import eu.etaxonomy.cdm.model.common.CdmBase;
import eu.etaxonomy.cdm.model.common.DefinedTerm;
import eu.etaxonomy.cdm.model.common.DefinedTermBase;
+import eu.etaxonomy.cdm.model.common.ISourceable;
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
import eu.etaxonomy.cdm.model.common.Language;
import eu.etaxonomy.cdm.model.common.OriginalSourceBase;
}
}
+<<<<<<< e12074844fd16df32275a14151d604461a15a064
+=======
+ /**
+ * Look if the Institution does already exist
+ * @param institutionCode: a string with the institutioncode
+ * @param config : the configurator
+ * @return the Institution (existing or new)
+ */
+ private Institution getInstitution(String institutionCode, Abcd206ImportState state) {
+ Abcd206ImportConfigurator config = state.getConfig();
+ Institution institution=null;
+ List<Institution> institutions;
+ try {
+ institutions = getAgentService().list(Institution.class, null, null, null, null);
+ } catch (Exception e) {
+ institutions = new ArrayList<Institution>();
+ logger.warn(e);
+ }
+ if (institutions.size() > 0 && config.isReUseExistingMetadata()) {
+ for (Institution institut:institutions){
+ try{
+ if (institut.getCode().equalsIgnoreCase(institutionCode)) {
+ institution=institut;
+ }
+ }catch(Exception e){logger.warn("no institution code in the db");}
+ }
+ }
+ if(DEBUG) {
+ if(institution !=null) {
+ logger.info("getinstitution " + institution.toString());
+ }
+ }
+ if (institution == null){
+ // create institution
+ institution = Institution.NewInstance();
+ institution.setCode(institutionCode);
+ institution.setTitleCache(institutionCode, true);
+ }
+ save(institution, state);
+ return institution;
+ }
+
+ /**
+ * Look if the Collection does already exist
+ * @param collectionCode
+ * @param collectionCode: a string
+ * @param config : the configurator
+ * @return the Collection (existing or new)
+ */
+ private Collection getCollection(Institution institution, String collectionCode, Abcd206ImportState state) {
+ Abcd206ImportConfigurator config = state.getConfig();
+ Collection collection = null;
+ List<Collection> collections;
+ try {
+ collections = getCollectionService().list(Collection.class, null, null, null, null);
+ } catch (Exception e) {
+ collections = new ArrayList<Collection>();
+ }
+ if (collections.size() > 0 && config.isReUseExistingMetadata()) {
+ for (Collection coll:collections){
+ if (coll.getCode() != null && coll.getInstitute() != null
+ && coll.getCode().equalsIgnoreCase(collectionCode) && coll.getInstitute().equals(institution)) {
+ collection = coll;
+ break;
+ }
+ }
+ }
+
+ if(collection == null){
+ collection =Collection.NewInstance();
+ collection.setCode(collectionCode);
+ collection.setInstitute(institution);
+ collection.setTitleCache(collectionCode);
+ }
+ save(collection, state);
+ return collection;
+ }
+
+
+ /**
+ * join DeterminationEvent to the Taxon Object
+ * @param state : the ABCD import state
+ * @param taxon: the current Taxon
+ * @param preferredFlag :if the current name is preferred
+ * @param derivedFacade : the derived Unit Facade
+ */
+ @SuppressWarnings("rawtypes")
+ private void linkDeterminationEvent(Abcd206ImportState state, Taxon taxon, boolean preferredFlag, DerivedUnitFacade derivedFacade) {
+ Abcd206ImportConfigurator config = state.getConfig();
+ if(DEBUG){
+ logger.info("start linkdetermination with taxon:" + taxon.getUuid()+", "+taxon);
+ }
+
