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dmp reference changes

This commit is contained in:
Efstratios Giannopoulos 2024-01-12 15:00:34 +02:00
parent df7a43d2de
commit 4b9b5cc056
17 changed files with 385 additions and 156 deletions
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8
dmp-backend/core/src/main/java/eu/eudat/commons/types/dmp/DmpBlueprintValueEntity.java
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@ -1,16 +1,18 @@
package eu.eudat.commons.types.dmp;
import java.util.UUID;
public class DmpBlueprintValueEntity {
private String fieldId;
private UUID fieldId;
private String value;
public String getFieldId() {
public UUID getFieldId() {
return fieldId;
}
public void setFieldId(String fieldId) {
public void setFieldId(UUID fieldId) {
this.fieldId = fieldId;
}

15
dmp-backend/core/src/main/java/eu/eudat/commons/types/dmpreference/DmpReferenceDataEntity.java Normal file
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@ -0,0 +1,15 @@
package eu.eudat.commons.types.dmpreference;
import java.util.UUID;
public class DmpReferenceDataEntity {
private UUID blueprintFieldId;
public UUID getBlueprintFieldId() {
return blueprintFieldId;
}
public void setBlueprintFieldId(UUID blueprintFieldId) {
this.blueprintFieldId = blueprintFieldId;
}
}

15
dmp-backend/core/src/main/java/eu/eudat/data/DescriptionReferenceEntity.java
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@ -18,10 +18,10 @@ public class DescriptionReferenceEntity extends TenantScopedBaseEntity {
public static final String _id = "id";
// @Column(name = "data")
// private String data;
//
// public static final String _data = "data";
@Column(name = "data")
private String data;
public static final String _data = "data";
@Column(name = "description_id", columnDefinition = "uuid", nullable = false)
private UUID descriptionId;
@ -97,4 +97,11 @@ public class DescriptionReferenceEntity extends TenantScopedBaseEntity {
this.isActive = isActive;
}
public String getData() {
return data;
}
public void setData(String data) {
this.data = data;
}
}

24
dmp-backend/core/src/main/java/eu/eudat/model/DmpReference.java
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@ -1,5 +1,7 @@
package eu.eudat.model;
import eu.eudat.model.dmpreference.DmpReferenceData;
import java.time.Instant;
import java.util.UUID;
@ -14,9 +16,6 @@ public class DmpReference {
private Reference reference;
public static final String _reference = "reference";
private String data;
public static final String _data = "data";
private Instant createdAt;
public static final String _createdAt = "createdAt";
@ -27,6 +26,9 @@ public class DmpReference {
public final static String _hash = "hash";
private String hash;
private DmpReferenceData data;
public static final String _data = "data";
public UUID getId() {
return id;
}
@ -51,14 +53,6 @@ public class DmpReference {
this.reference = reference;
}
public String getData() {
return data;
}
public void setData(String data) {
this.data = data;
}
public Instant getCreatedAt() { return createdAt;}
public void setCreatedAt(Instant createdAt) {this.createdAt = createdAt;}
@ -74,4 +68,12 @@ public class DmpReference {
public void setHash(String hash) {
this.hash = hash;
}
public void setData(DmpReferenceData data) {
this.data = data;
}
public DmpReferenceData getData() {
return data;
}
}

19
dmp-backend/core/src/main/java/eu/eudat/model/builder/DmpReferenceBuilder.java
View File

