import org.apache.log4j.Logger;
import org.hibernate.Hibernate;
+import org.joda.time.DateTime;
+import org.joda.time.Partial;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.stereotype.Service;
import eu.etaxonomy.cdm.api.service.exception.RegistrationValidationException;
import eu.etaxonomy.cdm.api.service.pager.Pager;
import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
+import eu.etaxonomy.cdm.api.utility.UserHelper;
+import eu.etaxonomy.cdm.database.PermissionDeniedException;
+import eu.etaxonomy.cdm.format.ReferenceEllypsisFormatter;
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
-import eu.etaxonomy.cdm.model.common.User;
import eu.etaxonomy.cdm.model.name.Registration;
import eu.etaxonomy.cdm.model.name.RegistrationStatus;
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
-import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
+import eu.etaxonomy.cdm.model.permission.CRUD;
import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.cdm.model.reference.ReferenceType;
+import eu.etaxonomy.cdm.persistence.dao.initializer.EntityInitStrategy;
import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
import eu.etaxonomy.cdm.persistence.query.MatchMode;
import eu.etaxonomy.cdm.persistence.query.OrderHint;
@Transactional(readOnly=true)
public class RegistrationWorkingSetService implements IRegistrationWorkingSetService {
- public static final List<String> REGISTRATION_DTO_INIT_STRATEGY = Arrays.asList(new String []{
+ public static final EntityInitStrategy REGISTRATION_DTO_INIT_STRATEGY = new EntityInitStrategy(Arrays.asList(new String []{
"blockedBy",
// typeDesignation
"typeDesignations.typeStatus",
"typeDesignations.typeSpecimen",
"typeDesignations.typeName.$",
"typeDesignations.citation",
- "typeDesignations.citation.authorship.$",
- "typeDesignations.annotations", // needed for AnnotatableEntity.clone() in DerivedUnitConverter.copyPropertiesTo
- "typeDesignations.markers", // needed for AnnotatableEntity.clone() in DerivedUnitConverter.copyPropertiesTo
+ "typeDesignations.annotations", // needed for AnnotatableEntity.clone() in DerivedUnitConverter.copyPropertiesTo
+ "typeDesignations.markers", // needed for AnnotatableEntity.clone() in DerivedUnitConverter.copyPropertiesTo
"typeDesignations.registrations", // DerivedUnitConverter.copyPropertiesTo(TARGET n)
// name
"name.$",
- "name.nomenclaturalReference.authorship.$",
- "name.nomenclaturalReference.inReference",
+ "name.nomenclaturalReference",
"name.rank",
"name.homotypicalGroup.typifiedNames",
"name.status.type",
// institution
"institution",
}
- );
+ ))
+ .extend("typeDesignations.citation", ReferenceEllypsisFormatter.INIT_STRATEGY, false)
+ .extend("name.nomenclaturalReference", ReferenceEllypsisFormatter.INIT_STRATEGY, false);
- public List<String> DERIVEDUNIT_INIT_STRATEGY = Arrays.asList(new String[]{
+ public EntityInitStrategy DERIVEDUNIT_INIT_STRATEGY = new EntityInitStrategy(Arrays.asList(new String[]{
"*", // initialize all related entities to allow DerivedUnit conversion, see DerivedUnitConverter.copyPropertiesTo()
"derivedFrom.$",
"derivedFrom.type", // TODO remove?
"derivedFrom.originals.derivationEvents", // important!!
"specimenTypeDesignations.typifiedNames.typeDesignations", // important!!
- "mediaSpecimen.sources",
+ "mediaSpecimen.sources.citation",
"collection.institute"// see CollectionCaptionGenerator
- });
+ })).extend("mediaSpecimen.sources.citation", ReferenceEllypsisFormatter.INIT_STRATEGY, false);
public List<String> FIELDUNIT_INIT_STRATEGY = Arrays.asList(new String[]{
"$",
"blockedBy.blockedBy",
// typeDesignation
"blockedBy.typeDesignations.typeStatus",
-// "typeDesignations.typifiedNames.typeDesignations", // important !!
