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package eu.etaxonomy.cdm;
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import java.io.FileInputStream;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.io.InputStream;
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import java.net.URI;
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import java.net.URISyntaxException;
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import java.util.ArrayList;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.apache.poi.hssf.usermodel.HSSFCell;
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import org.apache.poi.hssf.usermodel.HSSFRow;
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import org.apache.poi.hssf.usermodel.HSSFSheet;
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import org.apache.poi.hssf.usermodel.HSSFWorkbook;
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import org.apache.poi.poifs.filesystem.POIFSFileSystem;
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import eu.etaxonomy.cdm.api.application.CdmApplicationController;
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import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
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import eu.etaxonomy.cdm.api.service.IDescriptionService;
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import eu.etaxonomy.cdm.api.service.IFeatureTreeService;
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import eu.etaxonomy.cdm.api.service.IIdentifiableEntityService;
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import eu.etaxonomy.cdm.api.service.IReferenceService;
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import eu.etaxonomy.cdm.api.service.ITaxonService;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.api.service.IVocabularyService;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.common.AccountStore;
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import eu.etaxonomy.cdm.database.CdmDataSource;
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import eu.etaxonomy.cdm.database.DatabaseTypeEnum;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.LanguageString;
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import eu.etaxonomy.cdm.model.common.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.FeatureNode;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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import eu.etaxonomy.cdm.model.description.Modifier;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.description.StateData;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.reference.IReference;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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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.persistence.dao.common.IDefinedTermDao;
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public class UseImport {
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public static final Logger logger = Logger.getLogger(UseImport.class);
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public void UseImport() {
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}
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public static ICdmDataSource dataSource() {
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DatabaseTypeEnum dbType = DatabaseTypeEnum.MySQL;
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String cdmServer = "localhost";
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String cdmDB = "palm_use_cdm_db";
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String cdmUserName = "root";
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return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, null);
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}
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private static ICdmDataSource makeDestination(DatabaseTypeEnum dbType,
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String cdmServer, String cdmDB, int port, String cdmUserName,
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String pwd) {
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// establish connection
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pwd = AccountStore.readOrStorePassword(cdmServer, cdmDB, cdmUserName,
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pwd);
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ICdmDataSource destination;
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if (dbType.equals(DatabaseTypeEnum.MySQL)) {
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destination = CdmDataSource.NewMySqlInstance(cdmServer, cdmDB,
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port, cdmUserName, pwd, null);
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} else if (dbType.equals(DatabaseTypeEnum.PostgreSQL)) {
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destination = CdmDataSource.NewPostgreSQLInstance(cdmServer, cdmDB,
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port, cdmUserName, pwd, null);
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} else {
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// TODO others
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throw new RuntimeException("Unsupported DatabaseType");
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}
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return destination;
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}
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public boolean importFromExcelSS(String xlsPath) {
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boolean success = true;
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CdmApplicationController applicationController = CdmApplicationController.NewInstance(dataSource());
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ConversationHolder conversation = applicationController.NewConversation();
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conversation.startTransaction();
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ITaxonService service = applicationController.getTaxonService();
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ITermService termService = applicationController.getTermService();
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IDescriptionService descService = applicationController.getDescriptionService();
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IReferenceService referenceService = applicationController.getReferenceService();
