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dmp migration changes

This commit is contained in:
Efstratios Giannopoulos 2023-11-23 14:40:44 +02:00
parent e47a370088
commit 9433beaaa6
7 changed files with 428 additions and 188 deletions
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3
dmp-backend/core/src/main/java/eu/eudat/data/DmpEntity.java
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@ -6,6 +6,7 @@ import eu.eudat.commons.enums.DmpVersionStatus;
import eu.eudat.commons.enums.IsActive; import eu.eudat.commons.enums.IsActive;
import eu.eudat.data.converters.enums.DmpAccessTypeConverter; import eu.eudat.data.converters.enums.DmpAccessTypeConverter;
import eu.eudat.data.converters.enums.DmpStatusConverter; 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.converters.enums.IsActiveConverter;
import eu.eudat.data.old.queryableentity.DataEntity; import eu.eudat.data.old.queryableentity.DataEntity;
import jakarta.persistence.*; import jakarta.persistence.*;
@ -35,7 +36,7 @@ public class DmpEntity implements DataEntity<DmpEntity, UUID> {
public static final String _version = "version"; public static final String _version = "version";
@Column(name = "version_status", nullable = false) @Column(name = "version_status", nullable = false)
@Convert(converter = DmpStatusConverter.class) @Convert(converter = DmpVersionStatusConverter.class)
private DmpVersionStatus versionStatus; private DmpVersionStatus versionStatus;
public static final String _versionStatus = "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 is_active = 1;
UPDATE public."DescriptionTemplate" SET status = 0 where is_active = 0;
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 select dt.id from public."DescriptionTemplate" as dt
where dt.version = where dt.version =
( (
select Max(f.version) select Max(f.version)
from public."DescriptionTemplate" as f where f.group_id=dt.group_id 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
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@ -9,7 +9,7 @@ CREATE TABLE IF NOT EXISTS public."DmpDescriptionTemplate"
"id" uuid NOT NULL, "id" uuid NOT NULL,
"dmp" uuid NOT NULL, "dmp" uuid NOT NULL,
"description_template" 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(), "created_at" timestamp without time zone NOT NULL DEFAULT now(),
"updated_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, "is_active" smallint NOT NULL DEFAULT 1,

2
dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/DatasetMigrationService.java
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@ -49,7 +49,7 @@ public class DatasetMigrationService {
public List<DatasetMigrationCollectedInfo> collectDatasetsInfo() throws JsonProcessingException { public List<DatasetMigrationCollectedInfo> collectDatasetsInfo() throws JsonProcessingException {
List<DatasetMigrationCollectedInfo> collectedInfoList = new ArrayList<>(); List<DatasetMigrationCollectedInfo> collectedInfoList = new ArrayList<>();
List<DatasetWizardModel> datasets = getDatasets(0, 4); List<DatasetWizardModel> datasets = getDatasets(0, Integer.MAX_VALUE);
for (DatasetWizardModel datasetWizardModel : datasets) { for (DatasetWizardModel datasetWizardModel : datasets) {
DatasetMigrationCollectedInfo datasetMigrationCollectedInfo = new DatasetMigrationCollectedInfo(); DatasetMigrationCollectedInfo datasetMigrationCollectedInfo = new DatasetMigrationCollectedInfo();

206
dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/DmpDatasetProfileMigrationService.java
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@ -3,87 +3,199 @@ package eu.old.eudat.migration;
import com.fasterxml.jackson.annotation.JsonIgnoreProperties; import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.core.JsonProcessingException;
import eu.eudat.commons.JsonHandlingService; import eu.eudat.commons.JsonHandlingService;
import eu.eudat.commons.enums.DescriptionStatus; import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.enums.IsActive; import eu.eudat.commons.enums.IsActive;
import eu.eudat.data.DescriptionEntity; 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.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.DMPDatasetProfile;
import eu.old.eudat.data.entities.Dataset; import eu.old.eudat.data.entities.Researcher;
import eu.old.eudat.logic.services.operations.DatabaseRepository; import eu.old.eudat.logic.services.operations.DatabaseRepository;
