ public class DatasetWizardModel implements DataModel<Dataset, DatasetWizardModel
return externalDatasetListingModel;
}).collect(Collectors.toList()) : new ArrayList<>();
this.modified = entity.getModified();
this.finalized = entity.getFinalizedAt();
return this;
}
@ -251,7 +269,11 @@ public class DatasetWizardModel implements DataModel<Dataset, DatasetWizardModel
entity.setDmpSectionIndex(this.dmpSectionIndex);
entity.setDescription(this.description);
entity.setCreated(this.created != null ? this.created : new Date());
UserInfo userInfo = new UserInfo();
userInfo.setId(this.createdBy);
entity.setCreator(userInfo);
entity.setModified(new Date());
entity.setFinalizedAt(this.finalized != null ? this.finalized : new Date());
DescriptionTemplate profile = new DescriptionTemplate();
profile.setId(this.profile.getId());
entity.setProfile(profile);

66
dmp-migration-tool/web/src/main/java/eu/old/eudat/publicapi/migration/MigrationController.java
View File

@ -3,8 +3,16 @@ package eu.old.eudat.publicapi.migration;
import com.fasterxml.jackson.core.JsonProcessingException;
import eu.old.eudat.migration.*;
import io.swagger.annotations.Api;
import jakarta.xml.bind.JAXBException;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.web.bind.annotation.*;
import org.springframework.web.bind.annotation.CrossOrigin;
import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RestController;
import org.xml.sax.SAXException;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
@Api(tags = "Migration")
@RestController
@ -21,22 +29,27 @@ public class MigrationController {
private final RegistryMigrationService registryMigrationService;
private final ResearcherMigrationService researcherMigrationService;
private final ServiceMigrationService serviceMigrationService;
private final DatasetMigrationService datasetMigrationService;
private final DmpDatasetProfileMigrationService dmpDatasetProfileMigrationService;
private final OrganizationMigrationService organizationMigrationService;
public MigrationController(
DmpMigrationService dmpMigrationService,
DataRepositoryMigrationService dataRepositoryMigrationService,
ExternalDatasetMigrationService externalDatasetMigrationService,
FunderMigrationService funderMigrationService,
GrantMigrationService grantMigrationService,
ProjectMigrationService projectMigrationService,
RegistryMigrationService registryMigrationService,
ResearcherMigrationService researcherMigrationService,
ServiceMigrationService serviceMigrationService,
DatasetMigrationService datasetMigrationService,
DmpDatasetProfileMigrationService dmpDatasetProfileMigrationService,
DataRepositoryMigrationService dataRepositoryMigrationService,
ExternalDatasetMigrationService externalDatasetMigrationService,
FunderMigrationService funderMigrationService,
GrantMigrationService grantMigrationService,
ProjectMigrationService projectMigrationService,
RegistryMigrationService registryMigrationService,
ResearcherMigrationService researcherMigrationService,
ServiceMigrationService serviceMigrationService,
OrganizationMigrationService organizationMigrationService
) {
this.dmpMigrationService = dmpMigrationService;
this.datasetMigrationService = datasetMigrationService;
this.dmpDatasetProfileMigrationService = dmpDatasetProfileMigrationService;
this.dataRepositoryMigrationService = dataRepositoryMigrationService;
this.externalDatasetMigrationService = externalDatasetMigrationService;
this.funderMigrationService = funderMigrationService;
@ -48,19 +61,28 @@ public class MigrationController {
this.organizationMigrationService = organizationMigrationService;
}
@GetMapping("dmps/migrate")
@GetMapping("dmps")
@Transactional
public String migrateDmps() throws JsonProcessingException {
return this.dmpMigrationService.migrate();
public boolean migrateDmps() throws JsonProcessingException {
this.dmpMigrationService.migrate();
return true;
}
@GetMapping("organizations")
@GetMapping("datasets/migrate")
@Transactional
public boolean migrateOrganizations() {
this.organizationMigrationService.migrate();
return true;
public String migrateDatasets() throws JsonProcessingException {
return this.datasetMigrationService.migrate();
}
@GetMapping("dmp-dataset-profiles")
@Transactional
public boolean migrateDmpDatasetProfiles() throws IOException, JAXBException, ParserConfigurationException, InstantiationException, IllegalAccessException, SAXException {
this.dmpDatasetProfileMigrationService.migrate();
return true;
}
@GetMapping("references")
@Transactional
public boolean migrateReferences() {
@ -74,8 +96,16 @@ public class MigrationController {
this.researcherMigrationService.migrate();
this.serviceMigrationService.migrate();
return true;
}
@GetMapping("organizations")
@Transactional
public boolean migrateOrganizations() {
this.organizationMigrationService.migrate();
return true;
}
@GetMapping("dataRepositories")
@Transactional
public boolean migrateDataRepositories() {