@ -1,12 +1,17 @@
package eu.eudat.model.builder;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.commons.JsonHandlingService;
import eu.eudat.commons.types.description.PropertyDefinitionEntity;
import eu.eudat.commons.types.dmpreference.DmpReferenceDataEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.data.DmpReferenceEntity;
import eu.eudat.model.Description;
import eu.eudat.model.Dmp;
import eu.eudat.model.DmpDescriptionTemplate;
import eu.eudat.model.DmpReference;
import eu.eudat.model.Reference;
import eu.eudat.model.builder.descriptionpropertiesdefinition.PropertyDefinitionBuilder;
import eu.eudat.model.builder.dmpreference.DmpReferenceDataBuilder;
import eu.eudat.query.DmpQuery;
import eu.eudat.query.ReferenceQuery;
import gr.cite.tools.data.builder.BuilderFactory;
@ -32,16 +37,18 @@ public class DmpReferenceBuilder extends BaseBuilder<DmpReference, DmpReferenceE
private final BuilderFactory builderFactory;
private final QueryFactory queryFactory;
private final JsonHandlingService jsonHandlingService;
private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
@Autowired
public DmpReferenceBuilder(
ConventionService conventionService,
BuilderFactory builderFactory, QueryFactory queryFactory) {
ConventionService conventionService,
BuilderFactory builderFactory, QueryFactory queryFactory, JsonHandlingService jsonHandlingService) {
super(conventionService, new LoggerService(LoggerFactory.getLogger(DmpReferenceBuilder.class)));
this.builderFactory = builderFactory;
this.queryFactory = queryFactory;
this.jsonHandlingService = jsonHandlingService;
}
public DmpReferenceBuilder authorize(EnumSet<AuthorizationFlags> values) {
@ -62,16 +69,20 @@ public class DmpReferenceBuilder extends BaseBuilder<DmpReference, DmpReferenceE
FieldSet dmpFields = fields.extractPrefixed(this.asPrefix(DmpReference._dmp));
Map<UUID, Dmp> dmpItemsMap = this.collectDmps(dmpFields, data);
FieldSet dataFields = fields.extractPrefixed(this.asPrefix(DmpReference._data));
List<DmpReference> models = new ArrayList<>();
for (DmpReferenceEntity d : data) {
DmpReference m = new DmpReference();
if (fields.hasField(this.asIndexer(DmpReference._id))) m.setId(d.getId());
if (fields.hasField(this.asIndexer(DmpReference._data))) m.setData(d.getData());
if (fields.hasField(this.asIndexer(DmpReference._createdAt))) m.setCreatedAt(d.getCreatedAt());
if (fields.hasField(this.asIndexer(DmpReference._updatedAt))) m.setUpdatedAt(d.getUpdatedAt());
if (fields.hasField(this.asIndexer(DmpReference._hash))) m.setHash(this.hashValue(d.getUpdatedAt()));
if (!referenceFields.isEmpty() && referenceItemsMap != null && referenceItemsMap.containsKey(d.getReferenceId())) m.setReference(referenceItemsMap.get(d.getReferenceId()));
if (!dmpFields.isEmpty() && dmpItemsMap != null && dmpItemsMap.containsKey(d.getDmpId())) m.setDmp(dmpItemsMap.get(d.getDmpId()));
if (!dataFields.isEmpty() && d.getData() != null){
DmpReferenceDataEntity propertyDefinition = this.jsonHandlingService.fromJsonSafe(DmpReferenceDataEntity.class, d.getData());
m.setData(this.builderFactory.builder(DmpReferenceDataBuilder.class).authorize(this.authorize).build(dataFields, propertyDefinition));
}
models.add(m);
}
this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));

56
dmp-backend/core/src/main/java/eu/eudat/model/builder/dmpreference/DmpReferenceDataBuilder.java Normal file
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@ -0,0 +1,56 @@
package eu.eudat.model.builder.dmpreference;
import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.commons.types.dmpreference.DmpReferenceDataEntity;
import eu.eudat.convention.ConventionService;
import eu.eudat.model.builder.BaseBuilder;
import eu.eudat.model.dmpreference.DmpReferenceData;
import gr.cite.tools.data.builder.BuilderFactory;
import gr.cite.tools.exception.MyApplicationException;
import gr.cite.tools.fieldset.FieldSet;
import gr.cite.tools.logging.DataLogEntry;
import gr.cite.tools.logging.LoggerService;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableBeanFactory;
import org.springframework.context.annotation.Scope;
import org.springframework.stereotype.Component;
import java.util.*;
@Component("referencedmpreferencedatabuilder")
@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public class DmpReferenceDataBuilder extends BaseBuilder<DmpReferenceData, DmpReferenceDataEntity> {
private EnumSet<AuthorizationFlags> authorize = EnumSet.of(AuthorizationFlags.None);
@Autowired
public DmpReferenceDataBuilder(
ConventionService conventionService) {
super(conventionService, new LoggerService(LoggerFactory.getLogger(DmpReferenceDataBuilder.class)));
}
public DmpReferenceDataBuilder authorize(EnumSet<AuthorizationFlags> values) {
this.authorize = values;
return this;
}
@Override
public List<DmpReferenceData> build(FieldSet fields, List<DmpReferenceDataEntity> data) throws MyApplicationException {
this.logger.debug("building for {} items requesting {} fields", Optional.ofNullable(data).map(List::size).orElse(0), Optional.ofNullable(fields).map(FieldSet::getFields).map(Set::size).orElse(0));
this.logger.trace(new DataLogEntry("requested fields", fields));
if (fields == null || data == null || fields.isEmpty())
return new ArrayList<>();
//Not Bulk Build because is XML no interaction with db
List<DmpReferenceData> models = new ArrayList<>();
for (DmpReferenceDataEntity d : data) {
DmpReferenceData m = new DmpReferenceData();
if (fields.hasField(this.asIndexer(DmpReferenceData._blueprintFieldId))) m.setBlueprintFieldId(d.getBlueprintFieldId());
models.add(m);
}
this.logger.debug("build {} items", Optional.of(models).map(List::size).orElse(0));
return models;
}
}

4
dmp-backend/core/src/main/java/eu/eudat/model/censorship/DmpReferenceCensor.java
View File