import eu.old.eudat.models.data.datasetwizard.DatasetWizardModel;
import eu.old.eudat.queryable.QueryableList; 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.persistence.EntityManager;
import jakarta.xml.bind.JAXBException;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service; 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.time.Instant;
import java.util.ArrayList; import java.util.*;
import java.util.List;
@Service @Service
public class DmpDatasetProfileMigrationService { public class DmpDatasetProfileMigrationService {
private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(DmpDatasetProfileMigrationService.class));
private final DatabaseRepository databaseRepository; private final DatabaseRepository databaseRepository;
private final JsonHandlingService jsonHandlingService; 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; private final EntityManager entityManager;
public DmpDatasetProfileMigrationService(DatabaseRepository databaseRepository, JsonHandlingService jsonHandlingService, EntityManager entityManager) { public DmpDatasetProfileMigrationService(DatabaseRepository databaseRepository, JsonHandlingService jsonHandlingService, QueryFactory queryFactory, XmlHandlingService xmlHandlingService, EntityManager entityManager) {
this.databaseRepository = databaseRepository; this.databaseRepository = databaseRepository;
this.jsonHandlingService = jsonHandlingService; this.jsonHandlingService = jsonHandlingService;
this.queryFactory = queryFactory;
this.xmlHandlingService = xmlHandlingService;
this.entityManager = entityManager; this.entityManager = entityManager;
} }
public QueryableList<DMPDatasetProfile> dmpDatasetProfileQueryableList() { public void migrate() throws IOException, JAXBException, ParserConfigurationException, InstantiationException, IllegalAccessException, SAXException {
return databaseRepository.getDmpDatasetProfileDao().asQueryable(); 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);
} }
public List<DMPDatasetProfile> getDatasets(Integer skip, Integer take) { for (DMPDatasetProfile item : items) {
return dmpDatasetProfileQueryableList() entityManager.detach(item);
// .orderBy((builder, root) -> builder.desc(root.get("created")))
.skip(skip) DmpDatasetProfileData profileData = jsonHandlingService.fromJson(DmpDatasetProfileData.class, item.getData());
.take(take)
.toList(); 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());
} }
public List<DmpDatasetProfileMigrationCollectedInfo> collectDatasetsInfo() throws JsonProcessingException { for (int sectionIndex: profileData.dmpSectionIndex) {
List<DmpDatasetProfileMigrationCollectedInfo> collectedInfoList = new ArrayList<>(); if (definition == null || definition.getSections() == null || definition.getSections().size() < sectionIndex) {
List<DMPDatasetProfile> dmpDatasetProfiles = getDatasets(0, 4); logger.error("Migrate DmpDatasetProfile " + item.getId() + " can nto found section id for section " + sectionIndex);
for (DMPDatasetProfile dmpDatasetProfile : dmpDatasetProfiles) { throw new MyApplicationException();
DmpDatasetProfileMigrationCollectedInfo dmpDatasetProfileMigrationCollectedInfo = new DmpDatasetProfileMigrationCollectedInfo();
DmpDatasetProfileData data = jsonHandlingService.fromJson(DmpDatasetProfileData.class, dmpDatasetProfile.getData());
//Collect basic information
DmpDescriptionTemplateEntity dmpDescriptionTemplateEntity = new DmpDescriptionTemplateEntity();
dmpDescriptionTemplateEntity.setDescriptionTemplateId(dmpDatasetProfile.getDatasetprofile().getId());
dmpDescriptionTemplateEntity.setDmpId(dmpDatasetProfile.getDmp().getId());
dmpDescriptionTemplateEntity.setCreatedAt(Instant.now());
dmpDescriptionTemplateEntity.setUpdatedAt(Instant.now());
dmpDescriptionTemplateEntity.setSectionId(null); //TODO
dmpDescriptionTemplateEntity.setIsActive(IsActive.Active);
dmpDatasetProfileMigrationCollectedInfo.dmpDescriptionTemplateEntity = dmpDescriptionTemplateEntity;
collectedInfoList.add(dmpDatasetProfileMigrationCollectedInfo);
} }
return collectedInfoList; 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();
} }
public String migrate() throws JsonProcessingException { DmpDescriptionTemplateEntity data = new DmpDescriptionTemplateEntity();
for (DmpDatasetProfileMigrationCollectedInfo collectedInfo : collectDatasetsInfo()) { data.setId(UUID.randomUUID());
