+++ /dev/null
-/**
-* Copyright (C) 2019 EDIT
-* European Distributed Institute of Taxonomy
-* http://www.e-taxonomy.eu
-*
-* The contents of this file are subject to the Mozilla Public License Version 1.1
-* See LICENSE.TXT at the top of this package for the full license terms.
-*/
-package eu.etaxonomy.cdm.io.pesi.fauEu2Cdm;
-
-import java.lang.reflect.Field;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.UUID;
-
-import org.apache.log4j.Logger;
-
-import eu.etaxonomy.cdm.api.application.CdmApplicationController;
-import eu.etaxonomy.cdm.api.application.ICdmRepository;
-import eu.etaxonomy.cdm.database.DbSchemaValidation;
-import eu.etaxonomy.cdm.io.common.CdmImportBase;
-import eu.etaxonomy.cdm.model.agent.AgentBase;
-import eu.etaxonomy.cdm.model.agent.Contact;
-import eu.etaxonomy.cdm.model.agent.Institution;
-import eu.etaxonomy.cdm.model.agent.InstitutionalMembership;
-import eu.etaxonomy.cdm.model.agent.Person;
-import eu.etaxonomy.cdm.model.agent.Team;
-import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
-import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
-import eu.etaxonomy.cdm.model.common.Annotation;
-import eu.etaxonomy.cdm.model.common.CdmBase;
-import eu.etaxonomy.cdm.model.common.Credit;
-import eu.etaxonomy.cdm.model.common.Extension;
-import eu.etaxonomy.cdm.model.common.ExtensionType;
-import eu.etaxonomy.cdm.model.common.IIntextReferencable;
-import eu.etaxonomy.cdm.model.common.IIntextReferenceTarget;
-import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
-import eu.etaxonomy.cdm.model.common.IdentifiableSource;
-import eu.etaxonomy.cdm.model.common.Identifier;
-import eu.etaxonomy.cdm.model.common.IntextReference;
-import eu.etaxonomy.cdm.model.common.Language;
-import eu.etaxonomy.cdm.model.common.LanguageString;
-import eu.etaxonomy.cdm.model.common.LanguageStringBase;
-import eu.etaxonomy.cdm.model.common.Marker;
-import eu.etaxonomy.cdm.model.common.MarkerType;
-import eu.etaxonomy.cdm.model.common.ReferencedEntityBase;
-import eu.etaxonomy.cdm.model.common.RelationshipBase;
-import eu.etaxonomy.cdm.model.common.SourcedEntityBase;
-import eu.etaxonomy.cdm.model.common.VersionableEntity;
-import eu.etaxonomy.cdm.model.description.CommonTaxonName;
-import eu.etaxonomy.cdm.model.description.DescriptionBase;
-import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
-import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
-import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
-import eu.etaxonomy.cdm.model.description.Distribution;
-import eu.etaxonomy.cdm.model.description.FeatureState;
-import eu.etaxonomy.cdm.model.description.SpecimenDescription;
-import eu.etaxonomy.cdm.model.description.State;
-import eu.etaxonomy.cdm.model.description.TaxonDescription;
-import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
-import eu.etaxonomy.cdm.model.description.TextData;
-import eu.etaxonomy.cdm.model.location.Country;
-import eu.etaxonomy.cdm.model.location.NamedArea;
-import eu.etaxonomy.cdm.model.media.ExternalLink;
-import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
-import eu.etaxonomy.cdm.model.media.Media;
-import eu.etaxonomy.cdm.model.media.Rights;
-import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
-import eu.etaxonomy.cdm.model.name.HybridRelationship;
-import eu.etaxonomy.cdm.model.name.NameRelationship;
-import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
-import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
-import eu.etaxonomy.cdm.model.name.Registration;
-import eu.etaxonomy.cdm.model.name.TaxonName;
-import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
-import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
-import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
-import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
-import eu.etaxonomy.cdm.model.permission.User;
-import eu.etaxonomy.cdm.model.reference.OriginalSourceBase;
-import eu.etaxonomy.cdm.model.reference.Reference;
-import eu.etaxonomy.cdm.model.taxon.Classification;
-import eu.etaxonomy.cdm.model.taxon.Synonym;
-import eu.etaxonomy.cdm.model.taxon.Taxon;
-import eu.etaxonomy.cdm.model.taxon.TaxonBase;
-import eu.etaxonomy.cdm.model.taxon.TaxonNode;
-import eu.etaxonomy.cdm.model.taxon.TaxonNodeAgentRelation;
-import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
-import eu.etaxonomy.cdm.model.term.DefinedTerm;
-import eu.etaxonomy.cdm.model.term.DefinedTermBase;
-import eu.etaxonomy.cdm.model.term.OrderedTermBase;
-import eu.etaxonomy.cdm.model.term.Representation;
-import eu.etaxonomy.cdm.model.term.TermBase;
-import eu.etaxonomy.cdm.model.term.TermCollection;
-import eu.etaxonomy.cdm.model.term.TermNode;
-import eu.etaxonomy.cdm.model.term.TermRelationBase;
-import eu.etaxonomy.cdm.model.term.TermVocabulary;
-import eu.etaxonomy.cdm.persistence.query.MatchMode;
-
-/**
- * @author a.mueller
- * @since 17.08.2019
- */
-public abstract class FauEu2CdmImportBase
- extends CdmImportBase<FauEu2CdmImportConfigurator, FauEu2CdmImportState> {
-
- private static final long serialVersionUID = 8917991155285743172L;
- private static final Logger logger = Logger.getLogger(FauEu2CdmImportBase.class);
-
- //quick and dirty
- private FauEu2CdmImportState state;
-
- //TODO move to state
- private Map<UUID, CdmBase> sessionCache = new HashMap<>();
-
-
- protected Set<CdmBase> toSave = new HashSet<>();
-
- protected ICdmRepository sourceRepo(FauEu2CdmImportState state){
- ICdmRepository repo = state.getSourceRepository();
- if (repo == null){
- System.out.println("start source repo");
- boolean omitTermLoading = true;
- repo = CdmApplicationController.NewInstance(state.getConfig().getSource(),
- DbSchemaValidation.VALIDATE, omitTermLoading);
- state.setSourceRepository(repo);