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InputStream inputStream = null;
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try {
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inputStream = new FileInputStream(xlsPath);
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} catch (FileNotFoundException e) {
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success = false;
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System.out.println("File not found in the specified path.");
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e.printStackTrace();
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}
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POIFSFileSystem fileSystem = null;
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try {
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fileSystem = new POIFSFileSystem(inputStream);
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HSSFWorkbook workBook = new HSSFWorkbook(fileSystem);
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HSSFSheet sheet = workBook.getSheetAt(0);
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Iterator rows = sheet.rowIterator();
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// Iterator rows = sheet.rowIterator();
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ArrayList<ArrayList<String>> lstUpdates = new ArrayList<ArrayList<String>>();
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Set<Integer> lstTaxonIDs = new HashSet<Integer>();
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//Set<Integer> lstTaxonIDs;
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while (rows.hasNext()) {
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HSSFRow row = (HSSFRow) rows.next();
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System.out.println("Row No.: " + row.getRowNum());
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Iterator cells = row.cellIterator();
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ArrayList<String> lstTaxon = new ArrayList<String>();
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while (cells.hasNext()) {
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HSSFCell cell = (HSSFCell) cells.next();
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int intCellType = cell.getCellType();
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switch (intCellType) {
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case 0:
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int cellValue = (int) cell.getNumericCellValue();
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lstTaxon.add(Integer.toString(cellValue));
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break;
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case 1:
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lstTaxon.add(cell.getStringCellValue());
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break;
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}
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}
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lstUpdates.add(lstTaxon);
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lstTaxonIDs.add(Integer.parseInt(lstTaxon.get(0)));
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}
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List<TaxonBase> taxa = service.findTaxaByID(lstTaxonIDs);
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for(TaxonBase idTaxa : taxa) {
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//System.out.println(idTaxa.getUuid().toString());
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System.out.println(idTaxa.getName());
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}
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MarkerType useMarkerType = (MarkerType) termService.find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
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Marker useMarker = Marker.NewInstance(useMarkerType, true);
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for (ArrayList<String> lstUpdate : lstUpdates) {
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System.out.println("-----------------------------------------------: " + lstUpdate.get(1));
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String idTaxonToUpdate = lstUpdate.get(1);
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TaxonDescription newUseDescription = TaxonDescription.NewInstance();
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newUseDescription.addMarker(useMarker);
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newUseDescription.setTitleCache(lstUpdate.get(2));
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Reference citation = ReferenceFactory.newGeneric();
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Team authorTeam = Team.NewInstance();
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authorTeam.setTitleCache(lstUpdate.get(3));
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citation.setAuthorTeam(authorTeam);
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citation.setTitle(lstUpdate.get(4));
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//citation.
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TimePeriod year = TimePeriod.NewInstance(Integer.parseInt(lstUpdate.get(5)));
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citation.setDatePublished(year);
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citation.setTitleCache(lstUpdate.get(6));
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//citation.
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for(TaxonBase taxon : taxa) {
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String taxonUUID = taxon.getUuid().toString();
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//System.out.println(idTaxonToUpdate + "|" + taxonUUID);
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if(idTaxonToUpdate.equals(taxonUUID)) {
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logger.info("Processing Taxn " + taxon.getTitleCache() + " with UUID: " + taxon.getUuid());
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if(taxon.isInstanceOf(Synonym.class)) {
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Taxon bestCandidate = null;
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Synonym synonym = CdmBase.deproxy(taxon, Synonym.class);
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Set<Taxon> acceptetdCandidates = synonym.getAcceptedTaxa();
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if(!acceptetdCandidates.isEmpty()){