@ -2,8 +2,8 @@ package eu.eudat.model.censorship;
import eu.eudat.authorization.Permission;
import eu.eudat.convention.ConventionService;
import eu.eudat.model.DmpDescriptionTemplate;
import eu.eudat.model.DmpReference;
import eu.eudat.model.censorship.dmpreference.DmpReferenceDataCensor;
import gr.cite.commons.web.authz.service.AuthorizationService;
import gr.cite.tools.data.censor.CensorFactory;
import gr.cite.tools.fieldset.FieldSet;
@ -43,6 +43,8 @@ public class DmpReferenceCensor extends BaseCensor {
this.censorFactory.censor(DmpCensor.class).censor(dmpFields, userId);
FieldSet templateFields = fields.extractPrefixed(this.asIndexerPrefix(DmpReference._reference));
this.censorFactory.censor(ReferenceCensor.class).censor(templateFields, userId);
FieldSet dataFields = fields.extractPrefixed(this.asIndexerPrefix(DmpReference._data));
this.censorFactory.censor(DmpReferenceDataCensor.class).censor(dataFields, userId);
}
}

42
dmp-backend/core/src/main/java/eu/eudat/model/censorship/dmpreference/DmpReferenceDataCensor.java Normal file
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@ -0,0 +1,42 @@
package eu.eudat.model.censorship.dmpreference;
import eu.eudat.authorization.Permission;
import eu.eudat.convention.ConventionService;
import eu.eudat.model.censorship.BaseCensor;
import gr.cite.commons.web.authz.service.AuthorizationService;
import gr.cite.tools.fieldset.FieldSet;
import gr.cite.tools.logging.DataLogEntry;
import gr.cite.tools.logging.LoggerService;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.config.ConfigurableBeanFactory;
import org.springframework.context.annotation.Scope;
import org.springframework.stereotype.Component;
import java.util.UUID;
@Component
@Scope(value = ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public class DmpReferenceDataCensor extends BaseCensor {
private static final LoggerService logger = new LoggerService(LoggerFactory.getLogger(DmpReferenceDataCensor.class));
protected final AuthorizationService authService;
@Autowired
public DmpReferenceDataCensor(ConventionService conventionService,
AuthorizationService authService) {
super(conventionService);
this.authService = authService;
}
public void censor(FieldSet fields, UUID userId) {
logger.debug(new DataLogEntry("censoring fields", fields));
if (fields == null || fields.isEmpty())
return;
this.authService.authorizeForce(Permission.BrowseDmpDescriptionTemplate);
}
}

16
dmp-backend/core/src/main/java/eu/eudat/model/dmpreference/DmpReferenceData.java Normal file
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@ -0,0 +1,16 @@
package eu.eudat.model.dmpreference;
import java.util.UUID;
public class DmpReferenceData {
private UUID blueprintFieldId;
public final static String _blueprintFieldId = "blueprintFieldId";
public UUID getBlueprintFieldId() {
return blueprintFieldId;
}
public void setBlueprintFieldId(UUID blueprintFieldId) {
this.blueprintFieldId = blueprintFieldId;
}
}

23
dmp-backend/core/src/main/java/eu/eudat/model/persist/DmpPersist.java
View File

@ -45,9 +45,9 @@ public class DmpPersist {
private DmpAccessType accessType;
private List<DmpReferencePersist> references;
public static final String _references = "references";
// private List<DmpReferencePersist> references;
//
// public static final String _references = "references";
private List<DmpDescriptionTemplatePersist> descriptionTemplates;
@ -105,14 +105,6 @@ public class DmpPersist {
this.language = language;
}
public List<DmpReferencePersist> getReferences() {
return references;
}
public void setReferences(List<DmpReferencePersist> references) {
this.references = references;
}
public UUID getBlueprint() {
return blueprint;
}
@ -201,15 +193,6 @@ public class DmpPersist {
.on(DmpPersist._properties)
.over(item.getProperties())
.using(() -> this.validatorFactory.validator(DmpPropertiesPersist.DmpPropertiesPersistValidator.class).setStatus(item.getStatus())),
this.spec()
.iff(() -> item.getStatus() == DmpStatus.Finalized)
.must(() -> !this.isNull(item.getReferences()))
.failOn(DmpPersist._references).failWith(messageSource.getMessage("Validation_Required", new Object[]{DmpPersist._references}, LocaleContextHolder.getLocale())),
this.navSpec()
.iff(() -> !this.isNull(item.getReferences()))
.on(DmpPersist._references)
.over(item.getReferences())
.using(() -> this.validatorFactory.validator(DmpReferencePersist.DmpReferencePersistValidator.class)),
this.spec()
.iff(() -> item.getStatus() == DmpStatus.Finalized)
.must(() -> !this.isNull(item.getDescriptionTemplates()))

50
dmp-backend/core/src/main/java/eu/eudat/model/persist/DmpReferencePersist.java
View File