- System.out.println("end source repo");
- }
- return repo;
- }
-
- protected Contact detache(Contact contact) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- contact = CdmBase.deproxy(contact);
- if (contact == null){
- return contact;
- }else{
- return handlePersistedContact(contact);
- }
- }
-
- protected IIntextReferencable detache(IIntextReferencable cdmBase, boolean onlyForDefinedSignature) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- return (IIntextReferencable)detache((CdmBase)cdmBase);
- }
- protected IIntextReferenceTarget detache(IIntextReferenceTarget cdmBase, boolean onlyForDefinedSignature) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- return (IIntextReferenceTarget)detache((CdmBase)cdmBase);
- }
-
- protected <T extends CdmBase> T detache(T cdmBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- return detache(cdmBase, false);
- }
-
- private Map<Class,Set<UUID>> existingObjects = new HashMap<>();
- protected <T extends CdmBase> T detache(T cdmBase, boolean notFromSource) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- cdmBase = CdmBase.deproxy(cdmBase);
- if (cdmBase == null ){
- return cdmBase;
- }else if(isInCache(cdmBase)){
- return getCached(cdmBase);
- }else {
- if (existingObjects.get(cdmBase.getClass()) == null){
- loadExistingUuids(cdmBase.getClass());
- }
- boolean exists = existingObjects.get(cdmBase.getClass()).contains(cdmBase.getUuid());
- if (exists){
- Class<T> clazz = (Class<T>)cdmBase.getClass();
- T existingObj = getCommonService().find(clazz, cdmBase.getUuid());
- if (existingObj != null){
- cache(existingObj);
- return existingObj;
- }else{
- logger.warn("Object should exist already but does not exist in target. This should not happen: " + cdmBase.getClass().getSimpleName() + "/" + cdmBase.getUuid());
- }
- }
- }
- if ( !cdmBase.isPersited()){
- logger.warn("Non persisted object not in cache and not in target DB. This should not happen: " + cdmBase.getUuid());
- return cdmBase; //should not happen anymore; either in cache or in target or persisted in source
- }else{
- return notFromSource? null : (T)handlePersisted(cdmBase);
- }
- }
-
- /**
- * @param class1
- * @return
- */
- private Set<UUID> loadExistingUuids(Class<? extends CdmBase> clazz) {
- List<UUID> list = getCommonService().listUuid(clazz);
- Set<UUID> result = new HashSet<>(list);
- existingObjects.put(clazz, result);
- return result;
- }
-
- protected <A extends CdmBase> CdmBase handlePersisted(A cdmBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- if(cdmBase instanceof TaxonNode){
- return handlePersistedTaxonNode((TaxonNode)cdmBase);
- }else if(cdmBase instanceof Taxon){
- return handlePersistedTaxon((Taxon)cdmBase);
- }else if(cdmBase instanceof Synonym){
- return handlePersistedSynonym((Synonym)cdmBase);
- }else if(cdmBase instanceof TaxonName){
- return handlePersistedTaxonName((TaxonName)cdmBase);
- }else if(cdmBase instanceof Team){
- return handlePersistedTeam((Team)cdmBase);
- }else if(cdmBase instanceof Person){
- return handlePersistedPerson((Person)cdmBase);
- }else if(cdmBase instanceof Classification){
- return handlePersistedClassification((Classification)cdmBase);
- }else if(cdmBase instanceof Reference){
- return handlePersistedReference((Reference)cdmBase);
- }else if(cdmBase instanceof SpecimenOrObservationBase){
- return handlePersistedSpecimenOrObservationBase((SpecimenOrObservationBase)cdmBase);
- }else if(cdmBase instanceof IdentifiableSource){
- return handlePersistedIdentifiableSource((IdentifiableSource)cdmBase);
- }else if(cdmBase instanceof DescriptionElementSource){
- return handlePersistedDescriptionElementSource((DescriptionElementSource)cdmBase);
- }else if(cdmBase instanceof CommonTaxonName){
- return handlePersistedCommonTaxonName((CommonTaxonName)cdmBase);
- }else if(cdmBase instanceof Distribution){
- return handlePersistedDistribution((Distribution)cdmBase);
- }else if(cdmBase instanceof TextData){
- return handlePersistedTextData((TextData)cdmBase);
- }else if(cdmBase instanceof HomotypicalGroup){
- return handlePersistedHomotypicalGroup((HomotypicalGroup)cdmBase);
- }else if(cdmBase instanceof TypeDesignationBase){
- return handlePersistedTypeDesignationBase((TypeDesignationBase)cdmBase);
- }else if(cdmBase instanceof TaxonDescription){
- return handlePersistedTaxonDescription((TaxonDescription)cdmBase);
- }else if(cdmBase instanceof NomenclaturalStatus){
- return handlePersistedNomenclaturalStatus((NomenclaturalStatus)cdmBase);
- }else if(cdmBase instanceof TaxonNameDescription){
- return handlePersistedTaxonNameDescription((TaxonNameDescription)cdmBase);
- }else if(cdmBase instanceof TaxonRelationship){
- return handlePersistedTaxonRelationship((TaxonRelationship)cdmBase);
- }else if(cdmBase instanceof HybridRelationship){
- return handlePersistedHybridRelationship((HybridRelationship)cdmBase);
- }else if(cdmBase instanceof NameRelationship){
- return handlePersistedNameRelationship((NameRelationship)cdmBase);
- }else if(cdmBase instanceof TaxonNodeAgentRelation){
- return handlePersistedTaxonNodeAgentRelation((TaxonNodeAgentRelation)cdmBase);
- }else if(cdmBase instanceof User){
- return handlePersistedUser((User)cdmBase);
- }else if(cdmBase instanceof Extension){
- return handlePersistedExtension((Extension)cdmBase);
- }else if(cdmBase instanceof Marker){
- return handlePersistedMarker((Marker)cdmBase);
- }else if(cdmBase instanceof Annotation){
- return handlePersistedAnnotation((Annotation)cdmBase);
- }else if(cdmBase instanceof LanguageString){
- return handlePersistedLanguageString((LanguageString)cdmBase);
- }else if(cdmBase instanceof TermVocabulary){
- return handlePersistedVocabulary((TermVocabulary<?>)cdmBase);
- }else if(cdmBase instanceof NamedArea){
- return handlePersistedNamedArea((NamedArea)cdmBase);