-// "typeDesignations.typeSpecimen",
-// "typeDesignations.typeName.$",
-// "typeDesignations.citation",
-// "typeDesignations.citation.authorship.$",
- // name
+// "typeDesignations.typifiedNames.typeDesignations", // important !?
// "blockedBy.name.$",
"blockedBy.name.nomenclaturalReference.authorship",
"blockedBy.name.nomenclaturalReference.inReference",
"blockedBy.name.rank",
-// "name.homotypicalGroup.typifiedNames",
-// "name.status.type",
-// "name.typeDesignations",
// institution
"blockedBy.institution",
}
@Qualifier("cdmRepository")
private CdmRepository repo;
+ @Autowired
+ private UserHelper userHelper;
+
@Autowired
protected IBeanInitializer defaultBeanInitializer;
*/
@Override
public RegistrationDTO loadDtoById(Integer id) {
- Registration reg = repo.getRegistrationService().load(id, REGISTRATION_DTO_INIT_STRATEGY);
+ Registration reg = repo.getRegistrationService().load(id, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
inititializeSpecimen(reg);
return new RegistrationDTO(reg);
}
*/
@Override
public RegistrationDTO loadDtoByUuid(UUID uuid) {
- Registration reg = repo.getRegistrationService().load(uuid, REGISTRATION_DTO_INIT_STRATEGY);
+ Registration reg = repo.getRegistrationService().load(uuid, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
inititializeSpecimen(reg);
return new RegistrationDTO(reg);
}
@Override
public Pager<RegistrationDTO> pageDTOs(String identifier, Integer pageIndex, Integer pageSize) throws IOException {
- Pager<Registration> regPager = repo.getRegistrationService().pageByIdentifier(identifier, pageIndex, pageSize, REGISTRATION_DTO_INIT_STRATEGY);
+ Pager<Registration> regPager = repo.getRegistrationService().pageByIdentifier(identifier, pageIndex, pageSize, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
return convertToDTOPager(regPager);
}
@Override
public Pager<RegistrationDTO> pageDTOs(Integer pageSize, Integer pageIndex) {
- return pageDTOs((User)null, null, null, null, null, pageSize, pageIndex, null);
+ return pageDTOs((UUID)null, null, null, null, null, null, pageSize, pageIndex, null);
+
}
/**
- * {@inheritDoc}
+ * @param submitterUuid
+ * Filter by the uuid of the {@link User} associated with the Registration as <code>Registration.submitter</code>
+ * @param includedStatus
+ * Filter by one or more {@link RegistrationStatus}. Multiple status will be combined with OR. In case the current user
+ * is not authenticated (i.e. the authentication is anonymous) the includedStatus will be set to {@link RegistrationStatus#PUBLISHED}
+ * to protect all other Registrations from being undisclosed.
+ * @param identifierFilterPattern
+ * Filter by the {@link Registration#getIdentifier() Registration.identifier}.
+ * The method matches Registrations which contain the the passed pattern in the identifier.
+ * @param taxonNameFilterPattern
+ * The method matches Registrations which contain the the passed pattern in the
+ * {@link Registration#getName() Registration.name}
+ * @param typeDesignationStatusUuids
+ * Filter by one or more {@link eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus} or {@link eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus}.
+ * Multiple status will be combined with OR.
