Revision 783428fc
Added by Patrick Plitzner almost 8 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportClassification.java | ||
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| 36 | 36 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; |
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/** |
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* |
| ... | ... | |
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String gueltString = rs.getString(RedListUtil.GUELT); |
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String taxZusatzString = rs.getString(RedListUtil.TAX_ZUSATZ); |
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String relationE = rs.getString(RedListUtil.E); |
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String relationW = rs.getString(RedListUtil.W); |
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String relationK = rs.getString(RedListUtil.K); |
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String relationAW = rs.getString(RedListUtil.AW); |
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String relationAO = rs.getString(RedListUtil.AO); |
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String relationR = rs.getString(RedListUtil.R); |
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String relationO = rs.getString(RedListUtil.O); |
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String relationS = rs.getString(RedListUtil.S); |
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|
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//Gesamtliste |
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TaxonBase<?> taxonBaseGL = state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class); |
| 136 | 146 |
TaxonBase<?> parentBaseGL = state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, parentId, TaxonBase.class); |
| ... | ... | |
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} |
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|
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//add taxa for concept relationships to E, W, K, AW, AO, R, O, S |
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addTaxonToClassification(classificationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, id, state); |
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addTaxonToClassification(classificationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, id, state); |
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addTaxonToClassification(classificationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, id, state); |
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addTaxonToClassification(classificationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, id, state); |
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addTaxonToClassification(classificationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, id, state); |
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addTaxonToClassification(classificationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, id, state); |
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addTaxonToClassification(classificationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, id, state); |
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addTaxonToClassification(classificationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, id, state); |
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addTaxonToClassification(classificationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, relationE, taxonBaseGL, taxonBaseCL, id, state);
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addTaxonToClassification(classificationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, relationW, taxonBaseGL, taxonBaseCL, id, state);
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addTaxonToClassification(classificationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, relationK, taxonBaseGL, taxonBaseCL, id, state);
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addTaxonToClassification(classificationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, relationAW, taxonBaseGL, taxonBaseCL, id, state);
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addTaxonToClassification(classificationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, relationAO, taxonBaseGL, taxonBaseCL, id, state);
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addTaxonToClassification(classificationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, relationR, taxonBaseGL, taxonBaseCL, id, state);
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addTaxonToClassification(classificationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, relationO, taxonBaseGL, taxonBaseCL, id, state);
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addTaxonToClassification(classificationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, relationS, taxonBaseGL, taxonBaseCL, id, state);
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} |
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private void addTaxonToClassification(Classification classification, String classificationNamespace, long id, RedListGefaesspflanzenImportState state){
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private void addTaxonToClassification(Classification classification, String classificationNamespace, String relationString, final TaxonBase<?> gesamtListeTaxon, final TaxonBase<?> checklisteTaxon, long id, RedListGefaesspflanzenImportState state){
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Taxon taxon = HibernateProxyHelper.deproxy(state.getRelatedObject(classificationNamespace, String.valueOf(id), TaxonBase.class), Taxon.class); |
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//add concept relation to gesamtliste and checkliste |
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if(CdmUtils.isNotBlank(relationString) && !relationString.equals(".")){
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//if the related concept in gesamtliste/checkliste is a synonym then we |
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//create a relation to the accepted taxon |
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Taxon acceptedGesamtListeTaxon = getAcceptedTaxon(gesamtListeTaxon); |
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Taxon acceptedChecklistTaxon = getAcceptedTaxon(checklisteTaxon); |
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String relationSubstring = relationString.substring(relationString.length()-1, relationString.length()); |
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TaxonRelationshipType taxonRelationshipTypeByKey = new RedListGefaesspflanzenTransformer().getTaxonRelationshipTypeByKey(relationSubstring); |
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if(taxonRelationshipTypeByKey==null){
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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(relationSubstring.equals("<")){
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if(acceptedGesamtListeTaxon!=null){
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acceptedGesamtListeTaxon.addTaxonRelation(taxon, taxonRelationshipTypeByKey, null, null); |
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} |
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if(acceptedChecklistTaxon!=null) {
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acceptedChecklistTaxon.addTaxonRelation(taxon, taxonRelationshipTypeByKey, null, null); |
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} |
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} |
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else{
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if(acceptedGesamtListeTaxon!=null){
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taxon.addTaxonRelation(acceptedGesamtListeTaxon, taxonRelationshipTypeByKey, null, null); |
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} |
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if(acceptedChecklistTaxon!=null) {
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taxon.addTaxonRelation(acceptedChecklistTaxon, taxonRelationshipTypeByKey, null, null); |
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} |
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} |
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} |
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if(taxon!=null){//not all taxa exist in these classifications
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taxon.setSec(classification.getReference()); |
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taxon.setTitleCache(null);//Reset title cache to reflect sec ref in title |
| app-import/src/main/java/eu/etaxonomy/cdm/io/redlist/gefaesspflanzen/RedListGefaesspflanzenImportNames.java | ||
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throws SQLException {
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long id = rs.getLong(RedListUtil.NAMNR); |
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String clTaxonString = rs.getString(RedListUtil.CL_TAXON); |
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String relationE = rs.getString(RedListUtil.E); |
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String relationW = rs.getString(RedListUtil.W); |
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String relationK = rs.getString(RedListUtil.K); |
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String relationAW = rs.getString(RedListUtil.AW); |
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String relationAO = rs.getString(RedListUtil.AO); |
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String relationR = rs.getString(RedListUtil.R); |
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String relationO = rs.getString(RedListUtil.O); |
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String relationS = rs.getString(RedListUtil.S); |
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//---NAME--- |
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NonViralName<?> name = importName(state, rs, namesToSave); |
| ... | ... | |
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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, 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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cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_E, taxaToSave, id, state);
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cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_W, taxaToSave, id, state);
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cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_K, taxaToSave, id, state);
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cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_AW, taxaToSave, id, state);
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cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_AO, taxaToSave, id, state);
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cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_R, taxaToSave, id, state);
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cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_O, taxaToSave, id, state);
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cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_S, 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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|
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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); |
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if(taxonRelationshipTypeByKey==null){
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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(gesamtListeTaxon, checkListenTaxon, taxonRelationshipTypeByKey, taxaToSave, id, classificationNamespace, true, false, state); |
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} |
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else{
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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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/** |
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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 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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private Taxon cloneTaxon(final TaxonBase<?> gesamtListeTaxon, String sourceNameSpace, Set<TaxonBase> taxaToSave, long id, RedListGefaesspflanzenImportState state){
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Taxon clonedTaxon = null; |
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if(gesamtListeTaxon.isInstanceOf(Taxon.class)){
|
| ... | ... | |
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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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} |
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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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} |
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|
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ImportHelper.setOriginalSource(clonedTaxon, state.getTransactionalSourceReference(), id, sourceNameSpace); |
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taxaToSave.add(clonedTaxon); |
| 236 | 179 |
return clonedTaxon; |
Also available in: Unified diff
#5448 Move import of concept relationships to classification import
class