Revision 766713c7
Added by Patrick Plitzner over 7 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java | ||
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} |
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//---CONCEPT RELATIONSHIPS--- |
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/*check if taxon/synonym also exists in other classification |
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* 1. create new taxon with the same name (in that classification) |
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* 2. create concept relationship between both |
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*/ |
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| 142 | 138 |
//checklist |
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TaxonBase<?> checklistTaxon = null; |
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if(CdmUtils.isNotBlank(clTaxonString) && !clTaxonString.trim().equals("-")){
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cloneTaxon(taxonBase, name, TaxonRelationshipType.CONGRUENT_TO(), taxaToSave, id, RedListUtil.TAXON_CHECKLISTE_NAMESPACE, false, true, state); |
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checklistTaxon = (TaxonBase<?>) taxonBase.clone(); |
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//TODO what to do with synonyms? |
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if(checklistTaxon.isInstanceOf(Taxon.class)){
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TaxonRelationship relation = HibernateProxyHelper.deproxy(checklistTaxon, Taxon.class).addTaxonRelation(HibernateProxyHelper.deproxy(taxonBase, Taxon.class), TaxonRelationshipType.CONGRUENT_TO(), null, null); |
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relation.setDoubtful(true); |
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} |
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ImportHelper.setOriginalSource(checklistTaxon, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_CHECKLISTE_NAMESPACE); |
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taxaToSave.add(checklistTaxon); |
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} |
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//E, W, K, AW, AO, R, O, S |
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addConceptRelation(relationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, taxonBase, name, taxaToSave, id, state);
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addConceptRelation(relationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, taxonBase, name, taxaToSave, id, state);
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addConceptRelation(relationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, taxonBase, name, taxaToSave, id, state);
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addConceptRelation(relationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, taxonBase, name, taxaToSave, id, state);
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addConceptRelation(relationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, taxonBase, name, taxaToSave, id, state);
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addConceptRelation(relationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, taxonBase, name, taxaToSave, id, state);
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addConceptRelation(relationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, taxonBase, name, taxaToSave, id, state);
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addConceptRelation(relationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, taxonBase, name, taxaToSave, id, state);
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addConceptRelation(relationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, taxonBase, checklistTaxon, taxaToSave, id, state);
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addConceptRelation(relationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, taxonBase, checklistTaxon, taxaToSave, id, state);
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addConceptRelation(relationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, taxonBase, checklistTaxon, taxaToSave, id, state);
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addConceptRelation(relationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, taxonBase, checklistTaxon, taxaToSave, id, state);
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addConceptRelation(relationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, taxonBase, checklistTaxon, taxaToSave, id, state);
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addConceptRelation(relationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, taxonBase, checklistTaxon, taxaToSave, id, state);
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addConceptRelation(relationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, taxonBase, checklistTaxon, taxaToSave, id, state);
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addConceptRelation(relationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, taxonBase, checklistTaxon, taxaToSave, id, state);
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//NOTE: the source has to be added after cloning or otherwise the clone would also get the source |
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ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE); |
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taxaToSave.add(taxonBase); |
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} |
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private void addConceptRelation(String relationString, String classificationNamespace, TaxonBase<?> taxonBase, TaxonNameBase<?,?> name, Set<TaxonBase<?>> taxaToSave, long id, RedListGefaesspflanzenImportState state){
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private void addConceptRelation(String relationString, String classificationNamespace, TaxonBase<?> gesamtListeTaxon, TaxonBase<?> checkListenTaxon, Set<TaxonBase<?>> taxaToSave, long id, RedListGefaesspflanzenImportState state){
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if(CdmUtils.isNotBlank(relationString) && !relationString.equals(".")){
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String substring = relationString.substring(relationString.length()-1, relationString.length()); |
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TaxonRelationshipType taxonRelationshipTypeByKey = new RedListGefaesspflanzenTransformer().getTaxonRelationshipTypeByKey(substring); |
| 165 | 170 |
if(taxonRelationshipTypeByKey==null){
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RedListUtil.logMessage(id, "Could not interpret relationship "+relationString+" for taxon "+taxonBase.generateTitle(), logger);
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RedListUtil.logMessage(id, "Could not interpret relationship "+relationString+" for taxon "+gesamtListeTaxon.generateTitle(), logger);
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} |
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//there is no type "included in" so we have to reverse the direction |
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if(substring.equals("<")){
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cloneTaxon(taxonBase, name, taxonRelationshipTypeByKey, taxaToSave, id, classificationNamespace, true, false, state);