+ * @param pageSize
+ * @param pageIndex
+ * @param orderHints
+ * @return
*/
- @Override
- public Pager<RegistrationDTO> pageDTOs(User submitter, Collection<RegistrationStatus> includedStatus,
- String identifierFilterPattern, String taxonNameFilterPattern, Set<TypeDesignationStatusBase> typeStatusFilter,
- Integer pageSize, Integer pageIndex, List<OrderHint> orderHints) {
-
- if(pageSize == null){
- pageSize = PAGE_SIZE;
- }
-
- if(orderHints == null){
- orderHints = Arrays.asList(new OrderHint("identifier", SortOrder.ASCENDING));
- }
-
- Pager<Registration> pager = repo.getRegistrationService().page(submitter, includedStatus, identifierFilterPattern, taxonNameFilterPattern,
- typeStatusFilter, PAGE_SIZE, pageIndex , orderHints, REGISTRATION_DTO_INIT_STRATEGY);
-
- Pager<RegistrationDTO> dtoPager = convertToDTOPager(pager);
- if(logger.isDebugEnabled()){
- logger.debug(String.format("pageDTOs() pageIndex: $1%d, pageSize: $2%d, includedStatus: $3%s, identifierFilterPattern: $4%s, taxonNameFilterPattern: $5%s, submitter: $6%s",
- pageIndex, pageSize, includedStatus, identifierFilterPattern, taxonNameFilterPattern, submitter));
- logger.debug("pageDTOs() result: " + pager.toString());
- }
- return dtoPager;
- }
@Override
public Pager<RegistrationDTO> pageDTOs(UUID submitterUuid, Collection<RegistrationStatus> includedStatus, String identifierFilterPattern,
- String taxonNameFilterPattern, Collection<UUID> typeDesignationStatusUuids, Integer pageSize,
- Integer pageIndex, List<OrderHint> orderHints){
+ String taxonNameFilterPattern, String referenceFilterPattern, Collection<UUID> typeDesignationStatusUuids,
+ Integer pageSize, Integer pageIndex, List<OrderHint> orderHints){
if(pageSize == null){
pageSize = PAGE_SIZE;
Pager<Registration> pager = repo.getRegistrationService().page(submitterUuid, includedStatus,
identifierFilterPattern, taxonNameFilterPattern,
- typeDesignationStatusUuids, PAGE_SIZE, pageIndex , orderHints, REGISTRATION_DTO_INIT_STRATEGY);
+ referenceFilterPattern, typeDesignationStatusUuids, PAGE_SIZE , pageIndex, orderHints, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
Pager<RegistrationDTO> dtoPager = convertToDTOPager(pager);
if(logger.isDebugEnabled()){
Pager<Registration> regPager = repo.getRegistrationService().pageTaxomicInclusion(null, includedStatus,
taxonNameFilterPattern, matchMode,
- pageSize, pageIndex, orderHints, REGISTRATION_DTO_INIT_STRATEGY);
+ pageSize, pageIndex, orderHints, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
return convertToDTOPager(regPager);
}
* @throws RegistrationValidationException
*/
@Override
- public RegistrationWorkingSet loadWorkingSetByReferenceUuid(UUID referenceUuid, boolean resolveSections) throws RegistrationValidationException {
+ public RegistrationWorkingSet loadWorkingSetByReferenceUuid(UUID referenceUuid, boolean resolveSections) throws RegistrationValidationException, PermissionDeniedException {
Reference reference = repo.getReferenceService().load(referenceUuid); // needed to use load to avoid the problem described in #7331
if(resolveSections){
reference = resolveSection(reference);
}
- Pager<Registration> pager = repo.getRegistrationService().page(Optional.of(reference), null, null, null, REGISTRATION_DTO_INIT_STRATEGY);
+ checkPermissions(reference);
+
+ Pager<Registration> pager = repo.getRegistrationService().page(Optional.of(reference), null, null, null, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
/* for debugging https://dev.e-taxonomy.eu/redmine/issues/7331 */
// debugIssue7331(pager);
- return new RegistrationWorkingSet(makeDTOs(pager.getRecords()));
+ RegistrationWorkingSet registrationWorkingSet;
+ if(pager.getCount() > 0) {
+ registrationWorkingSet = new RegistrationWorkingSet(makeDTOs(pager.getRecords()));
+ } else {
+ registrationWorkingSet = new RegistrationWorkingSet(reference);
+ }
+ return registrationWorkingSet;
+ }
+
+
+ /**
+ * @param reference
+ */