@ -5,6 +5,7 @@ import eu.eudat.commons.validation.ValidatorFactory;
import eu.eudat.commons.validation.specification.Specification;
import eu.eudat.convention.ConventionService;
import eu.eudat.errorcode.ErrorThesaurusProperties;
import eu.eudat.model.persist.dmpreference.DmpReferenceDataPersist;
import org.springframework.beans.factory.config.ConfigurableBeanFactory;
import org.springframework.context.MessageSource;
import org.springframework.context.annotation.Scope;
@ -17,27 +18,15 @@ import java.util.UUID;
public class DmpReferencePersist {
private UUID id;
private ReferencePersist reference;
public static final String _reference = "reference";
private String data;
private DmpReferenceDataPersist data;
public static final String _data = "data";
private String hash;
public static final String _hash = "hash";
public UUID getId() {
return id;
}
public void setId(UUID id) {
this.id = id;
}
public ReferencePersist getReference() {
return reference;
@ -47,22 +36,14 @@ public class DmpReferencePersist {
this.reference = reference;
}
public String getData() {
public DmpReferenceDataPersist getData() {
return data;
}
public void setData(String data) {
public void setData(DmpReferenceDataPersist data) {
this.data = data;
}
public String getHash() {
return hash;
}
public void setHash(String hash) {
this.hash = hash;
}
@Component(DmpReferencePersistValidator.ValidatorName)
@Scope(ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public static class DmpReferencePersistValidator extends BaseValidator<DmpReferencePersist> {
@ -87,26 +68,25 @@ public class DmpReferencePersist {
@Override
protected List<Specification> specifications(DmpReferencePersist item) {
return Arrays.asList(
this.spec()
.iff(() -> this.isValidGuid(item.getId()))
.must(() -> this.isValidHash(item.getHash()))
.failOn(DmpReferencePersist._hash).failWith(messageSource.getMessage("Validation_Required", new Object[]{DmpReferencePersist._hash}, LocaleContextHolder.getLocale())),
this.spec()
.iff(() -> !this.isValidGuid(item.getId()))
.must(() -> !this.isValidHash(item.getHash()))
.failOn(DmpReferencePersist._hash).failWith(messageSource.getMessage("Validation_OverPosting", new Object[]{}, LocaleContextHolder.getLocale())),
this.spec()
.must(() -> !this.isNull(item.getData()))
.failOn(DmpReferencePersist._data).failWith(messageSource.getMessage("Validation_Required", new Object[]{DmpReferencePersist._data}, LocaleContextHolder.getLocale())),
this.spec()
.must(() -> !this.isNull(item.getReference()))
.failOn(DmpReferencePersist._reference).failWith(messageSource.getMessage("Validation_Required", new Object[]{DescriptionPersist._properties}, LocaleContextHolder.getLocale())),
.failOn(DmpReferencePersist._reference).failWith(messageSource.getMessage("Validation_Required", new Object[]{DmpReferencePersist._reference}, LocaleContextHolder.getLocale())),
this.refSpec()
.iff(() -> !this.isNull(item.getReference()))
.on(DmpReferencePersist._reference)
.over(item.getReference())
.using(() -> this.validatorFactory.validator(ReferencePersist.ReferencePersistValidator.class))
.using(() -> this.validatorFactory.validator(ReferencePersist.ReferencePersistValidator.class)),
this.spec()
.must(() -> !this.isNull(item.getData()))
.failOn(DmpReferencePersist._data).failWith(messageSource.getMessage("Validation_Required", new Object[]{DmpReferencePersist._data}, LocaleContextHolder.getLocale())),
this.refSpec()
.iff(() -> !this.isNull(item.getData()))
.on(DmpReferencePersist._data)
.over(item.getData())
.using(() -> this.validatorFactory.validator(DmpReferenceDataPersist.DmpReferenceDataPersistValidator.class))
);
}

53
dmp-backend/core/src/main/java/eu/eudat/model/persist/dmpproperties/DmpBlueprintValuePersist.java
View File