- }else if(cdmBase instanceof TermNode){
- return handlePersistedTermNode((TermNode)cdmBase);
- }else if(cdmBase instanceof Representation){
- return handlePersistedRepresentation((Representation)cdmBase);
- }else if(cdmBase instanceof InstitutionalMembership){
- return handlePersistedInstitutionalMembership((InstitutionalMembership)cdmBase);
- }else if(cdmBase instanceof Institution){
- return handlePersistedInstitution((Institution)cdmBase);
- }else if(cdmBase instanceof IntextReference){
- return handlePersistedIntextReference((IntextReference)cdmBase);
- }else if(cdmBase instanceof ExtensionType){
- return handlePersistedExtensionType((ExtensionType)cdmBase);
- }else if(cdmBase instanceof NomenclaturalStatusType){
- return handlePersistedNomenclaturalStatusType((NomenclaturalStatusType)cdmBase);
- }else if(cdmBase instanceof MarkerType){
- return handlePersistedMarkerType((MarkerType)cdmBase);
- }else if(cdmBase instanceof DefinedTerm){
- return handlePersistedDefinedTerm((DefinedTerm)cdmBase);
- }else if(cdmBase instanceof DefinedTermBase){
- return handlePersistedTerm((DefinedTermBase<?>)cdmBase);
- }else {
- throw new RuntimeException("Type not yet supported: " + cdmBase.getClass().getCanonicalName());
- }
- }
-
-
- protected TaxonNode handlePersistedTaxonNode(TaxonNode node) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
-
- TaxonNode result = handlePersisted((AnnotatableEntity)node);
- if (result ==null){
- return result;
- }
- //complete
- handleCollection(result, TaxonNode.class, "agentRelations", TaxonNodeAgentRelation.class);
- result.setTaxon(detache(result.getTaxon()));
- result.setReference(detache(node.getReference()));
- result.setSynonymToBeUsed(detache(result.getSynonymToBeUsed()));
- handleMap(result, TaxonNode.class, "excludedNote", Language.class, LanguageString.class);
- //classification, parent, children
- this.setInvisible(node, "classification", detache(node.getClassification()));
- handleParentTaxonNode(result);
- setNewCollection(node, TaxonNode.class, "childNodes", TaxonNode.class);
- return result;
- }
-
- private void handleParentTaxonNode(TaxonNode childNode) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- TaxonNode parent = detache(childNode.getParent(), true);
- //TODO
- String microReference = null;
- Reference reference = null;
- if (parent == null && childNode.getClassification().getRootNode().equals(childNode)){
- //do nothing
- }else if (parent == null ){
- childNode.getClassification().addChildNode(childNode, reference, microReference) ;
- }else{
- parent.addChildNode(childNode, reference, microReference);
- }
- }
-
- protected Taxon handlePersistedTaxon(Taxon taxon) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- Taxon result = handlePersisted((TaxonBase)taxon);
- //complete
- handleCollection(result, Taxon.class, "synonyms", Synonym.class);
-// handleCollection(result, Taxon.class, "taxonNodes", TaxonNode.class);
- setNewCollection(result, Taxon.class, "taxonNodes", TaxonNode.class);
- handleCollection(result, Taxon.class, "relationsFromThisTaxon", TaxonRelationship.class);
- handleCollection(result, Taxon.class, "relationsToThisTaxon", TaxonRelationship.class);
- if (this.doDescriptions(state)){
- handleCollection(result, Taxon.class, "descriptions", TaxonDescription.class);
- }else{
- setNewCollection(result, Taxon.class, "descriptions", TaxonDescription.class);
- }
- return result;
- }
-
- protected boolean doDescriptions(FauEu2CdmImportState state) {
- return false;
- }
-
- protected Synonym handlePersistedSynonym(Synonym synonym) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- Synonym result = handlePersisted((TaxonBase)synonym);
- //complete
- setInvisible(result, "acceptedTaxon", detache(result.getAcceptedTaxon()));
- result.setType(detache(result.getType()));
- return result;
- }
-
- protected TaxonRelationship handlePersistedTaxonRelationship(TaxonRelationship taxRel) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- TaxonRelationship result = handlePersisted((RelationshipBase)taxRel);
- //complete
- result.setFromTaxon(detache(result.getFromTaxon()));
- result.setToTaxon(detache(result.getToTaxon()));
- result.setType(detache(result.getType()));
- return result;
- }
-
- protected NameRelationship handlePersistedNameRelationship(NameRelationship rel) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- NameRelationship result = handlePersisted((RelationshipBase)rel);
- //complete
- setInvisible(result, "relatedFrom", detache(result.getFromName()));
- setInvisible(result, "relatedTo", detache(result.getToName()));
-// result.setFromName(detache(result.getFromName()));
-// result.setToName(detache(result.getToName()));
- result.setType(detache(result.getType()));
- return result;
- }
-
- protected HybridRelationship handlePersistedHybridRelationship(HybridRelationship rel) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- HybridRelationship result = handlePersisted((RelationshipBase)rel);
- //complete
- setInvisible(result, "relatedFrom", detache(result.getParentName()));
- setInvisible(result, "relatedTo", detache(result.getHybridName()));
-// result.setFromName(detache(result.getFromName()));
-// result.setToName(detache(result.getToName()));
- result.setType(detache(result.getType()));
- return result;
- }
-
- protected NomenclaturalStatus handlePersistedNomenclaturalStatus(NomenclaturalStatus status) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- NomenclaturalStatus result = handlePersisted((ReferencedEntityBase)status);
- //complete
- result.setType(detache(result.getType()));
- return result;
- }
-
- protected TypeDesignationBase handlePersistedTypeDesignationBase(TypeDesignationBase<?> designation) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- TypeDesignationBase result = handlePersisted((SourcedEntityBase)designation);