+ DeterminationEvent determinationEvent = DeterminationEvent.NewInstance();
+ determinationEvent.setTaxonName(taxon.getName());
+ determinationEvent.setPreferredFlag(preferredFlag);
+
+ determinationEvent.setIdentifiedUnit(state.getDerivedUnitBase());
+ state.getDerivedUnitBase().addDetermination(determinationEvent);
+
+ if(DEBUG){
+ logger.info("NB TYPES INFO: "+ state.getDataHolder().statusList.size());
+ }
+ for (SpecimenTypeDesignationStatus specimenTypeDesignationstatus : state.getDataHolder().statusList) {
+ if (specimenTypeDesignationstatus != null) {
+ if(DEBUG){
+ logger.info("specimenTypeDesignationstatus :"+ specimenTypeDesignationstatus);
+ }
+
+ ICdmApplicationConfiguration cdmAppController = config.getCdmAppController();
+ if(cdmAppController == null){
+ cdmAppController = this;
+ }
+ specimenTypeDesignationstatus = (SpecimenTypeDesignationStatus) cdmAppController.getTermService().find(specimenTypeDesignationstatus.getUuid());
+ //Designation
+ TaxonNameBase<?,?> name = taxon.getName();
+ SpecimenTypeDesignation designation = SpecimenTypeDesignation.NewInstance();
+
+ designation.setTypeStatus(specimenTypeDesignationstatus);
+ designation.setTypeSpecimen(state.getDerivedUnitBase());
+ name.addTypeDesignation(designation, true);
+ }
+ }
+
+ for (String[] fullReference : state.getDataHolder().referenceList) {
+
+
+ String strReference=fullReference[0];
+ String citationDetail = fullReference[1];
+ String citationURL = fullReference[2];
+ List<Reference> references = getReferenceService().listByTitle(Reference.class, "strReference", MatchMode.EXACT, null, null, null, null, null);
+
+ if (!references.isEmpty()){
+ Reference reference = null;
+ for (Reference refe: references) {
+ if (refe.getTitleCache().equalsIgnoreCase(strReference)) {
+ reference =refe;
+ break;
+ }
+ }
+ if (reference ==null){
+ reference = ReferenceFactory.newGeneric();
+ reference.setTitleCache(strReference, true);
+ save(reference, state);
+ }
+ determinationEvent.addReference(reference);
+ }
+ }
+ save(state.getDerivedUnitBase(), state);
+
+ if (config.isAddIndividualsAssociationsSuchAsSpecimenAndObservations() && preferredFlag) {
+ //do not add IndividualsAssociation to non-preferred taxa
+ if(DEBUG){
+ logger.info("isDoCreateIndividualsAssociations");
+ }
+
+ makeIndividualsAssociation(state, taxon, determinationEvent);
+
+ save(state.getDerivedUnitBase(), state);
+ }
+ }
+
+ /**
+ * create and link each association (specimen, observation..) to the accepted taxon
+ * @param state : the ABCD import state
+ * @param taxon: the current Taxon
+ * @param determinationEvent:the determinationevent
+ */
+ private void makeIndividualsAssociation(Abcd206ImportState state, Taxon taxon, DeterminationEvent determinationEvent) {
+ Abcd206ImportConfigurator config = state.getConfig();
+ SpecimenUserInteraction sui = config.getSpecimenUserInteraction();
+
+ if (DEBUG) {
+ logger.info("MAKE INDIVIDUALS ASSOCIATION");
+ }
+
+ TaxonDescription taxonDescription = null;
+ Set<TaxonDescription> descriptions= taxon.getDescriptions();
+ if (((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
+ if(!state.isDescriptionGroupSet()){
+ taxonDescription = sui.askForDescriptionGroup(descriptions);
+ state.setDescriptionGroup(taxonDescription);
+ state.setDescriptionGroupSet(true);
+ }else{
+ taxonDescription=state.getDescriptionGroup();
+ }
+ } else {
+ for (TaxonDescription description : descriptions){