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bestCandidate = acceptetdCandidates.iterator().next();
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if(acceptetdCandidates.size() == 1){
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logger.info(acceptetdCandidates.size() + " Accepted taxa found for synonym " + taxon.getTitleCache() + ", using first one: " + bestCandidate.getTitleCache());
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Set<TaxonDescription> taxonDescriptions = bestCandidate.getDescriptions();
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if(!taxonDescriptions.isEmpty()) {
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TaxonDescription firstDescription = taxonDescriptions.iterator().next();
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//newUseSummary.addSource(null, null, citation, null);
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//firstDescription.addElement(newUseSummary);
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}
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else {
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logger.warn("No description container for: " + bestCandidate.getName());
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}
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} else {
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logger.info("using accepted Taxon " + bestCandidate.getTitleCache() + "for synonym " + taxon.getTitleCache());
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//List<DescriptionElementBase> descriptionElements = descService.getDescriptionElementsForTaxon((Taxon) bestCandidate, null, null, null, null, null);
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Set<TaxonDescription> taxonDescriptions = bestCandidate.getDescriptions();
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if(!taxonDescriptions.isEmpty()) {
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TaxonDescription firstDescription = taxonDescriptions.iterator().next();
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//newUseSummary.addSource(null, null, citation, null);
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//firstDescription.addElement(newUseSummary);
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}
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else {
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logger.warn("No description container for: " + bestCandidate.getName());
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}
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}
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}
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}
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else {
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Taxon taxonAccepted = (Taxon) taxon;
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/*Set<TaxonDescription> taxonDescriptions = taxonAccepted.getDescriptions();
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if(!taxonDescriptions.isEmpty()) {
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TaxonDescription firstDescription = taxonDescriptions.iterator().next();
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//newUseSummary.addSource(null, null, citation, null);
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//firstDescription.addElement(newUseSummary);
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}
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else {
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logger.warn("No description container for: " + taxonAccepted.getName());
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}*/
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taxonAccepted.addDescription(newUseDescription);
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service.saveOrUpdate(taxonAccepted);
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}
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}
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}
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}
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conversation.commit(false);
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} catch (IOException e) {
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success = false;
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e.printStackTrace();
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}
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return success;
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}
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private boolean loadUses() {
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boolean success = true;
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//String xslUseSummaryPathString = "C://workspace//Matched_UseSummary_referenceIdTaxEd_TaxonName.xls";
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String xslUseSummaryPathString = "C://workspace//testUseSummaries.xls";
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//String xslUseSummaryPathString = "//Users//alextheys//Projects//CDM_Trunk//Palm_Use_Data_Extension//UseImport//Matched_UseSummary_referenceIdTaxEd_TaxonName.xls";
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//String xslUseRecordPathString = "C://workspace//UseRecordTerms_UseSummaryId.xls";
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String xslUseRecordPathString = "C://workspace//testUseRecords.xls";
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//String xslUseRecordPathString = "C://workspace//test_useRecord.xls";
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//String xslUseRecordPathString = "//Users//alextheys//Projects//CDM_Trunk//Palm_Use_Data_Extension//UseImport//UseRecordTerms_UseSummaryId.xls";
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InputStream inputStream = null;
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CdmApplicationController applicationController = CdmApplicationController.NewInstance(dataSource());
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ConversationHolder conversation = applicationController.NewConversation();
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conversation.startTransaction();
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ITaxonService taxonService = applicationController.getTaxonService();
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ITermService termService = applicationController.getTermService();
