323 lines
9.4 KiB
Java
323 lines
9.4 KiB
Java
package org.gcube.portlets.user.speciesdiscovery.server.service;
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import java.util.ArrayList;
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import java.util.List;
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import org.apache.log4j.Logger;
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import org.gcube.application.framework.core.session.ASLSession;
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import org.gcube.data.spd.model.products.TaxonomyItem;
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import org.gcube.data.spd.model.util.ElementProperty;
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import org.gcube.portlets.user.speciesdiscovery.client.ConstantsSpeciesDiscovery;
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import org.gcube.portlets.user.speciesdiscovery.server.TaxonomySearchServiceImpl;
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import org.gcube.portlets.user.speciesdiscovery.server.stream.Converter;
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import org.gcube.portlets.user.speciesdiscovery.shared.CommonName;
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import org.gcube.portlets.user.speciesdiscovery.shared.ItemParameter;
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import org.gcube.portlets.user.speciesdiscovery.shared.LightTaxonomyRow;
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import org.gcube.portlets.user.speciesdiscovery.shared.TaxonomyRow;
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import org.gcube.portlets.user.speciesdiscovery.shared.util.NormalizeString;
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/**
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*
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* @author Francesco Mangiacrapa francesco.mangiacrapa@isti.cnr.it
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*
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*/
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public class TaxonomyItemConverter implements Converter<TaxonomyItem, TaxonomyRow> {
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protected Logger logger = Logger.getLogger(TaxonomyItemConverter.class);
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protected int id = 0;
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private ASLSession session;
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/**
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* @param dataProviderId
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*/
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public TaxonomyItemConverter(ASLSession session) {
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this.session = session;
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}
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@Override
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public TaxonomyRow convert(TaxonomyItem input) throws Exception {
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TaxonomyRow taxonomy = createTaxonomyRow(input);
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//SET PARENTS
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// System.out.println("Convert Taxonomy parent for: "+taxonomy.getId());
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taxonomy.setParent(convertParentsTaxonomy(input));
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//SET BASE TAXON
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taxonomy.setBaseTaxonValue(NormalizeString.lowerCaseUpFirstChar(getTaxonomyValue(TaxonomySearchServiceImpl.BASETAXONOMY,taxonomy)));
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// System.out.println("#############################PARENT ID: " + taxonomy.getParent().getId());
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if(taxonomy.getParents()!=null && taxonomy.getParents().size()>0)
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taxonomy.setParentID(""+taxonomy.getParents().get(0).getId());
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return taxonomy;
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}
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public LightTaxonomyRow convertLightTaxonomy(TaxonomyItem input) throws Exception {
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LightTaxonomyRow taxonomy = createLightTaxonomyRow(input);
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//SET PARENTS
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// System.out.println("Convert Taxonomy parent for: "+taxonomy.getId());
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taxonomy.setParent(convertParentsLightTaxonomy(input));
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//SET BASE TAXON
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taxonomy.setBaseTaxonValue(NormalizeString.lowerCaseUpFirstChar(getTaxonomyValue(TaxonomySearchServiceImpl.BASETAXONOMY,taxonomy)));
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if(taxonomy.getParents()!=null && taxonomy.getParents().size()>0)
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taxonomy.setParentID(""+taxonomy.getParents().get(0).getId());
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return taxonomy;
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}
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protected LightTaxonomyRow createLightTaxonomyRow(TaxonomyItem input) throws Exception{
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LightTaxonomyRow tax = new LightTaxonomyRow(id++);
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if(input.getId()!=null){
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tax.setServiceId(input.getId());
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}
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if(input.getProvider()!=null && !input.getProvider().isEmpty()){
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tax.setDataProviderId(input.getProvider());
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tax.setDataProviderName(input.getProvider());
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}else{
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tax.setDataProviderId(ConstantsSpeciesDiscovery.NOT_FOUND);
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tax.setDataProviderName(ConstantsSpeciesDiscovery.NOT_FOUND);
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}
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if(input.getRank()!=null && !input.getRank().isEmpty()){
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tax.setRank(NormalizeString.lowerCaseUpFirstChar(input.getRank()));
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}else{
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tax.setRank(ConstantsSpeciesDiscovery.NOT_FOUND);
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}