+ Set<IdentifiableSource> sources = new HashSet<>();
+ sources.addAll(description.getTaxon().getSources());
+ sources.addAll(description.getSources());
+ for (IdentifiableSource source:sources){
+ if(state.getRef().equals(source.getCitation())) {
+ taxonDescription = description;
+ }
+ }
+ }
+ }
+ if (taxonDescription == null){
+ taxonDescription = TaxonDescription.NewInstance(taxon, false);
+ if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
+ taxonDescription.addSource(OriginalSourceType.Import, null, null, state.getRef(), null);
+ }
+ state.setDescriptionGroup(taxonDescription);
+ taxon.addDescription(taxonDescription);
+ }
+
+ //PREPARE REFERENCE QUESTIONS
+
+ Map<String,OriginalSourceBase<?>> sourceMap = new HashMap<String, OriginalSourceBase<?>>();
+
+ List<IdentifiableSource> issTmp = new ArrayList<>();//getCommonService().list(IdentifiableSource.class, null, null, null, null);
+ List<DescriptionElementSource> issTmp2 = new ArrayList<>();//getCommonService().list(DescriptionElementSource.class, null, null, null, null);
+
+ Set<OriginalSourceBase> osbSet = new HashSet<OriginalSourceBase>();
+ if(issTmp2!=null) {
+ osbSet.addAll(issTmp2);
+ }
+ if(issTmp!=null) {
+ osbSet.addAll(issTmp);
+ }
+
+
+ addToSourceMap(sourceMap, osbSet);
+
+ if (((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
+ List<OriginalSourceBase<?>> res = null;
+ if(!state.isDescriptionSourcesSet()){
+ res = sui.askForSource(sourceMap, "the description group ("+taxon+")",
+ "The current reference is "+state.getRef().getTitleCache(),getReferenceService(), state.getDataHolder().docSources);
+ state.setDescriptionRefs(res);
+ state.setDescriptionSourcesSet(true);
+ }
+ else{
+ res=state.getDescriptionRefs();
+ }
+ if(res !=null) {
+ for (OriginalSourceBase<?> sour:res){
+ if(sour.isInstanceOf(IdentifiableSource.class)){
+ try {
+ if(sourceNotLinkedToElement(taxonDescription,sour)) {
+ taxonDescription.addSource((IdentifiableSource)sour.clone());
+ }
+ } catch (CloneNotSupportedException e) {
+ logger.warn("no cloning?");
+ }
+ }else{
+ if(sourceNotLinkedToElement(taxonDescription,sour)) {
+ taxonDescription.addSource(OriginalSourceType.Import,null, null, sour.getCitation(),sour.getCitationMicroReference());
+ }
+ }
+ }
+ }
+ }
+ else {
+ if(sourceNotLinkedToElement(taxonDescription,state.getRef(),null)) {
+ taxonDescription.addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
+ }
+ }
+ state.setDescriptionGroup(taxonDescription);
+
+ IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();
+ Feature feature = makeFeature(state.getDerivedUnitBase());
+ indAssociation.setAssociatedSpecimenOrObservation(state.getDerivedUnitBase());
+ indAssociation.setFeature(feature);
+
+ if (((Abcd206ImportConfigurator) state.getConfig()).isInteractWithUser()){
+ sourceMap = new HashMap<String, OriginalSourceBase<?>>();
+
+ issTmp = getCommonService().list(IdentifiableSource.class, null, null, null, null);
+ issTmp2 = getCommonService().list(DescriptionElementSource.class, null, null, null, null);
+
+ osbSet = new HashSet<OriginalSourceBase>();
+ if(issTmp2!=null) {
+ osbSet.addAll(issTmp2);
+ }
+ if(issTmp!=null) {
+ osbSet.addAll(issTmp);
+ }
+
+
+ addToSourceMap(sourceMap, osbSet);
+
+ List<OriginalSourceBase<?>> sources =null;
+ if(!state.isAssociationSourcesSet()) {
+ sources = sui.askForSource(sourceMap, "descriptive element (association) ",taxon.toString(),