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IDescriptionService descService = applicationController.getDescriptionService();
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IReferenceService referenceService = applicationController.getReferenceService();
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ArrayList<ArrayList<String>> lstUseSummaries = loadSpreadsheet(xslUseSummaryPathString);
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ArrayList<ArrayList<String>> lstUseRecords = loadSpreadsheet(xslUseRecordPathString);
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MarkerType useMarkerType = (MarkerType) termService.find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
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Feature featureUseRecord = (Feature) termService.find(UUID.fromString("8125a59d-b4d5-4485-89ea-67306297b599"));
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Feature featureUseSummary = (Feature) termService.find(UUID.fromString("6acb0348-c070-4512-a37c-67bcac016279"));
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Pager<DefinedTermBase> notAvailModPager = (Pager<DefinedTermBase> ) termService.findByTitle(Modifier.class, "N/A", null, null, null, null, null, null);
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Pager<DefinedTermBase> notAvailStatePager = (Pager<DefinedTermBase> ) termService.findByTitle(State.class, "N/A", null, null, null, null, null, null);
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Modifier notAvailMod = (Modifier) notAvailModPager.getRecords().get(0);
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State notAvailState = (State) notAvailStatePager.getRecords().get(0);
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int i = 0;
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int j = 0;
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try {
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for (ArrayList<String> lstUseSummary : lstUseSummaries) {
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i++;
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String idTaxonToUpdate = lstUseSummary.get(3);
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TaxonBase taxon = taxonService.find(UUID.fromString(idTaxonToUpdate));
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if (taxon != null) {
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TaxonDescription newUseDescription = TaxonDescription.NewInstance();
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Marker useMarker = Marker.NewInstance(useMarkerType, true);
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newUseDescription.addMarker(useMarker);
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Reference useReference = null;
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Pager<Reference> reference = referenceService.findByTitle(Reference.class, lstUseSummary.get(5), null, null, null, null, null, null);
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if(reference.getCount() == 0) {
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System.out.println("Reference title: " + lstUseSummary.get(5) + " not found.");
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} else if(reference.getCount() > 0 ) {
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useReference = reference.getRecords().get(0);
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}
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IdentifiableSource source =IdentifiableSource.NewInstance(useReference, null);
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source.setOriginalNameString(taxon.getName().toString());
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newUseDescription.addSource(source);
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TextData useSummary = TextData.NewInstance(featureUseSummary);
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LanguageString languageString = LanguageString.NewInstance(lstUseSummary.get(1), Language.ENGLISH());
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useSummary.putText(languageString);
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descService.saveDescriptionElement(useSummary);
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newUseDescription.addElement(useSummary);
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for (ArrayList<String> lstUseRecord : lstUseRecords) {
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j++;
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//System.out.println("Processing UseSummary#: " + i + " ID:" + lstUseSummary.get(0) + "UseRecord: " + lstUseRecord.get(1));
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if(lstUseSummary.get(0).equals(lstUseRecord.get(0))) {
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CategoricalData useRecord = CategoricalData.NewInstance();
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useRecord.setFeature(featureUseRecord);
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String modifyingText = "";
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if(lstUseRecord.get(3) != null && lstUseRecord.get(3).length() > 0) {
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Pager<DefinedTermBase> useCategoryPager = termService.findByTitle(State.class, lstUseRecord.get(3), null, null, null, null, null, null);
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State useCategory = null;
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if(useCategoryPager.getCount() > 0) {
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useCategory = (State) useCategoryPager.getRecords().get(0);
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} else {
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useCategory = notAvailState;
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}
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StateData stateCatData = StateData.NewInstance(useCategory);
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stateCatData.setState(useCategory);
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stateCatData.putModifyingText(Language.ENGLISH(), "Use Category");
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modifyingText += useCategory.toString() + ";";
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useRecord.addState(stateCatData);
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//useRecord.addState(stateData);
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} else {
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State useCategory = notAvailState;
