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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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

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";

58
dmp-db-scema/updates/00.01.010_Align_DescriptionTemplate_table.sql
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@ -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 "Label" TO label;
ALTER TABLE public."DescriptionTemplate" RENAME "ID" TO id;
ALTER TABLE public."DescriptionTemplate" RENAME "Definition" TO definition;
ALTER TABLE public."DescriptionTemplate" RENAME "Label" TO label;
ALTER TABLE public."DescriptionTemplate" RENAME "Status" TO status;
ALTER TABLE public."DescriptionTemplate" RENAME "Definition" TO definition;
ALTER TABLE public."DescriptionTemplate" RENAME "Created" TO created_at;
ALTER TABLE public."DescriptionTemplate" RENAME "Status" TO status;
ALTER TABLE public."DescriptionTemplate" RENAME "Modified" TO updated_at;
ALTER TABLE public."DescriptionTemplate" RENAME "Created" TO created_at;
ALTER TABLE public."DescriptionTemplate" RENAME "Description" TO description;
ALTER TABLE public."DescriptionTemplate" RENAME "Modified" TO updated_at;
ALTER TABLE public."DescriptionTemplate" RENAME "GroupId" TO group_id;
ALTER TABLE public."DescriptionTemplate" RENAME "Description" TO description;
ALTER TABLE public."DescriptionTemplate" RENAME "Version" TO version;
ALTER TABLE public."DescriptionTemplate" RENAME "GroupId" TO group_id;
ALTER TABLE public."DescriptionTemplate" RENAME "Language" TO "language";
ALTER TABLE public."DescriptionTemplate" RENAME "Version" TO version;
ALTER TABLE public."DescriptionTemplate" RENAME "Type" TO "type";
ALTER TABLE public."DescriptionTemplate" RENAME "Language" TO "language";
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN created_at TYPE timestamp without time zone ;
ALTER TABLE public."DescriptionTemplate" RENAME "Type" TO "type";
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN updated_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 group_id DROP DEFAULT;
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN updated_at TYPE timestamp without time zone ;
ALTER TABLE public."DescriptionTemplate" ADD COLUMN is_active smallint;
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN group_id DROP DEFAULT;
UPDATE public."DescriptionTemplate" SET is_active = 1;
ALTER TABLE public."DescriptionTemplate" ADD COLUMN is_active smallint;
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 = 1;
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN is_active SET NOT NULL;
UPDATE public."DescriptionTemplate" SET is_active = 0 where status = 99;
UPDATE public."DescriptionTemplate" SET status = 0 where is_active = 0;
ALTER TABLE public."DescriptionTemplate" ADD COLUMN version_status smallint;
ALTER TABLE public."DescriptionTemplate" ALTER COLUMN is_active SET NOT NULL;
UPDATE public."DescriptionTemplate" SET version_status = 1;
ALTER TABLE public."DescriptionTemplate" ADD COLUMN version_status smallint;
UPDATE public."DescriptionTemplate" SET version_status = 0 where id in (
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
)
);
);
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(){
@ -50,6 +59,8 @@ public class DataRepositoryMigrationService {
String[] referenceParts = item.getReference().split(":", 2);
boolean isInternal = referenceParts[0].equals(InternalReferenceSource);
ReferenceEntity data = new ReferenceEntity();
data.setId(item.getId());
data.setLabel(item.getLabel());
@ -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
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@ -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;
}
}
}

245
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);
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();
DataManagementPlan model = new DataManagementPlan();
model.fromDataModel(item);
DmpPropertiesEntity dmpProperties = new DmpPropertiesEntity();
dmpProperties.setDmpBlueprintValues(new ArrayList<>());
dmpProperties.setContacts(new ArrayList<>());
//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) {
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) dataManagementPlan.getExtraProperties().get("contact"));
contactEntity.setUserId((String) model.getExtraProperties().get("contact"));
dmpProperties.getContacts().add(contactEntity);
}
}
if (dataManagementPlan.getProperties() != null) {
dataManagementPlan.getProperties().forEach((key,val) -> {
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 (dataManagementPlan.getStatus() == 99) {
dmpEntity.setIsActive(IsActive.Inactive);
if (model.getStatus() == 99) {
data.setIsActive(IsActive.Inactive);
data.setStatus(DmpStatus.Draft);
} else {
dmpEntity.setIsActive(IsActive.Active);
dmpEntity.setStatus(DmpStatus.of((short) dataManagementPlan.getStatus()));
data.setIsActive(IsActive.Active);
data.setStatus(DmpStatus.of((short) model.getStatus()));
}
dmpEntity.setProperties(jsonHandlingService.toJson(dmpProperties));
dmpMigrationCollectedInfo.dmpEntity = dmpEntity;
data.setProperties(jsonHandlingService.toJson(dmpProperties));
//Collect dmp Organization info
collectedInfoList.add(dmpMigrationCollectedInfo);
if (data.getAccessType() == null) {
logger.warn("AccessType not found set to default for dmp " + item.getId());
data.setAccessType(DmpAccessType.Restricted); //TODO
}
return collectedInfoList;
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;
}
@Transactional
public String migrate() throws JsonProcessingException {
for (DmpMigrationCollectedInfo collectedInfo : collectDmpsInfo()) {
this.entityManager.persist(collectedInfo.dmpEntity);
}
this.entityManager.persist(data);
this.entityManager.flush();
return "Migrated dmps";
}
public static class DmpMigrationCollectedInfo {
public DmpEntity dmpEntity;
page++;
}
} while (items != null && !items.isEmpty() && !TestMode);
}
// 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 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);

52
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
@ -21,11 +29,14 @@ 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,
DatasetMigrationService datasetMigrationService,
DmpDatasetProfileMigrationService dmpDatasetProfileMigrationService,
DataRepositoryMigrationService dataRepositoryMigrationService,
ExternalDatasetMigrationService externalDatasetMigrationService,
FunderMigrationService funderMigrationService,
@ -37,6 +48,8 @@ public class MigrationController {
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();
}
@GetMapping("organizations")
@Transactional
public boolean migrateOrganizations() {
this.organizationMigrationService.migrate();
public boolean migrateDmps() throws JsonProcessingException {
this.dmpMigrationService.migrate();
return true;
}
@GetMapping("datasets/migrate")
@Transactional
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() {
@ -76,6 +98,14 @@ public class MigrationController {
return true;
}
@GetMapping("organizations")
@Transactional
public boolean migrateOrganizations() {
this.organizationMigrationService.migrate();
return true;
}
@GetMapping("dataRepositories")
@Transactional
public boolean migrateDataRepositories() {