Revision 59ef8f07
Added by Andreas Müller about 8 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/edaphobase/EdaphobaseClassificationImport.java | ||
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import eu.etaxonomy.cdm.io.common.IPartitionedIO; |
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.taxon.Classification; |
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import eu.etaxonomy.cdm.model.taxon.Synonym; |
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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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|
| ... | ... | |
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Set<TaxonBase> taxaToSave = new HashSet<>(); |
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try {
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while (rs.next()){
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Integer id = rs.getInt("taxon_id");
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int id = rs.getInt("taxon_id");
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//parentTaxonFk |
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boolean isValid = rs.getBoolean("valid");
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// boolean idDeleted = rs.getBoolean("deleted");
|
| ... | ... | |
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// boolean isGroup = rs.getBoolean("taxonomic_group");
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Integer parentTaxonFk = nullSafeInt(rs, "parent_taxon_fk"); |
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if (id != null && parentTaxonFk != null){
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if (isValid){
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Taxon child = state.getRelatedObject(TAXON_NAMESPACE, id.toString(), Taxon.class); |
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Taxon parent = state.getRelatedObject(TAXON_NAMESPACE, parentTaxonFk.toString(), Taxon.class); |
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if (parent != null){
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classification.addParentChild(parent, child, sourceReference, null); |
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}else{
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logger.warn("Parent taxon " + parentTaxonFk + " not found for taxon " + id );
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} |
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if (parentTaxonFk != null){
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TaxonBase<?> parent = state.getRelatedObject(TAXON_NAMESPACE, parentTaxonFk.toString(), TaxonBase.class); |
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if (parent == null){
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logger.warn("Parent taxon " + parentTaxonFk + " not found for taxon " + id );
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}else{
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Synonym synonym = state.getRelatedObject(TAXON_NAMESPACE, id.toString(), Synonym.class); |
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if (synonym == null){
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logger.warn("Synonym " + id + " not found for taxon ");
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} |
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Taxon accepted = state.getRelatedObject(TAXON_NAMESPACE, parentTaxonFk.toString(), Taxon.class); |
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if (accepted != null){
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accepted.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF()); |
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TaxonNameBase<?,?> parentName = parent.getName(); |
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TaxonBase<?> child = state.getRelatedObject(TAXON_NAMESPACE, String.valueOf(id), TaxonBase.class); |
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// TaxonNameBase<?,?> childName = child.getName(); |
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// handleMissingNameParts(CdmBase.deproxy(childName, NonViralName.class), CdmBase.deproxy(parentName, NonViralName.class)); |
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if (isValid){
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if (parent.isInstanceOf(Synonym.class)){
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logger.warn("Parent taxon (" + parentTaxonFk + " is not valid for valid child " + id);
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}else{
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Taxon accParent = CdmBase.deproxy(parent, Taxon.class); |
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classification.addParentChild(accParent, (Taxon)child, sourceReference, null); |
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taxaToSave.add(accParent); |
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} |
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}else{
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logger.warn("Accepted(parent) taxon " + parentTaxonFk + " not found for taxon " + id );
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// Synonym synonym = CdmBase.deproxy(child, Synonym.class); |
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// if (synonym == null){
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// logger.warn("Synonym " + id + " not found for taxon ");
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// } |
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// if(parent.isInstanceOf(Synonym.class)){
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// String message = "Taxon ("+parentTaxonFk+") is not accepted but synonym. Can't add synonym ("+id+")";
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// logger.warn(message); |
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// }else{
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// Taxon accepted = CdmBase.deproxy(parent, Taxon.class); |
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//// accepted.addSynonym(synonym, SynonymRelationshipType.SYNONYM_OF()); |
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// taxaToSave.add(accepted); |
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// } |
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} |
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} |
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|
|
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} |
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|
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// //id |
| ... | ... | |
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|
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} |
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} catch (SQLException e) {
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// TODO Auto-generated catch block |
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e.printStackTrace(); |
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} |
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|
| ... | ... | |
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return true; |
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} |
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// /** |
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// * @param childName |
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// * @param parentName |
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// */ |
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// private void handleMissingNameParts(NonViralName<?> childName, NonViralName<?> parentName) {
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// if (childName.getGenusOrUninomial()) |
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// } |
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@Override |
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, |
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EdaphobaseImportState state) {
|
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