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if(input.getScientificName()!=null && !input.getScientificName().isEmpty()){
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tax.setName(input.getScientificName());
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}else{
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tax.setName(ConstantsSpeciesDiscovery.NOT_FOUND);
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}
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if(input.getStatus()!=null){
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if(input.getStatus().getRefId()!=null && !input.getStatus().getRefId().isEmpty()){
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tax.setStatusRefId(input.getStatus().getRefId());
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}else{
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tax.setStatusRefId("");
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}
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if(input.getStatus().getStatusAsString()!=null && !input.getStatus().getStatusAsString().isEmpty()){
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tax.setStatusRemarks(input.getStatus().getStatusAsString());
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}else{
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tax.setStatusRemarks(ConstantsSpeciesDiscovery.NOT_FOUND);
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}
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if(input.getStatus().getStatus()!=null){
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if(input.getStatus().getStatus().name()!=null && !input.getStatus().getStatus().name().isEmpty()){
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tax.setStatusName(input.getStatus().getStatus().name());
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}else{
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tax.setStatusName(ConstantsSpeciesDiscovery.NOT_FOUND);
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}
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}
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}
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return tax;
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}
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protected TaxonomyRow createTaxonomyRow(TaxonomyItem input) throws Exception{
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TaxonomyRow tax = new TaxonomyRow(id++);
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//Retrieve Properties
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List<ElementProperty> listProperties = input.getProperties();
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//Fill properties
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if(listProperties!=null){
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for (ElementProperty elementProperty : listProperties)
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tax.getProperties().add(new ItemParameter(elementProperty.getName(), elementProperty.getValue()));
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tax.setExistsProperties(true);
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}
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if(input.getId()!=null){
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tax.setServiceId(input.getId());
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}
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if(input.getScientificNameAuthorship()!=null && !input.getScientificNameAuthorship().isEmpty()){
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tax.setScientificNameAuthorship(input.getScientificNameAuthorship());
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}
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else
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tax.setScientificNameAuthorship(ConstantsSpeciesDiscovery.NOT_FOUND);
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if(input.getCredits()!=null && !input.getCredits().isEmpty()){
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tax.setCredits(input.getCredits());
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}
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else
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tax.setCredits(ConstantsSpeciesDiscovery.NOT_FOUND);
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if(input.getLsid()!=null && !input.getLsid().isEmpty()){
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tax.setLsid(input.getLsid());
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}
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else
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tax.setLsid(ConstantsSpeciesDiscovery.NOT_FOUND);
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if(input.getProvider()!=null && !input.getProvider().isEmpty()){
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tax.setDataProviderId(input.getProvider());
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tax.setDataProviderName(input.getProvider());
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}else{
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tax.setDataProviderId(ConstantsSpeciesDiscovery.NOT_FOUND);
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tax.setDataProviderName(ConstantsSpeciesDiscovery.NOT_FOUND);
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}
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if(input.getCitation()!=null && !input.getCitation().isEmpty()){
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tax.setDataSetCitation(input.getCitation());
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}else{
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tax.setDataSetCitation(ConstantsSpeciesDiscovery.NOT_FOUND);
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}
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if(input.getRank()!=null && !input.getRank().isEmpty()){
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tax.setRank(NormalizeString.lowerCaseUpFirstChar(input.getRank()));
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}else{
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tax.setRank(ConstantsSpeciesDiscovery.NOT_FOUND);
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}
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if(input.getScientificName()!=null && !input.getScientificName().isEmpty()){
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tax.setName(input.getScientificName());
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}else{
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tax.setName(ConstantsSpeciesDiscovery.NOT_FOUND);
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}
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if(input.getStatus()!=null){
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if(input.getStatus().getRefId()!=null && !input.getStatus().getRefId().isEmpty()){
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tax.setStatusRefId(input.getStatus().getRefId());