@ -4,37 +4,35 @@ import eu.eudat.commons.validation.BaseValidator;
import eu.eudat.commons.validation.specification.Specification;
import eu.eudat.convention.ConventionService;
import eu.eudat.errorcode.ErrorThesaurusProperties;
import eu.eudat.model.persist.ReferencePersist;
import org.springframework.beans.factory.config.ConfigurableBeanFactory;
import org.springframework.context.MessageSource;
import org.springframework.context.annotation.Scope;
import org.springframework.context.i18n.LocaleContextHolder;
import org.springframework.stereotype.Component;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.UUID;
public class DmpBlueprintValuePersist {
private UUID fieldId;
private String fieldId;
private String fieldName;
public static final String _fieldId = "fieldId";
private String fieldValue;
public static final String _fieldValue = "fieldValue";
private List<ReferencePersist> references;
public static final String _references = "references";
public String getFieldId() {
public UUID getFieldId() {
return fieldId;
}
public void setFieldId(String fieldId) {
public void setFieldId(UUID fieldId) {
this.fieldId = fieldId;
}
public String getFieldName() {
return fieldName;
}
public void setFieldName(String fieldName) {
this.fieldName = fieldName;
}
public String getFieldValue() {
return fieldValue;
}
@ -43,14 +41,25 @@ public class DmpBlueprintValuePersist {
this.fieldValue = fieldValue;
}
public List<ReferencePersist> getReferences() {
return references;
}
public void setReferences(List<ReferencePersist> references) {
this.references = references;
}
@Component(DmpBlueprintValuePersistValidator.ValidatorName)
@Scope(ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public static class DmpBlueprintValuePersistValidator extends BaseValidator<DmpBlueprintValuePersist> {
private final MessageSource messageSource;
public static final String ValidatorName = "DmpBlueprintValuePersistValidator";
protected DmpBlueprintValuePersistValidator(ConventionService conventionService, ErrorThesaurusProperties errors) {
protected DmpBlueprintValuePersistValidator(ConventionService conventionService, ErrorThesaurusProperties errors, MessageSource messageSource) {
super(conventionService, errors);
this.messageSource = messageSource;
}
@Override
@ -60,7 +69,19 @@ public class DmpBlueprintValuePersist {
@Override
protected List<Specification> specifications(DmpBlueprintValuePersist item) {
return new ArrayList<>();
return Arrays.asList(
this.spec()
.must(() -> !this.isValidGuid(item.getFieldId()))
.failOn(DmpBlueprintValuePersist._fieldId).failWith(messageSource.getMessage("Validation_Required", new Object[]{DmpBlueprintValuePersist._fieldId}, LocaleContextHolder.getLocale())),
this.spec()
.iff(() -> this.isNull(item.getReferences()) || item.getReferences().isEmpty())
.must(() -> !this.isEmpty(item.getFieldValue()))
.failOn(DmpBlueprintValuePersist._fieldValue).failWith(messageSource.getMessage("Validation_Required", new Object[]{DmpBlueprintValuePersist._fieldValue}, LocaleContextHolder.getLocale())),
this.spec()
.iff(() -> !this.isNull(item.getReferences()) && !item.getReferences().isEmpty())
.must(() -> this.isEmpty(item.getFieldValue()))
.failOn(DmpBlueprintValuePersist._fieldValue).failWith(messageSource.getMessage("Validation_UnexpectedValue", new Object[]{DmpBlueprintValuePersist._fieldValue}, LocaleContextHolder.getLocale()))
);
}
}

59
dmp-backend/core/src/main/java/eu/eudat/model/persist/dmpreference/DmpReferenceDataPersist.java Normal file
View File

@ -0,0 +1,59 @@
package eu.eudat.model.persist.dmpreference;
import eu.eudat.commons.validation.BaseValidator;
import eu.eudat.commons.validation.specification.Specification;
import eu.eudat.convention.ConventionService;
import eu.eudat.errorcode.ErrorThesaurusProperties;
import eu.eudat.model.persist.ReferencePersist;
import org.springframework.beans.factory.config.ConfigurableBeanFactory;
import org.springframework.context.MessageSource;
import org.springframework.context.annotation.Scope;
import org.springframework.context.i18n.LocaleContextHolder;
import org.springframework.stereotype.Component;
import java.util.Arrays;
import java.util.List;
import java.util.UUID;
public class DmpReferenceDataPersist {
private UUID blueprintFieldId;
public static final String _blueprintFieldId = "blueprintFieldId";
public UUID getBlueprintFieldId() {
return blueprintFieldId;
}
public void setBlueprintFieldId(UUID blueprintFieldId) {
this.blueprintFieldId = blueprintFieldId;
}
@Component(DmpReferenceDataPersistValidator.ValidatorName)
@Scope(ConfigurableBeanFactory.SCOPE_PROTOTYPE)
public static class DmpReferenceDataPersistValidator extends BaseValidator<DmpReferenceDataPersist> {
public static final String ValidatorName = "DmpReferenceDataPersistValidator";
private final MessageSource messageSource;
protected DmpReferenceDataPersistValidator(ConventionService conventionService, ErrorThesaurusProperties errors, MessageSource messageSource) {
super(conventionService, errors);
this.messageSource = messageSource;
}
@Override
protected Class<DmpReferenceDataPersist> modelClass() {
return DmpReferenceDataPersist.class;
}
@Override
protected List<Specification> specifications(DmpReferenceDataPersist item) {
return Arrays.asList(
this.spec()
.must(() -> !this.isNull(item.getBlueprintFieldId()))
.failOn(DmpReferenceDataPersist._blueprintFieldId).failWith(messageSource.getMessage("Validation_Required", new Object[]{DmpReferenceDataPersist._blueprintFieldId}, LocaleContextHolder.getLocale()))
);
}
}
}

1
dmp-backend/core/src/main/java/eu/eudat/query/DmpReferenceQuery.java
View File

@ -4,7 +4,6 @@ import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.authorization.Permission;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.scope.user.UserScope;
import eu.eudat.data.DescriptionEntity;
import eu.eudat.data.DmpEntity;
import eu.eudat.data.DmpReferenceEntity;
import eu.eudat.data.ReferenceEntity;

149
dmp-backend/core/src/main/java/eu/eudat/service/dmp/DmpServiceImpl.java
View File