- //complete
- result.setCitation(detache(result.getCitation()));
- handleCollection(result, TypeDesignationBase.class, "registrations", Registration.class);
- handleCollection(result, TypeDesignationBase.class, "typifiedNames", TaxonName.class);
- result.setTypeStatus(detache(result.getTypeStatus()));
- return result;
- }
-
- protected InstitutionalMembership handlePersistedInstitutionalMembership(InstitutionalMembership institutionalMembership) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- InstitutionalMembership result = handlePersisted((VersionableEntity)institutionalMembership);
- //complete
-// result.setPerson(detache(result.getPerson()));
- setInvisible(result, "person", detache(result.getPerson()));
- result.setInstitute(detache(result.getInstitute()));
- return result;
- }
-
- protected Institution handlePersistedInstitution(Institution institution) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- Institution result = handlePersisted((AgentBase)institution);
- //complete
- result.setIsPartOf(detache(result.getIsPartOf()));
- handleCollection(result, Institution.class, "types", DefinedTerm.class);
- return result;
- }
-
- protected TaxonNodeAgentRelation handlePersistedTaxonNodeAgentRelation(TaxonNodeAgentRelation nodeAgentRel) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- TaxonNodeAgentRelation result = handlePersisted((AnnotatableEntity)nodeAgentRel);
- //complete
- result.setAgent(detache(result.getAgent()));
- result.setType(detache(result.getType()));
- setInvisible(result, "taxonNode", detache(result.getTaxonNode()));
- return result;
- }
-
-
- protected TaxonName handlePersistedTaxonName(TaxonName taxonName) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- @SuppressWarnings("rawtypes")
- TaxonName result = handlePersisted((IdentifiableEntity)taxonName);
- //complete
- result.setRank(detache(result.getRank()));
- result.setCombinationAuthorship(detache(result.getCombinationAuthorship()));
- result.setExCombinationAuthorship(detache(result.getExCombinationAuthorship()));
- result.setBasionymAuthorship(detache(result.getBasionymAuthorship()));
- result.setExBasionymAuthorship(detache(result.getExBasionymAuthorship()));
- result.setInBasionymAuthorship(detache(result.getInBasionymAuthorship()));
- result.setInCombinationAuthorship(detache(result.getInCombinationAuthorship()));
-
- result.setNomenclaturalReference(detache(result.getNomenclaturalReference()));
- result.setNomenclaturalSource(detache(result.getNomenclaturalSource()));
- result.setHomotypicalGroup(detache(result.getHomotypicalGroup()));
- handleCollection(result, TaxonName.class, "descriptions", TaxonNameDescription.class);
- handleCollection(result, TaxonName.class, "hybridChildRelations", HybridRelationship.class);
- handleCollection(result, TaxonName.class, "hybridParentRelations", HybridRelationship.class);
- handleCollection(result, TaxonName.class, "relationsFromThisName", NameRelationship.class);
- handleCollection(result, TaxonName.class, "relationsToThisName", NameRelationship.class);
- handleCollection(result, TaxonName.class, "status", NomenclaturalStatus.class);
-
- handleCollection(result, TaxonName.class, "registrations", Registration.class);
- handleCollection(result, TaxonName.class, "typeDesignations", TypeDesignationBase.class);
-
- handleCollection(result, TaxonName.class, "taxonBases", TaxonBase.class);
-
- return result;
- }
-
- protected HomotypicalGroup handlePersistedHomotypicalGroup(HomotypicalGroup group) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- HomotypicalGroup result = handlePersisted((AnnotatableEntity)group);
- //complete
- handleCollection(result, HomotypicalGroup.class, "typifiedNames", TaxonName.class);
- return result;
- }
-
- protected Annotation handlePersistedAnnotation(Annotation annotation) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- Annotation result = handlePersisted((AnnotatableEntity)annotation);
- //complete
- result.setAnnotationType(detache(annotation.getAnnotationType()));
- result.setCommentator(detache(result.getCommentator()));
- handleCollection(result, Annotation.class, "intextReferences", IntextReference.class);
- return result;
- }
-
- protected Extension handlePersistedExtension(Extension extension) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- Extension result = handlePersisted((VersionableEntity)extension);
- //complete
- result.setType(detache(extension.getType()));
- return result;
- }
-
- protected Marker handlePersistedMarker(Marker marker) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- Marker result = handlePersisted((VersionableEntity)marker);
- //complete
- result.setMarkerType(detache(marker.getMarkerType()));
- return result;
- }
-
- protected Team handlePersistedTeam(Team team) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- Team result = handlePersisted((TeamOrPersonBase)team);
- //complete
- handleCollection(result, Team.class, "teamMembers", Person.class);
- return result;
- }
-
- protected Contact handlePersistedContact(Contact contact) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- Contact result = contact; // getTarget(contact);
- if (result ==null){
- return result;
- }
- if (!contact.getAddresses().isEmpty() || !contact.getEmailAddresses().isEmpty()
- || !contact.getFaxNumbers().isEmpty() ||!contact.getPhoneNumbers().isEmpty()
- ||!contact.getUrls().isEmpty()){
- logger.warn("Addresses not yet implemented");
- }
- setInvisible(result, "addresses", new HashSet<>());
-// handleCollection(result, Contact.class, "", Address.class);
- setInvisible(result, "faxNumbers", new ArrayList<>());
- setInvisible(result, "phoneNumbers", new ArrayList<>());
- setInvisible(result, "emailAddresses", new ArrayList<>());