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}else{
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tax.setStatusRefId("");
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}
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if(input.getStatus().getStatusAsString()!=null && !input.getStatus().getStatusAsString().isEmpty()){
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tax.setStatusRemarks(input.getStatus().getStatusAsString());
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}else{
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tax.setStatusRemarks(ConstantsSpeciesDiscovery.NOT_FOUND);
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}
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if(input.getStatus().getStatus()!=null){
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if(input.getStatus().getStatus().name()!=null && !input.getStatus().getStatus().name().isEmpty()){
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tax.setStatusName(input.getStatus().getStatus().name());
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}else{
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tax.setStatusName(ConstantsSpeciesDiscovery.NOT_FOUND);
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}
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}
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}
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if(input.getModified()!=null){
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tax.setDateModified(input.getModified().getTime().toString());
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}
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if(input.getCommonNames()!=null){
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for (org.gcube.data.spd.model.CommonName commonName : input.getCommonNames()){
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CommonName com = new CommonName(commonName.getName(), commonName.getLanguage(), tax.getId());
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// DaoSession.createOrUpdateCommonName(com, session);
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tax.getCommonNames().add(com);
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tax.setExistsCommonName(true);
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}
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}
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// System.out.println("convert completed: " +tax);
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return tax;
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}
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private String getTaxonomyValue(String rank, TaxonomyRow taxon){
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List<TaxonomyRow> listTaxonomy = taxon.getParents();
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for (TaxonomyRow taxonomyRow : listTaxonomy) {
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if(taxonomyRow.getRank().compareToIgnoreCase(rank)==0)
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return taxonomyRow.getName();
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}
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return TaxonomySearchServiceImpl.TAXONOMYUNKNOWN;
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}
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private String getTaxonomyValue(String rank, LightTaxonomyRow taxon){
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List<LightTaxonomyRow> listTaxonomy = taxon.getParents();
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for (LightTaxonomyRow taxonomyRow : listTaxonomy) {
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if(taxonomyRow.getRank().compareToIgnoreCase(rank)==0)
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return taxonomyRow.getName();
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}
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return TaxonomySearchServiceImpl.TAXONOMYUNKNOWN;
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}
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protected List<LightTaxonomyRow> convertParentsLightTaxonomy(TaxonomyItem taxon) throws Exception
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{
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if (taxon == null) return null;
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List<LightTaxonomyRow> listTaxonomy = new ArrayList<LightTaxonomyRow>();
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TaxonomyItem parent = taxon.getParent();
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int i=0;
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while(parent!=null){
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LightTaxonomyRow row = createLightTaxonomyRow(parent);
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row.setParent(true);
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row.setParentIndex(i++);
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// System.out.println("Insert Taxonomy parent id: "+row.getId() + ", row.getParentIndex: "+row.getParentIndex());
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listTaxonomy.add(row);
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parent = parent.getParent();
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}
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return listTaxonomy;
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}
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protected List<TaxonomyRow> convertParentsTaxonomy(TaxonomyItem taxon) throws Exception
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{
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if (taxon == null) return null;
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List<TaxonomyRow> listTaxonomy = new ArrayList<TaxonomyRow>();
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TaxonomyItem parent = taxon.getParent();
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int i=0;
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while(parent!=null){
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TaxonomyRow row = createTaxonomyRow(parent);
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row.setParent(true);
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row.setParentIndex(i++);
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// System.out.println("Insert Taxonomy parent id: "+row.getId() + ", row.getParentIndex: "+row.getParentIndex());
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listTaxonomy.add(row);
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parent = parent.getParent();
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}
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return listTaxonomy;
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}
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}
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