@ -12,6 +12,7 @@ import eu.eudat.commons.types.actionconfirmation.DmpInvitationEntity;
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.dmpreference.DmpReferenceDataEntity;
import eu.eudat.commons.types.notification.*;
import eu.eudat.commons.types.reference.DefinitionEntity;
import eu.eudat.commons.types.reference.FieldEntity;
@ -37,6 +38,7 @@ import eu.eudat.model.persist.actionconfirmation.DmpInvitationPersist;
import eu.eudat.model.persist.dmpproperties.DmpBlueprintValuePersist;
import eu.eudat.model.persist.dmpproperties.DmpContactPersist;
import eu.eudat.model.persist.dmpproperties.DmpPropertiesPersist;
import eu.eudat.model.persist.dmpreference.DmpReferenceDataPersist;
import eu.eudat.model.persist.referencedefinition.DefinitionPersist;
import eu.eudat.model.persist.referencedefinition.FieldPersist;
import eu.eudat.query.*;
@ -159,7 +161,7 @@ public class DmpServiceImpl implements DmpService {
DmpEntity data = this.patchAndSave(model);
this.patchAndSaveReferences(model.getReferences(), data.getId());
this.patchAndSaveReferences(this.buildDmpReferencePersists(model.getProperties()), data.getId());
this.patchAndSaveTemplates(data.getId(), model.getDescriptionTemplates());
@ -250,7 +252,7 @@ public class DmpServiceImpl implements DmpService {
List<DmpEntity> latestVersionDmps = latestVersionDmpEntityQuery.collect();
if (latestVersionDmps.isEmpty()) throw new MyValidationException("Previous dmp not found");
if (latestVersionDmps.size() > 1) throw new MyValidationException("Multiple previous dmps found");
if (!latestVersionDmps.get(0).getVersion().equals(oldDmpEntity.getVersion())){
if (!latestVersionDmps.getFirst().getVersion().equals(oldDmpEntity.getVersion())){
throw new MyValidationException(this.errors.getDmpNewVersionConflict().getCode(), this.errors.getDmpNewVersionConflict().getMessage());
}
@ -490,9 +492,8 @@ public class DmpServiceImpl implements DmpService {
@Override
public ResponseEntity<byte[]> export(UUID id, String exportType) throws InvalidApplicationException, IOException {
HttpHeaders headers = new HttpHeaders();
String type = exportType;
FileEnvelope fileEnvelope = this.fileTransformerService.exportDmp(id, type);
FileEnvelope fileEnvelope = this.fileTransformerService.exportDmp(id, exportType);
headers.add("Content-Disposition", "attachment;filename=" + fileEnvelope.getFilename());
byte[] data = Files.readAllBytes(fileEnvelope.getFile().toPath());
headers.setContentType(MediaType.APPLICATION_OCTET_STREAM);
@ -563,7 +564,7 @@ public class DmpServiceImpl implements DmpService {
if (!this.conventionService.isListNullOrEmpty(persist.getDmpBlueprintValues())){
data.setDmpBlueprintValues(new ArrayList<>());
for (DmpBlueprintValuePersist fieldValuePersist: persist.getDmpBlueprintValues()) {
data.getDmpBlueprintValues().add(this.buildDmpBlueprintValueEntity(fieldValuePersist));
if (!this.conventionService.isNullOrEmpty(fieldValuePersist.getFieldValue())) data.getDmpBlueprintValues().add(this.buildDmpBlueprintValueEntity(fieldValuePersist));
}
}
return data;
@ -591,71 +592,98 @@ public class DmpServiceImpl implements DmpService {
return data;
}
private @NotNull List<DmpReferencePersist> buildDmpReferencePersists(DmpPropertiesPersist persist){
List<DmpReferencePersist> dmpReferencePersists = new ArrayList<>();
if (!this.conventionService.isListNullOrEmpty(persist.getDmpBlueprintValues())){
for (DmpBlueprintValuePersist fieldValuePersist: persist.getDmpBlueprintValues()) {
if (this.conventionService.isNullOrEmpty(fieldValuePersist.getFieldValue()) && !this.conventionService.isListNullOrEmpty( fieldValuePersist.getReferences())) {
for (ReferencePersist referencePersist : fieldValuePersist.getReferences()) {
DmpReferencePersist dmpReferencePersist = new DmpReferencePersist();
dmpReferencePersist.setData(new DmpReferenceDataPersist());
dmpReferencePersist.getData().setBlueprintFieldId(fieldValuePersist.getFieldId());
dmpReferencePersist.setReference(referencePersist);
}
}
}
}
return dmpReferencePersists;
}
private void patchAndSaveReferences(List<DmpReferencePersist> models, UUID dmpId) throws InvalidApplicationException {
if (models == null || models.isEmpty())
return;
if (models == null) models = new ArrayList<>();
List<DmpReferenceEntity> references = this.queryFactory.query(DmpReferenceQuery.class).dmpIds(dmpId).collect();
Map<UUID, List<DmpReferenceEntity>> referencesLookup = this.conventionService.toDictionaryOfList(references, DmpReferenceEntity::getDmpId);
List<DmpReferenceEntity> dmpReferences = this.queryFactory.query(DmpReferenceQuery.class).dmpIds(dmpId).collect();
Map<UUID, List<DmpReferenceEntity>> dmpReferenceEntityByReferenceId = new HashMap<>();
for (DmpReferenceEntity dmpReferenceEntity : dmpReferences){
List<DmpReferenceEntity> dmpReferenceEntities = dmpReferenceEntityByReferenceId.getOrDefault(dmpReferenceEntity.getReferenceId(), null);
if (dmpReferenceEntities == null) {
dmpReferenceEntities = new ArrayList<>();
dmpReferenceEntityByReferenceId.put(dmpReferenceEntity.getReferenceId(), dmpReferenceEntities);
}
dmpReferenceEntities.add(dmpReferenceEntity);
}
List<ReferenceEntity> existingReferences;
if (referencesLookup.containsKey(dmpId))
existingReferences = this.queryFactory.query(ReferenceQuery.class).ids(referencesLookup.get(dmpId).stream().map(DmpReferenceEntity::getId).toList()).collect();
else
existingReferences = new ArrayList<>();
List<UUID> updatedReferencesIds = models.stream().map(x -> x.getReference().getId()).filter(this.conventionService::isValidGuid).distinct().toList();
List<ReferenceEntity> toDelete = existingReferences.stream().filter(x -> !updatedReferencesIds.contains(x.getId())).toList();