+ private void checkPermissions(Reference reference) throws PermissionDeniedException {
+
+ boolean permissionDenied = isPermissionDenied(reference);
+ if(permissionDenied) {
+ throw new PermissionDeniedException("Access to the workingset is denied for the current user.");
+ }
+ }
+
+
+ /**
+ * @param reference
+ * @return
+ */
+ public boolean isPermissionDenied(Reference reference) {
+ boolean permissionDenied = false;
+ if(!checkReferencePublished(reference)){
+ permissionDenied = !userHelper.userHasPermission(reference, CRUD.UPDATE);
+ }
+ return permissionDenied;
+ }
+
+
+
+ /**
+ * @param reference
+ * @return
+ */
+ public boolean checkReferencePublished(Reference reference) {
+
+ if(reference.getDatePublished() == null){
+ return false;
+ }
+ Partial pubPartial = null;
+ if(reference.getDatePublished().getStart() != null){
+ pubPartial = reference.getDatePublished().getStart();
+ } else {
+ pubPartial = reference.getDatePublished().getEnd();
+ }
+ if(pubPartial == null){
+ return !reference.getDatePublished().getFreeText().isEmpty();
+ }
+
+ DateTime nowLocal = new DateTime();
+ //LocalDateTime nowUTC = nowLocal.withZone(DateTimeZone.UTC).toLocalDateTime();
+
+ DateTime pubDateTime = pubPartial.toDateTime(null);
+ return nowLocal.isAfter(pubDateTime);
+
}
* @throws RegistrationValidationException
*/
@Override
- public RegistrationWorkingSet loadWorkingSetByReferenceID(Integer referenceID, boolean resolveSections) throws RegistrationValidationException {
+ public RegistrationWorkingSet loadWorkingSetByReferenceID(Integer referenceID, boolean resolveSections) throws RegistrationValidationException, PermissionDeniedException {
Reference reference = repo.getReferenceService().find(referenceID);
if(resolveSections){
reference = resolveSection(reference);
}
+
+ checkPermissions(reference);
+
repo.getReferenceService().load(reference.getUuid()); // needed to avoid the problem described in #7331
- Pager<Registration> pager = repo.getRegistrationService().page(Optional.of(reference), null, null, null, REGISTRATION_DTO_INIT_STRATEGY);
+ Pager<Registration> pager = repo.getRegistrationService().page(Optional.of(reference), null, null, null, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
/* for debugging https://dev.e-taxonomy.eu/redmine/issues/7331 */
// debugIssue7331(pager);
return new RegistrationWorkingSet(makeDTOs(pager.getRecords()));
}
+ @Override
+ public Pager<RegistrationDTO> pageWorkingSetsByNameUUID(Collection<UUID> taxonNameUuids, Integer pageIndex, Integer pageSize, List<OrderHint> orderHints) throws RegistrationValidationException, PermissionDeniedException {
+
+ if(orderHints == null){
+ orderHints = Arrays.asList(new OrderHint("identifier", SortOrder.ASCENDING));
+ }
+
+ Pager<Registration> pager = repo.getRegistrationService().page((UUID)null, null, taxonNameUuids, pageSize, pageIndex, orderHints, REGISTRATION_DTO_INIT_STRATEGY.getPropertyPaths());
+
+ return new DefaultPagerImpl<RegistrationDTO>(pager.getCurrentIndex(), pager.getCount(), pager.getPageSize(), makeDTOs(pager.getRecords()));
+ }
+
/**
* @param pager
* @param regs
* @return
*/
- private List<RegistrationDTO> makeDTOs(List<Registration> regs) {
+ @Override
+ public List<RegistrationDTO> makeDTOs(Collection<Registration> regs) {
initializeSpecimens(regs);
List<RegistrationDTO> dtos = new ArrayList<>(regs.size());
regs.forEach(reg -> {dtos.add(new RegistrationDTO(reg));});
/**
* @param regs
*/
- public void initializeSpecimens(List<Registration> regs) {
+ public void initializeSpecimens(Collection<Registration> regs) {
for(Registration reg : regs){
inititializeSpecimen(reg);
}
continue;
}
if(DerivedUnit.class.isAssignableFrom(sob.getClass())) {
- defaultBeanInitializer.initialize(sob, DERIVEDUNIT_INIT_STRATEGY);
+ defaultBeanInitializer.initialize(sob, DERIVEDUNIT_INIT_STRATEGY.getPropertyPaths());
nextSobs = ((DerivedUnit)sob).getOriginals();
}
if(sob instanceof FieldUnit){
BGBM BDI Projects / cdmlib.git / blobdiff