+ getReferenceService(),state.getDataHolder().docSources);
+ state.setAssociationRefs(sources);
+ state.setAssociationSourcesSet(true);
+ }
+ else{
+ sources=state.getAssociationRefs();
+ }
+ if(sources !=null) {
+ for (OriginalSourceBase<?> source: sources) {
+ if(source !=null) {
+ if(source.isInstanceOf(DescriptionElementSource.class)){
+ try {
+ if(sourceNotLinkedToElement(indAssociation,source)) {
+ indAssociation.addSource((DescriptionElementSource)source.clone());
+ }
+ } catch (CloneNotSupportedException e) {
+ logger.warn("clone forbidden?");
+ }
+ }else{
+ if(sourceNotLinkedToElement(indAssociation,source)) {
+ indAssociation.addSource(OriginalSourceType.Import,null, null, source.getCitation(),source.getCitationMicroReference());
+ }
+ try {
+ if(sourceNotLinkedToElement(state.getDerivedUnitBase(), source)) {
+ state.getDerivedUnitBase().addSource((IdentifiableSource) source.clone());
+ }
+ } catch (CloneNotSupportedException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+
+ }
+ }
+ }
+ }else {
+ if(sourceNotLinkedToElement(indAssociation,state.getRef(),null)) {
+ indAssociation.addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
+ }
+ if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getRef(),null)) {
+ state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
+ }
+ for (Reference citation : determinationEvent.getReferences()) {
+ if(sourceNotLinkedToElement(indAssociation,citation,null))
+ {
+ indAssociation.addSource(DescriptionElementSource.NewInstance(OriginalSourceType.Import, null, null, citation, null));
+ }
+ if(sourceNotLinkedToElement(state.getDerivedUnitBase(), state.getRef(),null)) {
+ state.getDerivedUnitBase().addSource(OriginalSourceType.Import,null, null, state.getRef(), null);
+ }
+ }
+ }
+
+ taxonDescription.addElement(indAssociation);
+
+ save(taxonDescription, state);
+ save(taxon, state);
+ state.getReport().addDerivate(state.getDerivedUnitBase(), config);
+ state.getReport().addIndividualAssociation(taxon, state.getDataHolder().unitID, state.getDerivedUnitBase());
+ }
+
+ private <T extends OriginalSourceBase<?>> boolean sourceNotLinkedToElement(ISourceable<T> sourcable, Reference reference, String microReference) {
+ Set<T> linkedSources = sourcable.getSources();
+ for (T is:linkedSources){
+ Reference unitReference = is.getCitation();
+ String unitMicroReference = is.getCitationMicroReference();
+
+ boolean refMatch=false;
+ boolean microMatch=false;
+
+ try{
+ if (unitReference==null && reference==null) {
+ refMatch=true;
+ }
+ if (unitReference!=null && reference!=null) {
+ if (unitReference.getTitleCache().equalsIgnoreCase(reference.getTitleCache())) {
+ refMatch=true;
+ }
+ }
+ }catch(Exception e){}
+
+ try{
+ if (unitMicroReference==null && microReference==null) {
+ microMatch=true;
+ }
+ if(unitMicroReference!=null && microReference!=null) {
+ if(unitMicroReference.equalsIgnoreCase(microReference)) {
+ microMatch=true;
+ }
+ }
+ }
+ catch(Exception e){}
+
+ if (microMatch && refMatch) {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ private <T extends OriginalSourceBase<?>> boolean sourceNotLinkedToElement(ISourceable<T> sourcable, OriginalSourceBase<?> source) {
+ return sourceNotLinkedToElement(sourcable, source.getCitation(), source.getCitationMicroReference());
+ }
+>>>>>>> fix #6001 Clean up multiple sourceNotLinked() methods
BGBM BDI Projects / cdmlib.git / commitdiff