// this.entityManager.persist(collectedInfo.dmpDescriptionTemplateEntity); 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(); this.entityManager.flush();
return "Migrated dmps";
page++;
} }
} while (items != null && !items.isEmpty() && !TestMode);
public static class DmpDatasetProfileMigrationCollectedInfo {
public DmpDescriptionTemplateEntity dmpDescriptionTemplateEntity;
} }
//
// 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"}) @JsonIgnoreProperties({"validationErrorModel"})
public static class DmpDatasetProfileData { public static class DmpDatasetProfileData {

241
dmp-migration-tool/web/src/main/java/eu/old/eudat/migration/DmpMigrationService.java
View File

@ -9,27 +9,43 @@ import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.types.dmp.DmpBlueprintValueEntity; import eu.eudat.commons.types.dmp.DmpBlueprintValueEntity;
import eu.eudat.commons.types.dmp.DmpContactEntity; import eu.eudat.commons.types.dmp.DmpContactEntity;
import eu.eudat.commons.types.dmp.DmpPropertiesEntity; 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.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.DMP;
import eu.old.eudat.data.entities.DMPDatasetProfile;
import eu.old.eudat.logic.services.operations.DatabaseRepository; import eu.old.eudat.logic.services.operations.DatabaseRepository;
import eu.old.eudat.models.data.dmp.DataManagementPlan; import eu.old.eudat.models.data.dmp.DataManagementPlan;
import eu.old.eudat.queryable.QueryableList; import eu.old.eudat.queryable.QueryableList;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.logging.LoggerService;
import jakarta.persistence.EntityManager; import jakarta.persistence.EntityManager;
import jakarta.xml.bind.JAXBException;
import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Service; import org.springframework.stereotype.Service;
import org.springframework.web.bind.annotation.PathVariable; import org.springframework.web.bind.annotation.PathVariable;
import org.xml.sax.SAXException;
import java.util.ArrayList; import javax.xml.parsers.ParserConfigurationException;
import java.util.List; import java.io.IOException;
import java.util.UUID; import java.time.Instant;
import java.util.*;
@Service @Service
public class DmpMigrationService { public class DmpMigrationService {
private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(DmpMigrationService.class));
private final DatabaseRepository databaseRepository; private final DatabaseRepository databaseRepository;
private final JsonHandlingService jsonHandlingService; private final JsonHandlingService jsonHandlingService;
private final EntityManager entityManager; private final EntityManager entityManager;
private static final int PageSize = 500;
private static final boolean TestMode = false;
public DmpMigrationService(DatabaseRepository databaseRepository, JsonHandlingService jsonHandlingService, EntityManager entityManager) { public DmpMigrationService(DatabaseRepository databaseRepository, JsonHandlingService jsonHandlingService, EntityManager entityManager) {
this.databaseRepository = databaseRepository; this.databaseRepository = databaseRepository;
@ -37,98 +53,189 @@ public class DmpMigrationService {
this.entityManager = entityManager; this.entityManager = entityManager;
} }
public QueryableList<DMP> dmpQueryableList() { public void migrate() throws JsonProcessingException {
return databaseRepository.getDmpDao().asQueryable(); DMPDao dmpDao = databaseRepository.getDmpDao();
} long total = dmpDao.asQueryable().count();
logger.debug("Migrate Dmp Total : " + total);
int page = 0;
public List<DataManagementPlan> getDmps(Integer skip, Integer take) { List<DMP> items;
List<DMP> dmps = dmpQueryableList() do {
.orderBy((builder, root) -> builder.desc(root.get("created"))) 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();
.skip(skip) if (items != null && !items.isEmpty()) {
.take(take) logger.debug("Migrate Dmp " + page * PageSize + " of " + total);
.toList();
return dmps.stream().map(x -> { for (DMP item : items) {
DataManagementPlan dmp = new DataManagementPlan(); //entityManager.detach(item);
dmp.fromDataModel(x);
return dmp;
}).toList();
}
public List<DmpMigrationCollectedInfo> collectDmpsInfo() throws JsonProcessingException { DataManagementPlan model = new DataManagementPlan();