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cloneTaxon(gesamtListeTaxon, checkListenTaxon, taxonRelationshipTypeByKey, taxaToSave, id, classificationNamespace, true, false, state);
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} |
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else{
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cloneTaxon(taxonBase, name, taxonRelationshipTypeByKey, taxaToSave, id, classificationNamespace, false, false, state);
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cloneTaxon(gesamtListeTaxon, checkListenTaxon, taxonRelationshipTypeByKey, taxaToSave, id, classificationNamespace, false, false, state);
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} |
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} |
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} |
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/** |
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* 1. clone new taxon of gesamtListeTaxon with the same name (in that classification)<br> |
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* 2. create concept relationship from clone to gesamtListeTaxon/checklisteTaxon or from its accepted taxon if it is synonym<br> |
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*<br> |
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* <b>NOTE:</b> the {@link TaxonRelationshipType} passed as parameter is
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* directed <b>from the clone</b> to the taxon.<br> |
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* This can be changed with parameter <i>reverseRelation</i> |
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* @return cloned taxon |
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*/ |
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private void cloneTaxon(TaxonBase<?> taxonBase, TaxonNameBase<?, ?> name, TaxonRelationshipType relationFromCloneToTaxon, Set<TaxonBase<?>> taxaToSave, long id, String sourceNameSpace, boolean reverseRelation, boolean doubtful, RedListGefaesspflanzenImportState state){
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TaxonBase<?> clone = (TaxonBase<?>) taxonBase.clone(); |
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if(taxonBase.isInstanceOf(Taxon.class)){
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TaxonRelationship taxonRelation; |
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if(reverseRelation){
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taxonRelation = ((Taxon) taxonBase).addTaxonRelation((Taxon) clone, relationFromCloneToTaxon, null, null); |
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private Taxon cloneTaxon(final TaxonBase<?> gesamtListeTaxon, final TaxonBase<?> checklisteTaxon, TaxonRelationshipType relationFromCloneToTaxon, Set<TaxonBase<?>> taxaToSave, long id, String sourceNameSpace, boolean reverseRelation, boolean doubtful, RedListGefaesspflanzenImportState state){
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Taxon acceptedGesamtListeTaxon = getAcceptedTaxon(gesamtListeTaxon); |
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Taxon acceptedChecklistTaxon = getAcceptedTaxon(checklisteTaxon); |
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Taxon clonedTaxon = null; |
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if(gesamtListeTaxon.isInstanceOf(Taxon.class)){
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clonedTaxon = HibernateProxyHelper.deproxy(gesamtListeTaxon.clone(), Taxon.class); |
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} |
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else if(gesamtListeTaxon.isInstanceOf(Synonym.class)){
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clonedTaxon = Taxon.NewInstance(gesamtListeTaxon.getName(), gesamtListeTaxon.getSec()); |
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} |
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else{
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RedListUtil.logMessage(id, "Taxon base "+gesamtListeTaxon+" is neither taxon nor synonym! Taxon could not be cloned", logger); |
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return null; |
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} |
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if(reverseRelation){
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if(acceptedGesamtListeTaxon!=null){
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TaxonRelationship taxonRelation = acceptedGesamtListeTaxon.addTaxonRelation(clonedTaxon, relationFromCloneToTaxon, null, null); |
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taxonRelation.setDoubtful(doubtful); |
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} |
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if(acceptedChecklistTaxon!=null) {
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TaxonRelationship taxonRelation = acceptedChecklistTaxon.addTaxonRelation(clonedTaxon, relationFromCloneToTaxon, null, null); |
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taxonRelation.setDoubtful(doubtful); |
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} |
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else {
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taxonRelation = ((Taxon) clone).addTaxonRelation((Taxon) taxonBase, relationFromCloneToTaxon, null, null); |
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} |
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else {
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if(acceptedGesamtListeTaxon!=null){
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TaxonRelationship taxonRelation = clonedTaxon.addTaxonRelation(acceptedGesamtListeTaxon, relationFromCloneToTaxon, null, null); |
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taxonRelation.setDoubtful(doubtful); |
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} |
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if(acceptedChecklistTaxon!=null) {
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TaxonRelationship taxonRelation = clonedTaxon.addTaxonRelation(acceptedChecklistTaxon, relationFromCloneToTaxon, null, null); |
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taxonRelation.setDoubtful(doubtful); |
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} |
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taxonRelation.setDoubtful(doubtful); |
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} |
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ImportHelper.setOriginalSource(clone, state.getTransactionalSourceReference(), id, sourceNameSpace); |
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taxaToSave.add(clone); |
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ImportHelper.setOriginalSource(clonedTaxon, state.getTransactionalSourceReference(), id, sourceNameSpace); |
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taxaToSave.add(clonedTaxon); |
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return clonedTaxon; |
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} |
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private TaxonBase<?> importTaxon(ResultSet rs, NonViralName<?> name) throws SQLException {
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Also available in: Unified diff
Import synonyms of other classifications #5448