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StateData stateCatData = StateData.NewInstance(useCategory);
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stateCatData.setState(useCategory);
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stateCatData.putModifyingText(Language.ENGLISH(), "Use Category");
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modifyingText += useCategory.toString() + ";";
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useRecord.addState(stateCatData);
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}
|
|
350 |
|
|
351 |
if(lstUseRecord.get(4) != null && lstUseRecord.get(4).length() > 0) {
|
|
352 |
Pager<DefinedTermBase> useSubCategoryPager = termService.findByTitle(State.class, lstUseRecord.get(4), null, null, null, null, null, null);
|
|
353 |
State useSubCategory = null;
|
|
354 |
if(useSubCategoryPager.getCount() > 0) {
|
|
355 |
useSubCategory = (State) useSubCategoryPager.getRecords().get(0);
|
|
356 |
|
|
357 |
} else {
|
|
358 |
useSubCategory = notAvailState;
|
|
359 |
}
|
|
360 |
StateData stateSubCatData = StateData.NewInstance(useSubCategory);
|
|
361 |
stateSubCatData.setState(useSubCategory);
|
|
362 |
stateSubCatData.putModifyingText(Language.ENGLISH(), "Use SubCategory");
|
|
363 |
modifyingText += useSubCategory.toString() + ";";
|
|
364 |
useRecord.addState(stateSubCatData);
|
|
365 |
|
|
366 |
}
|
|
367 |
else {
|
|
368 |
State useSubCategory = notAvailState;
|
|
369 |
StateData stateSubCatData = StateData.NewInstance(useSubCategory);
|
|
370 |
stateSubCatData.setState(useSubCategory);
|
|
371 |
stateSubCatData.putModifyingText(Language.ENGLISH(), "Use SubCategory");
|
|
372 |
modifyingText += useSubCategory.toString() + ";";
|
|
373 |
useRecord.addState(stateSubCatData);
|
|
374 |
|
|
375 |
}
|
|
376 |
if(lstUseRecord.get(5) != null && lstUseRecord.get(5).length() > 0) {
|
|
377 |
Pager<DefinedTermBase> countryPager = termService.findByTitle(Modifier.class, lstUseRecord.get(5), null, null, null, null, null, null);
|
|
378 |
Modifier country = null;
|
|
379 |
if(countryPager.getCount() > 0) {
|
|
380 |
country = (Modifier) countryPager.getRecords().get(0);
|
|
381 |
} else {
|
|
382 |
country = notAvailMod;
|
|
383 |
}
|
|
384 |
modifyingText += country.toString() + ";";
|
|
385 |
useRecord.addModifier(country);
|
|
386 |
} else {
|
|
387 |
Modifier country = notAvailMod;
|
|
388 |
modifyingText += country.toString() + ";";
|
|
389 |
useRecord.addModifier(country);
|
|
390 |
}
|
|
391 |
|
|
392 |
if(lstUseRecord.get(6) != null && lstUseRecord.get(6).length() > 0) {
|
|
393 |
Pager<DefinedTermBase> plantPartPager = termService.findByTitle(Modifier.class, lstUseRecord.get(6), null, null, null, null, null, null);
|
|
394 |
Modifier plantPart = null;
|
|
395 |
if(plantPartPager.getCount() > 0) {
|
|
396 |
plantPart = (Modifier) plantPartPager.getRecords().get(0);
|
|
397 |
} else {
|
|
398 |
plantPart = notAvailMod;
|
|
399 |
}
|
|
400 |
modifyingText += plantPart.toString() + ";";
|
|
401 |
useRecord.addModifier(plantPart);
|
|
402 |
}else {
|
|
403 |
Modifier plantPart = notAvailMod;
|
|
404 |
modifyingText += plantPart.toString() + ";";
|
|
405 |
useRecord.addModifier(plantPart);
|
|
406 |
}
|
|
407 |
if(lstUseRecord.get(7) != null && lstUseRecord.get(7).length() > 0) {
|
|
408 |
Pager<DefinedTermBase> humanGroupPager = termService.findByTitle(Modifier.class, lstUseRecord.get(7), null, null, null, null, null, null);
|
|
409 |
Modifier humanGroup = null;
|
|
410 |
if(humanGroupPager.getCount() > 0) {
|
|
411 |
humanGroup = (Modifier) humanGroupPager.getRecords().get(0);
|
|
412 |
} else {
|
|
413 |
humanGroup = notAvailMod;
|
|
414 |
}
|
|
415 |
modifyingText += humanGroup.toString() + ";";
|
|
416 |
useRecord.addModifier(humanGroup);
|
|
417 |
} else {
|
|
418 |
Modifier humanGroup = notAvailMod;
|
|
419 |
modifyingText += humanGroup.toString() + ";";
|
|
420 |
useRecord.addModifier(humanGroup);
|
|
421 |
}
|
|
422 |
if(lstUseRecord.get(8) != null && lstUseRecord.get(8).length() > 0) {
|
|
423 |
Pager<DefinedTermBase> ethnicGroupPager = termService.findByTitle(Modifier.class, lstUseRecord.get(8), null, null, null, null, null, null);
|
|
424 |
Modifier ethnicGroup = null;
|
|
425 |
if(ethnicGroupPager.getCount() > 0) {
|
|
426 |
ethnicGroup = (Modifier) ethnicGroupPager.getRecords().get(0);
|
|
427 |
modifyingText += ethnicGroup.toString() + ";";
|
|
428 |
} else {
|
|
429 |
ethnicGroup = notAvailMod;
|
|
430 |
}
|
|
431 |
useRecord.addModifier(ethnicGroup);
|
|
432 |
}
|
|
433 |
else {
|
|
434 |
Modifier ethnicGroup = notAvailMod;
|
|
435 |
modifyingText += ethnicGroup.toString() + ";";
|
|
436 |
useRecord.addModifier(ethnicGroup);
|
|
437 |
}
|
|
438 |
useRecord.putModifyingText(Language.ENGLISH(), modifyingText);
|
|
439 |
descService.saveDescriptionElement(useRecord);
|
|
440 |
newUseDescription.addElement(useRecord);
|
|
441 |
}
|
|
442 |
}
|
|
443 |
|
|
444 |
|
|
445 |
|
|
446 |
if (taxon.isInstanceOf(Synonym.class)){
|
|
447 |
Taxon bestCandidate = null;
|
|
448 |
Synonym synonym = CdmBase.deproxy(taxon, Synonym.class);
|
|
449 |
Set<Taxon> acceptetdCandidates = synonym.getAcceptedTaxa();
|
|
450 |
if(!acceptetdCandidates.isEmpty()){
|
|
451 |
bestCandidate = acceptetdCandidates.iterator().next();
|
|
452 |
if(acceptetdCandidates.size() == 1){
|
|
453 |
logger.info(acceptetdCandidates.size() + " Accepted taxa found for synonym " + taxon.getTitleCache() + ", using first one: " + bestCandidate.getTitleCache());
|
|
454 |
bestCandidate.addDescription(newUseDescription);
|
|
455 |
taxonService.saveOrUpdate(bestCandidate);
|
|
456 |
conversation.commit();
|
|
457 |
}
|
|
458 |
else {
|
|
459 |
logger.info("using accepted Taxon " + bestCandidate.getTitleCache() + "for synonym " + taxon.getTitleCache());
|
|
460 |
bestCandidate.addDescription(newUseDescription);
|
|
461 |
taxonService.saveOrUpdate(bestCandidate);
|
|
462 |
conversation.commit();
|
|
463 |
}
|
|
464 |
}
|
|
465 |
} else {
|
|
466 |
Taxon taxonAccepted = (Taxon) taxon;
|
|
467 |
taxonAccepted.addDescription(newUseDescription);
|
|
468 |
taxonService.saveOrUpdate(taxonAccepted);
|
|
469 |
conversation.commit();
|
|
470 |
}
|
|
471 |
}
|
|
472 |
else {
|
|
473 |
System.out.println("Processing UseSummary#: " + i + " ID:" + lstUseSummary.get(0));
|
|
474 |
}
|
|
475 |
}
|
|
476 |
|
|
477 |
conversation.close();
|
|
478 |
applicationController.close();
|
|
479 |
|
|
480 |
} catch (Exception e) {
|
|
481 |
success = false;
|
|
482 |
e.printStackTrace();
|
|
483 |
}
|
|
484 |
return success;
|
|
485 |
|
|
486 |
}
|
|
487 |
|
|
488 |
//Completed and tested!