List<DmpMigrationCollectedInfo> collectedInfoList = new ArrayList<>(); model.fromDataModel(item);
List<DataManagementPlan> dmps = getDmps(0, 4);
for (DataManagementPlan dataManagementPlan : dmps) {
DmpMigrationCollectedInfo dmpMigrationCollectedInfo = new DmpMigrationCollectedInfo();
DmpPropertiesEntity dmpProperties = new DmpPropertiesEntity(); DmpPropertiesEntity dmpProperties = new DmpPropertiesEntity();
dmpProperties.setDmpBlueprintValues(new ArrayList<>()); dmpProperties.setDmpBlueprintValues(new ArrayList<>());
dmpProperties.setContacts(new ArrayList<>()); dmpProperties.setContacts(new ArrayList<>());
//Collect basic dmp information DmpEntity data = new DmpEntity();
DmpEntity dmpEntity = new DmpEntity(); data.setId(model.getId());
dmpEntity.setId(dataManagementPlan.getId()); data.setLabel(model.getLabel());
dmpEntity.setLabel(dataManagementPlan.getLabel()); data.setDescription(model.getDescription());
dmpEntity.setDescription(dataManagementPlan.getDescription()); if (model.getCreator() != null)
if (dataManagementPlan.getCreator() != null) data.setCreatorId(model.getCreator().getId());
dmpEntity.setCreatorId(dataManagementPlan.getCreator().getId()); data.setGroupId(model.getGroupId());
dmpEntity.setGroupId(dataManagementPlan.getGroupId()); data.setVersion((short) model.getVersion());
dmpEntity.setVersion((short) dataManagementPlan.getVersion()); data.setVersionStatus(DmpVersionStatus.of((short) model.getVersionStatus()));
dmpEntity.setVersionStatus(DmpVersionStatus.of((short) dataManagementPlan.getVersionStatus())); if (model.getCreated() != null)
if (dataManagementPlan.getCreated() != null) data.setCreatedAt(model.getCreated().toInstant());
dmpEntity.setCreatedAt(dataManagementPlan.getCreated().toInstant()); if (model.getModified() != null)
if (dataManagementPlan.getModified() != null) data.setUpdatedAt(model.getModified().toInstant());
dmpEntity.setUpdatedAt(dataManagementPlan.getModified().toInstant()); if (model.getFinalized() != null)
if (dataManagementPlan.getFinalized() != null) data.setFinalizedAt(model.getFinalized().toInstant());
dmpEntity.setFinalizedAt(dataManagementPlan.getFinalized().toInstant()); data.setBlueprintId(model.getProfile().getId());
dmpEntity.setBlueprintId(dataManagementPlan.getProfile().getId()); if (model.getExtraProperties() != null) {
if (dataManagementPlan.getExtraProperties() != null) { if (model.getExtraProperties().containsKey("language") && model.getExtraProperties().get("language") != null)
if (dataManagementPlan.getExtraProperties().containsKey("language") && dataManagementPlan.getExtraProperties().get("language") != null) data.setLanguage((String) model.getExtraProperties().get("language"));
dmpEntity.setLanguage((String) dataManagementPlan.getExtraProperties().get("language")); if (model.getExtraProperties().containsKey("visible") && model.getExtraProperties().get("visible") != null)
if (dataManagementPlan.getExtraProperties().containsKey("visible") && dataManagementPlan.getExtraProperties().get("visible") != null) data.setAccessType((boolean) model.getExtraProperties().get("visible") ? DmpAccessType.Public : DmpAccessType.Restricted);
dmpEntity.setAccessType((boolean) dataManagementPlan.getExtraProperties().get("visible") ? DmpAccessType.Public : DmpAccessType.Restricted); if (model.getExtraProperties().containsKey("contact") && model.getExtraProperties().get("contact") != null) {
if (dataManagementPlan.getExtraProperties().containsKey("contact") && dataManagementPlan.getExtraProperties().get("contact") != null) {
DmpContactEntity contactEntity = new DmpContactEntity(); DmpContactEntity contactEntity = new DmpContactEntity();
contactEntity.setUserId((String) dataManagementPlan.getExtraProperties().get("contact")); contactEntity.setUserId((String) model.getExtraProperties().get("contact"));
dmpProperties.getContacts().add(contactEntity); dmpProperties.getContacts().add(contactEntity);
} }
} }
if (dataManagementPlan.getProperties() != null) { if (model.getProperties() != null) {
dataManagementPlan.getProperties().forEach((key,val) -> { model.getProperties().forEach((key,val) -> {
DmpBlueprintValueEntity valueEntity = new DmpBlueprintValueEntity(); DmpBlueprintValueEntity valueEntity = new DmpBlueprintValueEntity();
valueEntity.setFieldId(key); valueEntity.setFieldId(key);
valueEntity.setValue((String) val); valueEntity.setValue((String) val);