- setInvisible(result, "urls", new ArrayList<>());
- return result;
- }
-
- protected Person handlePersistedPerson(Person person) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- Person result = handlePersisted((TeamOrPersonBase)person);
- //complete
- handleCollection(result, Person.class, "institutionalMemberships", InstitutionalMembership.class);
- return result;
- }
-
- protected NamedArea handlePersistedNamedArea(NamedArea area) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- NamedArea result = handlePersisted((OrderedTermBase)area);
- //complete
- handleCollection(result, NamedArea.class, "countries", Country.class);
- result.setLevel(detache(result.getLevel()));
- result.setType(detache(result.getType()));
- result.setShape(detache(result.getShape()));
- return result;
- }
-
- protected Classification handlePersistedClassification(Classification classification) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- Classification result = handlePersisted((IdentifiableEntity)classification);
- //complete
- result.setName(detache(classification.getName()));
- result.setReference(detache(classification.getReference()));
- result.setRootNode(detache(classification.getRootNode()));
- handleCollection(result, Classification.class, "geoScopes", NamedArea.class);
- handleMap(result, Classification.class, "description", Language.class, LanguageString.class);
- return result;
- }
-
- protected Reference handlePersistedReference(Reference reference) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- Reference result = handlePersisted((IdentifiableMediaEntity)reference);
- result.setAuthorship(detache(result.getAuthorship()));
- result.setInstitution(detache(result.getInstitution()));
- result.setSchool(detache(result.getSchool()));
- result.setInReference(detache(result.getInReference()));
- return result;
- }
-
- protected SpecimenOrObservationBase<?> handlePersistedSpecimenOrObservationBase(SpecimenOrObservationBase specimen) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- //TODO implement for classes
- SpecimenOrObservationBase<?> result = handlePersisted((IdentifiableEntity)specimen);
- //complete
- result.setSex(detache(result.getSex()));
- result.setLifeStage(detache(result.getLifeStage()));
- result.setKindOfUnit(detache(result.getKindOfUnit()));
- handleCollection(result, SpecimenOrObservationBase.class, "determinations", DeterminationEvent.class);
- handleCollection(result, SpecimenOrObservationBase.class, "descriptions", SpecimenDescription.class);
- handleCollection(result, SpecimenOrObservationBase.class, "derivationEvents", DerivationEvent.class);
- handleMap(result, SpecimenOrObservationBase.class, "definition", Language.class, LanguageString.class);
- return result;
- }
-
- protected IdentifiableSource handlePersistedIdentifiableSource(IdentifiableSource source) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- IdentifiableSource result = handlePersisted((OriginalSourceBase)source);
- //complete
- return result;
- }
-
- protected DescriptionElementSource handlePersistedDescriptionElementSource(DescriptionElementSource source) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- DescriptionElementSource result = handlePersisted((OriginalSourceBase)source);
- //complete
- result.setNameUsedInSource(detache(result.getNameUsedInSource()));
- return result;
- }
-
- protected <T extends CommonTaxonName> T handlePersistedCommonTaxonName(CommonTaxonName element) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((DescriptionElementBase)element);
- //complete
- result.setLanguage(detache(result.getLanguage()));
- result.setArea(detache(result.getArea()));
- return result;
- }
-
- protected <T extends TextData> T handlePersistedTextData(TextData element) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((DescriptionElementBase)element);
- //complete
- result.setFormat(detache(result.getFormat()));
- handleMap(result, TextData.class, "multilanguageText", Language.class, LanguageString.class);
- return result;
- }
-
- protected <T extends Distribution> T handlePersistedDistribution(Distribution element) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((DescriptionElementBase)element);
- //complete
- result.setArea(detache(result.getArea()));
- result.setStatus(detache(result.getStatus()));
- return result;
- }
-
- protected ExtensionType handlePersistedExtensionType(ExtensionType term) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- ExtensionType result = handlePersisted((DefinedTermBase)term);
- //complete
- return result;
- }
-
- protected MarkerType handlePersistedMarkerType(MarkerType term) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- MarkerType result = handlePersisted((DefinedTermBase)term);
- //complete
- return result;
- }
-
- protected NomenclaturalStatusType handlePersistedNomenclaturalStatusType(NomenclaturalStatusType term) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- NomenclaturalStatusType result = handlePersisted((OrderedTermBase)term);
- //complete
- return result;
- }
-
- protected DefinedTerm handlePersistedDefinedTerm(DefinedTerm term) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- DefinedTerm result = handlePersisted((DefinedTermBase)term);
- //complete
- return result;
- }
-
- //placeholder for not implemented methods for subclasses
- protected DefinedTermBase<?> handlePersistedTerm(DefinedTermBase term) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- DefinedTermBase<?> result = handlePersisted(term);
- logger.warn("Class not yet handled: " + term.getClass().getSimpleName());
- return result;
- }
-
- protected TermVocabulary<?> handlePersistedVocabulary(TermVocabulary voc) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- TermVocabulary<?> result = (TermVocabulary<?>)handlePersisted((TermCollection)voc);