|
|
489 |
private boolean loadTerms() {
|
|
490 |
boolean success = true;
|
|
491 |
|
|
492 |
String xslPathString = "C://workspace//terms.xls";
|
|
493 |
//String xslPathString = "//Users//alextheys//Projects//CDM_Trunk//Palm_Use_Data_Extension//UseImport//terms.xls";
|
|
494 |
|
|
495 |
CdmApplicationController applicationController = CdmApplicationController.NewInstance(dataSource());
|
|
496 |
ConversationHolder conversation = applicationController.NewConversation();
|
|
497 |
conversation.startTransaction();
|
|
498 |
|
|
499 |
ITaxonService service = applicationController.getTaxonService();
|
|
500 |
ITermService termService = applicationController.getTermService();
|
|
501 |
IVocabularyService vocabularyService = applicationController.getVocabularyService();
|
|
502 |
IReferenceService referenceService = applicationController.getReferenceService();
|
|
503 |
|
|
504 |
TermVocabulary<State> stateVocabulary = (TermVocabulary<State>) vocabularyService.find(UUID.fromString("67430d7c-fd43-4e9d-af5e-d0dca3f74931"));
|
|
505 |
TermVocabulary<Modifier> countryVocabulary = (TermVocabulary<Modifier>) vocabularyService.find(UUID.fromString("116c51f1-e63a-46f7-a258-e1149a42868b"));
|
|
506 |
TermVocabulary<Modifier> plantPartVocabulary = (TermVocabulary<Modifier>) vocabularyService.find(UUID.fromString("369914fe-d54b-4063-99ce-abc81d30ad35"));
|
|
507 |
TermVocabulary<Modifier> humanGroupVocabulary = (TermVocabulary<Modifier>) vocabularyService.find(UUID.fromString("ca46cea5-bdf7-438d-9cd8-e2793d2178dc"));
|
|
508 |
|
|
509 |
IDescriptionService descService = applicationController.getDescriptionService();
|
|
510 |
InputStream inputStream = null;
|
|
511 |
|
|
512 |
try {
|
|
513 |
inputStream = new FileInputStream(xslPathString);
|
|
514 |
|
|
515 |
} catch (FileNotFoundException e) {
|
|
516 |
success = false;
|
|
517 |
System.out.println("File not found in the specified path.");
|
|
518 |
e.printStackTrace();
|
|
519 |
}
|
|
520 |
|
|
521 |
POIFSFileSystem fileSystem = null;
|
|
522 |
|
|
523 |
try {
|
|
524 |
fileSystem = new POIFSFileSystem(inputStream);
|
|
525 |
|
|
526 |
HSSFWorkbook workBook = new HSSFWorkbook(fileSystem);
|
|
527 |
HSSFSheet sheet = workBook.getSheetAt(0);
|
|
528 |
Iterator rows = sheet.rowIterator();
|
|
529 |
|
|
530 |
ArrayList<ArrayList<String>> lstUpdates = new ArrayList<ArrayList<String>>();
|
|
531 |
|
|
532 |
while (rows.hasNext()) {
|
|
533 |
|
|
534 |
HSSFRow row = (HSSFRow) rows.next();
|
|
535 |
System.out.println("Row No.: " + row.getRowNum());
|
|
536 |
Iterator cells = row.cellIterator();
|
|
537 |
ArrayList<String> lstTerms = new ArrayList<String>();
|
|
538 |
while (cells.hasNext()) {
|
|
539 |
HSSFCell cell = (HSSFCell) cells.next();
|
|
540 |
|
|
541 |
int intCellType = cell.getCellType();
|
|
542 |
switch (intCellType) {