dmpProperties.getDmpBlueprintValues().add(valueEntity); dmpProperties.getDmpBlueprintValues().add(valueEntity);
}); });
} }
if (dataManagementPlan.getStatus() == 99) { if (model.getStatus() == 99) {
dmpEntity.setIsActive(IsActive.Inactive); data.setIsActive(IsActive.Inactive);
data.setStatus(DmpStatus.Draft);
} else { } else {
dmpEntity.setIsActive(IsActive.Active); data.setIsActive(IsActive.Active);
dmpEntity.setStatus(DmpStatus.of((short) dataManagementPlan.getStatus())); data.setStatus(DmpStatus.of((short) model.getStatus()));
} }
dmpEntity.setProperties(jsonHandlingService.toJson(dmpProperties)); data.setProperties(jsonHandlingService.toJson(dmpProperties));
dmpMigrationCollectedInfo.dmpEntity = dmpEntity;
//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;
} }
public String migrate() throws JsonProcessingException {
for (DmpMigrationCollectedInfo collectedInfo : collectDmpsInfo()) { this.entityManager.persist(data);
this.entityManager.persist(collectedInfo.dmpEntity);
}
this.entityManager.flush(); this.entityManager.flush();
return "Migrated dmps";
} }
public static class DmpMigrationCollectedInfo { page++;
public DmpEntity dmpEntity;
} }
} 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;
//
// }
} }

32
dmp-migration-tool/web/src/main/java/eu/old/eudat/publicapi/migration/MigrationController.java
View File

@ -3,11 +3,16 @@ package eu.old.eudat.publicapi.migration;
import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.core.JsonProcessingException;
import eu.old.eudat.migration.*; import eu.old.eudat.migration.*;
import io.swagger.annotations.Api; import io.swagger.annotations.Api;
import jakarta.xml.bind.JAXBException;
import org.springframework.transaction.annotation.Transactional; import org.springframework.transaction.annotation.Transactional;
import org.springframework.web.bind.annotation.CrossOrigin; import org.springframework.web.bind.annotation.CrossOrigin;
import org.springframework.web.bind.annotation.GetMapping; import org.springframework.web.bind.annotation.GetMapping;
import org.springframework.web.bind.annotation.RequestMapping; import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RestController; import org.springframework.web.bind.annotation.RestController;
import org.xml.sax.SAXException;
import javax.xml.parsers.ParserConfigurationException;
import java.io.IOException;
@Api(tags = "Migration") @Api(tags = "Migration")
@RestController @RestController
@ -56,10 +61,11 @@ public class MigrationController {
this.organizationMigrationService = organizationMigrationService; this.organizationMigrationService = organizationMigrationService;
} }
@GetMapping("dmps/migrate") @GetMapping("dmps")
@Transactional @Transactional
public String migrateDmps() throws JsonProcessingException { public boolean migrateDmps() throws JsonProcessingException {
return this.dmpMigrationService.migrate(); this.dmpMigrationService.migrate();
return true;
} }
@GetMapping("datasets/migrate") @GetMapping("datasets/migrate")
@ -68,19 +74,15 @@ public class MigrationController {
return this.datasetMigrationService.migrate(); return this.datasetMigrationService.migrate();
} }
@GetMapping("dmp-dataset-profiles/migrate") @GetMapping("dmp-dataset-profiles")
@Transactional @Transactional
public String migrateDmpDatasetProfiles() throws JsonProcessingException { public boolean migrateDmpDatasetProfiles() throws IOException, JAXBException, ParserConfigurationException, InstantiationException, IllegalAccessException, SAXException {
return this.dmpDatasetProfileMigrationService.migrate(); this.dmpDatasetProfileMigrationService.migrate();
}
@GetMapping("organizations/migrate")
@Transactional
public boolean migrateOrganizations() {
this.organizationMigrationService.migrate();
return true; return true;
} }
@GetMapping("references") @GetMapping("references")
@Transactional @Transactional
public boolean migrateReferences() { public boolean migrateReferences() {
@ -96,6 +98,14 @@ public class MigrationController {
return true; return true;
} }
@GetMapping("organizations")
@Transactional
public boolean migrateOrganizations() {
this.organizationMigrationService.migrate();
return true;
}
@GetMapping("dataRepositories") @GetMapping("dataRepositories")
@Transactional @Transactional
public boolean migrateDataRepositories() { public boolean migrateDataRepositories() {