- handleCollection(result, TermVocabulary.class, "terms", DefinedTermBase.class);
- return result;
- }
-
- protected TermNode<?> handlePersistedTermNode(TermNode node) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- TermNode<?> result = (TermNode<?>)handlePersisted((TermRelationBase)node);
- //complete
- setInvisible(result, "parent", detache(result.getParent()));
- handleCollection(result, TermNode.class, "inapplicableIf", FeatureState.class);
- handleCollection(result, TermNode.class, "onlyApplicableIf", FeatureState.class);
- handleCollection(result, TermNode.class, "inapplicableIf_old", State.class);
- handleCollection(result, TermNode.class, "onlyApplicableIf_old", State.class);
- handleCollection(result, TermNode.class, "children", TermNode.class);
-
- return result;
- }
-
- protected Representation handlePersistedRepresentation(Representation representation) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- Representation result = (Representation)handlePersisted((LanguageStringBase)representation);
- return result;
- }
-
- protected <T extends TermBase> T handlePersisted(TermBase termBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((IdentifiableEntity)termBase);
- //complete
- handleCollection(result, TermBase.class, "representations", Representation.class);
- return result;
- }
-
- protected <T extends TermCollection> T handlePersisted(TermCollection termCollection) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((TermBase)termCollection);
- //complete
- handleCollection(result, TermCollection.class, "termRelations", TermRelationBase.class);
- return result;
- }
-
- protected <T extends TermRelationBase> T handlePersisted(TermRelationBase termRelationBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((VersionableEntity)termRelationBase);
- result.setTerm(detache(result.getTerm()));
- setInvisible(result, TermRelationBase.class, "graph", detache(result.getGraph()));
- return result;
- }
-
- protected User handlePersistedUser(User user) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException, InvocationTargetException, NoSuchMethodException {
- User result = (User)handlePersistedCdmBase(user);
- if (result.getUsername().equals("admin")){
- result = getUserService().listByUsername("admin", MatchMode.EXACT, null, null, null, null, null).iterator().next();
- getState().putPermanent(user.getUuid(), result);
- cache(result); //necessary?
- toSave.add(result);
- toSave.remove(user);
- }
- if (!result.isPersited()){
- result.setAuthorities(new HashSet<>());
- result.setGrantedAuthorities(new HashSet<>());
- setInvisible(result, "groups", new HashSet<>());
- }
- return result;
- }
-
-
- protected LanguageString handlePersistedLanguageString(LanguageString languageString) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- LanguageString result = handlePersisted((LanguageStringBase)languageString);
- //complete
- handleCollection(result, LanguageString.class, "intextReferences", IntextReference.class);
- return result;
- }
-
- protected IntextReference handlePersistedIntextReference(IntextReference intextReference) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- IntextReference result = handlePersisted((VersionableEntity)intextReference);
- result.setReferencedEntity(detache(result.getReferencedEntity(), false));
- Method targetMethod = IntextReference.class.getDeclaredMethod("setTarget", IIntextReferenceTarget.class);
- targetMethod.setAccessible(true);
- targetMethod.invoke(result, detache(result.getTarget(), false));
- return result;
- }
-
- protected <T extends TaxonDescription> T handlePersistedTaxonDescription(TaxonDescription taxDescription) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((DescriptionBase)taxDescription);
- //complete
- setInvisible(taxDescription, "taxon", detache(taxDescription.getTaxon()));
- handleCollection(taxDescription, TaxonDescription.class, "geoScopes", NamedArea.class);
- handleCollection(taxDescription, TaxonDescription.class, "scopes", DefinedTerm.class);
- return result;
- }
-
- protected <T extends TaxonDescription> T handlePersistedTaxonNameDescription(TaxonNameDescription nameDescription) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((DescriptionBase)nameDescription);
- //complete
- setInvisible(nameDescription, "taxonName", detache(nameDescription.getTaxonName()));
- return result;
- }
-
-
-// ***************************** BASE CLASSES ********************************************/
-
- protected <T extends CdmBase> T handlePersistedCdmBase(CdmBase cdmBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = (T)getTarget(cdmBase);
- //complete
- cdmBase.setCreatedBy(detache(cdmBase.getCreatedBy()));
- return result;
- }
-
- protected <T extends VersionableEntity> T handlePersisted(VersionableEntity entity) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = (T)handlePersistedCdmBase((CdmBase)entity);
- //complete
- entity.setUpdatedBy(detache(entity.getUpdatedBy()));
- return result;
- }
-
- protected <T extends AnnotatableEntity> T handlePersisted(AnnotatableEntity entity) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((VersionableEntity)entity);
- //complete
- handleCollection(result, AnnotatableEntity.class, "annotations", Annotation.class);
- handleCollection(result, AnnotatableEntity.class, "markers", Marker.class);
- return result;
- }
-
- protected <T extends SourcedEntityBase> T handlePersisted(SourcedEntityBase sourcedEntity) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- int originalId = sourcedEntity.getId();
- T result = handlePersisted((AnnotatableEntity)sourcedEntity);
- if (!result.isPersited() && getState().getConfig().isAddSources()){
- result.addImportSource(String.valueOf(originalId), sourcedEntity.getClass().getSimpleName(),