|
|
543 |
case 0:
|
|
544 |
int cellValue = (int) cell.getNumericCellValue();
|
|
545 |
lstTerms.add(Integer.toString(cellValue));
|
|
546 |
break;
|
|
547 |
case 1:
|
|
548 |
lstTerms.add(cell.getStringCellValue());
|
|
549 |
break;
|
|
550 |
}
|
|
551 |
}
|
|
552 |
lstUpdates.add(lstTerms);
|
|
553 |
//lstTaxonIDs.add(Integer.parseInt(lstTaxon.get(0)));
|
|
554 |
}
|
|
555 |
for (ArrayList<String> lstUpdate : lstUpdates) {
|
|
556 |
int termType = Integer.parseInt(lstUpdate.get(0));
|
|
557 |
switch (termType) {
|
|
558 |
//Case 0 = UseCategory
|
|
559 |
case 0:
|
|
560 |
Pager<State> useCategoryPager = termService.findByRepresentationText(lstUpdate.get(1), State.class, null, null);
|
|
561 |
State useCategory = null;
|
|
562 |
State useSubCat = null;
|
|
563 |
if (useCategoryPager.getCount()>0) {
|
|
564 |
useCategory = useCategoryPager.getRecords().get(0);
|
|
565 |
}
|
|
566 |
if(useCategory == null) {
|
|
567 |
useCategory = State.NewInstance(lstUpdate.get(1), lstUpdate.get(1), null);
|
|
568 |
}
|
|
569 |
//State useCategory = (State) termService.
|
|
570 |
if(lstUpdate.size() > 2) {
|
|
571 |
useSubCat = State.NewInstance(lstUpdate.get(2), lstUpdate.get(2), null);
|
|
572 |
useCategory.addIncludes(useSubCat);
|
|
573 |
}
|
|
574 |
stateVocabulary.addTerm(useCategory);
|
|
575 |
vocabularyService.saveOrUpdate(stateVocabulary);
|
|
576 |
conversation.commit(true);
|
|
577 |
break;
|
|
578 |
|
|
579 |
//case 1: = HumanGroup
|
|
580 |
case 1:
|
|
581 |
Pager<Modifier> humanGroupPager = termService.findByRepresentationText(lstUpdate.get(1), Modifier.class, null, null);
|
|
582 |
|
|
583 |
Modifier humanGroup = null;
|
|
584 |
Modifier ethnicGroup = null;
|
|
585 |
if(humanGroupPager.getCount()>0) {
|
|
586 |
humanGroup = humanGroupPager.getRecords().get(0);
|
|
587 |
}
|
|
588 |
|
|
589 |
if(humanGroup == null) {
|
|
590 |
humanGroup = Modifier.NewInstance(lstUpdate.get(1), lstUpdate.get(1), null);
|
|
591 |
}
|
|
592 |
|
|
593 |
if(lstUpdate.size() >2) {
|
|
594 |
ethnicGroup = Modifier.NewInstance(lstUpdate.get(2), lstUpdate.get(2), null);
|
|
595 |
humanGroup.addIncludes(ethnicGroup);
|
|
596 |
}
|
|
597 |
humanGroupVocabulary.addTerm(humanGroup);
|
|
598 |
vocabularyService.saveOrUpdate(humanGroupVocabulary);
|
|
599 |
conversation.commit(true);
|
|
600 |
break;
|
|
601 |
|
|
602 |
//case 2: = Country
|
|
603 |
case 2:
|
|
604 |
Pager<Modifier> countryPager = termService.findByRepresentationText(lstUpdate.get(1), Modifier.class, null, null);
|
|
605 |
Modifier country = null;
|
|
606 |
|
|
607 |
if(countryPager.getCount()>0) {
|
|
608 |
country = countryPager.getRecords().get(0);
|
|
609 |
}
|
|
610 |
|
|
611 |
if(country == null) {
|
|
612 |
country = Modifier.NewInstance(lstUpdate.get(1), lstUpdate.get(1), null);
|
|
613 |
countryVocabulary.addTerm(country);