List<DmpReferenceEntity> dmpReferenceRecordsToDelete = this.queryFactory.query(DmpReferenceQuery.class).referenceIds(toDelete.stream().map(ReferenceEntity::getId).toList()).collect();
this.deleterFactory.deleter(DmpReferenceDeleter.class).delete(dmpReferenceRecordsToDelete);
Map<UUID, ReferenceEntity> existingReferencesLookup = existingReferences.stream().collect(Collectors.toMap(ReferenceEntity::getId, x -> x));
Map<UUID, DmpReferenceDataEntity> dmpReferenceDataEntityMap = new HashMap<>();
for (DmpReferenceEntity dmpReferenceEntity : dmpReferences){
dmpReferenceDataEntityMap.put(dmpReferenceEntity.getDmpId(), this.jsonHandlingService.fromJsonSafe(DmpReferenceDataEntity.class, dmpReferenceEntity.getData()));
}
List<UUID> updatedCreatedIds = new ArrayList<>();
for (DmpReferencePersist model : models) {
ReferencePersist referenceModel = model.getReference();
Boolean isUpdate = this.conventionService.isValidGuid(referenceModel.getId());
ReferenceEntity data;
if (isUpdate) {
if (!existingReferencesLookup.containsKey(referenceModel.getId()))
throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{referenceModel.getId(), Reference.class.getSimpleName()}, LocaleContextHolder.getLocale()));
data = existingReferencesLookup.get(referenceModel.getId());
if (data == null)
throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{referenceModel.getId(), Reference.class.getSimpleName()}, LocaleContextHolder.getLocale()));
if (!this.conventionService.hashValue(data.getUpdatedAt()).equals(referenceModel.getHash()))
throw new MyValidationException(this.errors.getHashConflict().getCode(), this.errors.getHashConflict().getMessage());
ReferencePersist referencePersist = model.getReference();
ReferenceEntity referenceEntity = null;
if (this.conventionService.isValidGuid(referencePersist.getId())){
referenceEntity = this.entityManager.find(ReferenceEntity.class, referencePersist.getId());
if (referenceEntity == null) throw new MyNotFoundException(messageSource.getMessage("General_ItemNotFound", new Object[]{referencePersist.getId(), Reference.class.getSimpleName()}, LocaleContextHolder.getLocale()));
} else {
data = new ReferenceEntity();
data.setId(UUID.randomUUID());
data.setIsActive(IsActive.Active);
data.setCreatedAt(Instant.now());
referenceEntity = this.queryFactory.query(ReferenceQuery.class).sourceTypes(referencePersist.getSourceType()).references(referencePersist.getReference()).first();
if (referenceEntity == null){
referenceEntity = new ReferenceEntity();
referenceEntity.setId(UUID.randomUUID());
referenceEntity.setIsActive(IsActive.Active);
referenceEntity.setCreatedAt(Instant.now());
DmpReferenceEntity dmpReference = new DmpReferenceEntity();
dmpReference.setReferenceId(data.getId());
dmpReference.setDmpId(dmpId);
dmpReference.setCreatedAt(Instant.now());
dmpReference.setUpdatedAt(Instant.now());
dmpReference.setIsActive(IsActive.Active);
dmpReference.setData(model.getData());
this.entityManager.persist(dmpReference);
referenceEntity.setDefinition(this.xmlHandlingService.toXmlSafe(this.buildDefinitionEntity(referencePersist.getDefinition())));
referenceEntity.setUpdatedAt(Instant.now());
referenceEntity.setReference(referencePersist.getReference());
referenceEntity.setAbbreviation(referencePersist.getAbbreviation());
referenceEntity.setSource(referencePersist.getSource());
referenceEntity.setSourceType(referencePersist.getSourceType());
this.entityManager.persist(referenceEntity);
}
}
data.setDefinition(this.xmlHandlingService.toXmlSafe(this.buildDefinitionEntity(referenceModel.getDefinition())));
DmpReferenceEntity data = null;
List<DmpReferenceEntity> dmpReferenceEntities = dmpReferenceEntityByReferenceId.getOrDefault(referenceEntity.getId(), new ArrayList<>());
for (DmpReferenceEntity dmpReferenceEntity : dmpReferenceEntities){
DmpReferenceDataEntity dmpReferenceDataEntity = dmpReferenceDataEntityMap.getOrDefault(dmpReferenceEntity.getId(), new DmpReferenceDataEntity());
if (Objects.equals(dmpReferenceDataEntity.getBlueprintFieldId(), model.getData().getBlueprintFieldId())){
data = dmpReferenceEntity;
break;
}
}
boolean isUpdate = data != null;
if (!isUpdate) {
data = new DmpReferenceEntity();
data.setReferenceId(referenceEntity.getId());
data.setDmpId(dmpId);
data.setCreatedAt(Instant.now());
data.setIsActive(IsActive.Active);
data.setData(this.jsonHandlingService.toJsonSafe(this.buildDmpReferenceDataEntity(model.getData())));
}
updatedCreatedIds.add(data.getId());
data.setUpdatedAt(Instant.now());
data.setReference(referenceModel.getReference());
data.setAbbreviation(referenceModel.getAbbreviation());
data.setSource(referenceModel.getSource());
data.setSourceType(referenceModel.getSourceType());
if (isUpdate)
this.entityManager.merge(data);
else
this.entityManager.persist(data);
if (isUpdate) this.entityManager.merge(data);
else this.entityManager.persist(data);
}
List<DmpReferenceEntity> toDelete = dmpReferences.stream().filter(x-> updatedCreatedIds.stream().noneMatch(y-> y.equals(x.getId()))).collect(Collectors.toList());
this.deleterFactory.deleter(DmpReferenceDeleter.class).delete(toDelete);
this.entityManager.flush();
}
@ -695,6 +723,13 @@ public class DmpServiceImpl implements DmpService {
return data;
}
private @NotNull DmpReferenceDataEntity buildDmpReferenceDataEntity(DmpReferenceDataPersist persist){
DmpReferenceDataEntity data = new DmpReferenceDataEntity();
if (persist == null) return data;
data.setBlueprintFieldId(persist.getBlueprintFieldId());
return data;
}
private @NotNull FieldEntity buildDmpContactEntity(FieldPersist persist){
FieldEntity data = new FieldEntity();
if (persist == null) return data;