- getSourceReference(getState()), null);
- }
- //complete
- handleCollection(result, SourcedEntityBase.class, "sources", OriginalSourceBase.class);
- return result;
- }
-
- protected <T extends IdentifiableEntity> T handlePersisted(IdentifiableEntity identifiableEntity) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((SourcedEntityBase)identifiableEntity);
- //complete
- handleCollection(result, IdentifiableEntity.class, "credits", Credit.class);
- handleCollection(result, IdentifiableEntity.class, "extensions", Extension.class);
- handleCollection(result, IdentifiableEntity.class, "identifiers", Identifier.class);
- handleCollection(result, IdentifiableEntity.class, "rights", Rights.class);
- return result;
- }
-
- protected <T extends DefinedTermBase> T handlePersisted(DefinedTermBase definedTermBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((TermBase)definedTermBase);
- //complete
- handleCollection(result, DefinedTermBase.class, "media", Media.class);
- handleCollection(result, DefinedTermBase.class, "generalizationOf", DefinedTermBase.class);
- handleCollection(result, DefinedTermBase.class, "includes", DefinedTermBase.class);
- result.setKindOf(detache(result.getKindOf()));
- result.setPartOf(detache(result.getPartOf()));
- setInvisible(result, DefinedTermBase.class, "vocabulary", detache(result.getVocabulary()));
-
- return result;
- }
-
- protected <T extends OriginalSourceBase> T handlePersisted(OriginalSourceBase source) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((ReferencedEntityBase)source);
- //complete
- handleCollection(result, OriginalSourceBase.class, "links", ExternalLink.class);
- return result;
- }
-
- protected <T extends LanguageStringBase> T handlePersisted(LanguageStringBase lsBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((AnnotatableEntity)lsBase);
- //complete
- result.setLanguage(detache(lsBase.getLanguage()));
- return result;
- }
-
- protected <T extends TeamOrPersonBase> T handlePersisted(TeamOrPersonBase teamOrPerson) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((AgentBase)teamOrPerson);
- //complete
- return result;
- }
-
- protected <T extends AgentBase> T handlePersisted(AgentBase agent) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((IdentifiableMediaEntity)agent);
- result.setContact(detache(result.getContact()));
- //complete
- return result;
- }
-
- protected <T extends TaxonBase> T handlePersisted(TaxonBase taxonBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((IdentifiableEntity)taxonBase);
- //complete
- result.setName(detache(taxonBase.getName()));
- result.setSec(detache(taxonBase.getSec()));
- return result;
- }
-
- protected <T extends IdentifiableMediaEntity> T handlePersisted(IdentifiableMediaEntity mediaEntity) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((IdentifiableEntity)mediaEntity);
- //complete
- handleCollection(result, IdentifiableMediaEntity.class, "media", Media.class);
- return result;
- }
-
- protected <T extends ReferencedEntityBase> T handlePersisted(ReferencedEntityBase referencedEntity) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((AnnotatableEntity)referencedEntity);
- //complete
- result.setCitation(detache(result.getCitation()));
- return result;
- }
-
- protected <T extends DescriptionBase> T handlePersisted(DescriptionBase descriptionBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((IdentifiableEntity)descriptionBase);
- //complete
- handleCollection(result, DescriptionBase.class, "descriptionElements", DescriptionElementBase.class);
- handleCollection(result, DescriptionBase.class, "descriptiveDataSets", DescriptiveDataSet.class);
- handleCollection(result, DescriptionBase.class, "descriptionSources", Reference.class);
- result.setDescribedSpecimenOrObservation(detache(descriptionBase.getDescribedSpecimenOrObservation()));
- return result;
- }
-
- protected <T extends DescriptionElementBase> T handlePersisted(DescriptionElementBase element) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((AnnotatableEntity)element);
- //complete
- result.setFeature(detache(result.getFeature()));
- setInvisible(result, DescriptionElementBase.class, "inDescription", detache(result.getInDescription()));
- handleCollection(result, DescriptionElementBase.class, "sources", DescriptionElementSource.class);
- handleCollection(result, DescriptionElementBase.class, "media", Media.class);
- handleCollection(result, DescriptionElementBase.class, "modifiers", DefinedTerm.class);
- handleMap(result, DescriptionElementBase.class, "modifyingText", Language.class, LanguageString.class);
-
- return result;
- }
-
- protected <T extends RelationshipBase> T handlePersisted(RelationshipBase relBase) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- T result = handlePersisted((ReferencedEntityBase)relBase);
- return result;
- }
-
-
-//************************** COLLECTIONS / MAPS ****************************************/
-
- protected <HOLDER extends CdmBase, ITEM extends CdmBase> void handleCollection(
- HOLDER holder, Class<? super HOLDER> declaringClass, String parameter, Class<ITEM> itemClass)
- throws NoSuchFieldException, IllegalAccessException, InvocationTargetException, NoSuchMethodException {
-
- Collection<ITEM> oldCollection = setNewCollection(holder, declaringClass, parameter, itemClass);
- Collection<ITEM> newCollection = getTargetCollection(itemClass, oldCollection);
- Field field = declaringClass.getDeclaredField(parameter);
- field.setAccessible(true);
- field.set(holder, newCollection);
- }
-
- protected <HOLDER extends CdmBase, KEY extends CdmBase, ITEM extends CdmBase>
- void handleMap(
- HOLDER holder, Class<? super HOLDER> declaringClass, String parameter,
- Class<KEY> keyClass, Class<ITEM> itemClass)
- throws NoSuchFieldException, IllegalAccessException, InvocationTargetException, NoSuchMethodException {
-
- //TODO we do not need to set the new map 2x
- Map<KEY,ITEM> oldMap = setNewMap(holder, declaringClass, parameter, keyClass, itemClass);
- Map<KEY,ITEM> newMap = getTargetMap(oldMap);
- Field field = declaringClass.getDeclaredField(parameter);
- field.setAccessible(true);
- field.set(holder, newMap);
- }
-
- protected <T extends CdmBase> Collection<T> setNewCollection(CdmBase obj, Class<?> holderClass,
- String parameter, Class<T> entityClass) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException {
- Field field = holderClass.getDeclaredField(parameter);
- field.setAccessible(true);
- Collection<T> oldValue = (Collection<T>)field.get(obj);
- Collection<T> newValue = null;
- if (Set.class.isAssignableFrom(field.getType())){
- newValue = new HashSet<>();
- }else if (List.class.isAssignableFrom(field.getType())){
- newValue = new ArrayList<>();
- }else{
- throw new RuntimeException("Unsupported collection type: " + field.getType().getCanonicalName());
- }
- field.set(obj, newValue);
- return oldValue;
- }
-
- protected <KEY extends CdmBase, ITEM extends CdmBase> Map<KEY,ITEM> setNewMap(CdmBase obj, Class<?> holderClass,
- String parameter, Class<KEY> keyClass, Class<ITEM> itemClass) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException {
- Field field = holderClass.getDeclaredField(parameter);
- field.setAccessible(true);
- Map<KEY,ITEM> oldValue = (Map<KEY,ITEM>)field.get(obj);
- Map<KEY,ITEM> newValue = null;
- if (Map.class.isAssignableFrom(field.getType())){
- newValue = new HashMap<>();
- }else{
- throw new RuntimeException("Unsupported map type: " + field.getType().getCanonicalName());
- }
- field.set(obj, newValue);
- return oldValue;
- }
-
-
- private <T extends Collection<S>, S extends CdmBase> Collection<S> getTargetCollection(Class<S> clazz, T sourceCollection) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- Collection<S> result = new ArrayList<>();
- if (Set.class.isAssignableFrom(sourceCollection.getClass())){
- result = new HashSet<>();
- }
- for (S entity : sourceCollection){
- S target = detache(entity);
- result.add(target);
- }
- return result;
- }
-
- private <K extends CdmBase, V extends CdmBase> Map<K,V> getTargetMap(Map<K,V> sourceMap) throws IllegalAccessException, InvocationTargetException, NoSuchFieldException, SecurityException, IllegalArgumentException, NoSuchMethodException {
- Map<K,V> result = new HashMap<>();
- for (K key : sourceMap.keySet()){
- K targetKey = detache(key);
- V targetValue = detache(sourceMap.get(key));
- result.put(targetKey, targetValue);
- }
- return result;
- }
-
-// ****************************** INVISIBLE **************************************/
-
- protected void setInvisible(Object holder, String fieldName, Object value) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException {
- setInvisible(holder, holder.getClass(), fieldName, value);
- }
- protected void setInvisible(Object holder, Class<?> holderClazz, String fieldName, Object value) throws NoSuchFieldException, SecurityException, IllegalArgumentException, IllegalAccessException {
- Field field = holderClazz.getDeclaredField(fieldName);
- field.setAccessible(true);
- field.set(holder, value);
- }
-
-// ************************* GET TARGET ******************************************/
-
-
- //TODO this should be cached for partition
- private <T extends CdmBase> T getTarget(T source) {
- if (source == null){
- return null;
- }
- T result = getCached(source);
-// if (result == null){
-// Class<T> clazz = (Class<T>)source.getClass();
-// result = getCommonService().find(clazz, source.getUuid());
-// }
- if (result == null){
- //Alternative: clone?
- result = CdmBase.deproxy(source);
- result.setId(0);
- cache(result);
- toSave.add(result);
- }
- return result;
- }
-
-// ******************* CACHE *******************************************************/
-
-
- protected void cache(CdmBase cdmBase) {
- if (cdmBase instanceof User || cdmBase instanceof DefinedTermBase){
- getState().putPermanent(cdmBase.getUuid(), cdmBase);
- }else{
- sessionCache.put(cdmBase.getUuid(), cdmBase);
- }
- addExistingObject(cdmBase);
-
- }
-
- private void addExistingObject(CdmBase cdmBase) {
- cdmBase = CdmBase.deproxy(cdmBase);
- Set<UUID> set = existingObjects.get(cdmBase.getClass());
- if (set == null){
- set = loadExistingUuids(cdmBase.getClass());
-// set = new HashSet<>();
-// existingObjects.put(cdmBase.getClass(), set);
- }
- set.add(cdmBase.getUuid());
- }
-
- protected boolean isInCache(CdmBase cdmBase) {
- return getCached(cdmBase) != null;
- }
-
- protected <T extends CdmBase> T getCached(T cdmBase) {
- T result = (T)sessionCache.get(cdmBase.getUuid());
- if (result == null){
- result = (T)getState().getPermanent(cdmBase.getUuid());
- }
- return result;
- }
-
- protected void clearCache() {
- sessionCache.clear();
- }
-
- private Reference getSourceReference(FauEu2CdmImportState state) {
- UUID uuid = state.getConfig().getSourceRefUuid();
- if (uuid == null){
- uuid = state.getConfig().getSourceReference().getUuid();
- state.getConfig().setSourceRefUuid(uuid);
- }
- Reference result = (Reference)sessionCache.get(uuid);
- if (result == null){
- result = (Reference)getState().getPermanent(uuid);
- }
- if (result == null){
- result = getReferenceService().find(uuid);
- }
- if (result == null){
- result = state.getConfig().getSourceReference();
- getReferenceService().save(result);
- sessionCache.put(result.getUuid(), result);
- }
- return result;
- }
-
- public FauEu2CdmImportState getState() {
- return state;
- }
-
- public void setState(FauEu2CdmImportState state) {
- this.state = state;
- }
-
-}
BGBM BDI Projects / cdmlib-apps.git / commitdiff