3
dmp-backend/core/src/main/java/eu/eudat/service/reference/ReferenceServiceImpl.java
View File

@ -9,6 +9,7 @@ import eu.eudat.authorization.AuthorizationFlags;
import eu.eudat.authorization.Permission;
import eu.eudat.commons.XmlHandlingService;
import eu.eudat.commons.enums.IsActive;
import eu.eudat.commons.enums.ReferenceSourceType;
import eu.eudat.commons.enums.ReferenceTypeExternalApiHTTPMethodType;
import eu.eudat.commons.enums.ReferenceTypeSourceType;
import eu.eudat.commons.exceptions.HugeResultSetException;
@ -223,7 +224,7 @@ public class ReferenceServiceImpl implements ReferenceService {
}
private List<Reference> fetchFromDb(ReferenceSearchLookup lookup){
ReferenceQuery query = lookup.enrich(this.queryFactory).authorize(AuthorizationFlags.OwnerOrDmpAssociatedOrPermissionOrPublic);
ReferenceQuery query = lookup.enrich(this.queryFactory).authorize(AuthorizationFlags.OwnerOrDmpAssociatedOrPermissionOrPublic).sourceTypes(ReferenceSourceType.Internal);
List<ReferenceEntity> data = query.collectAs(lookup.getProject());
return this.builderFactory.builder(ReferenceBuilder.class).authorize(AuthorizationFlags.OwnerOrDmpAssociatedOrPermissionOrPublic).build(lookup.getProject(), data);
}

4
dmp-backend/web/src/main/java/eu/eudat/controllers/v2/ReferenceController.java
View File

@ -68,7 +68,6 @@ public class ReferenceController extends BaseController {
private final MessageSource messageSource;
private final AuthorizationService authorizationService;
@Autowired
public ReferenceController(
@ -78,7 +77,7 @@ public class ReferenceController extends BaseController {
AuditService auditService,
CensorFactory censorFactory,
QueryFactory queryFactory,
MessageSource messageSource, AuthorizationService authorizationService) {
MessageSource messageSource) {
super(apiContext);
this.builderFactory = builderFactory;
this.referenceService = referenceService;
@ -86,7 +85,6 @@ public class ReferenceController extends BaseController {
this.censorFactory = censorFactory;
this.queryFactory = queryFactory;
this.messageSource = messageSource;
this.authorizationService = authorizationService;
}
@PostMapping("query")