|
|
614 |
vocabularyService.saveOrUpdate(countryVocabulary);
|
|
615 |
}
|
|
616 |
conversation.commit(true);
|
|
617 |
break;
|
|
618 |
|
|
619 |
//case 3: //plantPart
|
|
620 |
case 3:
|
|
621 |
Pager<Modifier> plantPartPager = termService.findByRepresentationText(lstUpdate.get(1), Modifier.class, null, null);
|
|
622 |
Modifier plantPart = null;
|
|
623 |
|
|
624 |
if(plantPartPager.getCount()>0) {
|
|
625 |
plantPart = plantPartPager.getRecords().get(0);
|
|
626 |
}
|
|
627 |
|
|
628 |
if(plantPart == null) {
|
|
629 |
plantPart = Modifier.NewInstance(lstUpdate.get(1), lstUpdate.get(1), null);
|
|
630 |
plantPartVocabulary.addTerm(plantPart);
|
|
631 |
vocabularyService.saveOrUpdate(plantPartVocabulary);
|
|
632 |
}
|
|
633 |
conversation.commit(true);
|
|
634 |
break;
|
|
635 |
|
|
636 |
}
|
|
637 |
}
|
|
638 |
conversation.close();
|
|
639 |
applicationController.close();
|
|
640 |
|
|
641 |
} catch (IOException e) {
|
|
642 |
success = false;
|
|
643 |
e.printStackTrace();
|
|
644 |
}
|
|
645 |
return success;
|
|
646 |
|
|
647 |
}
|
|
648 |
|
|
649 |
private ArrayList<ArrayList<String>> loadSpreadsheet(String xslPathString) {
|
|
650 |
ArrayList<ArrayList<String>> lstUpdates = new ArrayList<ArrayList<String>>();
|
|
651 |
InputStream inputStream = null;
|
|
652 |
|
|
653 |
try {
|
|
654 |
inputStream = new FileInputStream(xslPathString);
|
|
655 |
|
|
656 |
} catch (FileNotFoundException e) {
|
|
657 |
System.out.println("File not found in the specified path.");
|
|
658 |
e.printStackTrace();
|
|
659 |
}
|
|
660 |
|
|
661 |
POIFSFileSystem fileSystem = null;
|
|
662 |
|
|
663 |
try {
|
|
664 |
fileSystem = new POIFSFileSystem(inputStream);
|
|
665 |
|
|
666 |
HSSFWorkbook workBook = new HSSFWorkbook(fileSystem);
|
|
667 |
HSSFSheet sheet = workBook.getSheetAt(0);
|
|
668 |
Iterator rows = sheet.rowIterator();
|
|
669 |
// Iterator rows = sheet.rowIterator();
|
|
670 |
//Set<Integer> lstTaxonIDs;
|
|
671 |
|
|
672 |
|
|
673 |
while (rows.hasNext()) {
|
|
674 |
|
|
675 |
HSSFRow row = (HSSFRow) rows.next();
|
|
676 |
System.out.println("Row No.: " + row.getRowNum());
|
|
677 |
Iterator cells = row.cellIterator();
|
|
678 |
ArrayList<String> lstTerms = new ArrayList<String>();
|
|
679 |
while (cells.hasNext()) {
|
|
680 |
HSSFCell cell = (HSSFCell) cells.next();
|
|
681 |
|
|
682 |
int intCellType = cell.getCellType();
|
|
683 |
switch (intCellType) {
|
|
684 |
case 0:
|
|
685 |
int cellValue = (int) cell.getNumericCellValue();
|
|
686 |
lstTerms.add(Integer.toString(cellValue));
|
|
687 |
break;
|
|
688 |
case 1:
|
|
689 |
lstTerms.add(cell.getStringCellValue());
|
|
690 |
break;
|
|
691 |
}
|
|
692 |
}
|
|
693 |
lstUpdates.add(lstTerms);
|
|
694 |
//lstTaxonIDs.add(Integer.parseInt(lstTaxon.get(0)));
|
|
695 |
}
|
|
696 |
} catch (IOException e) {
|
|
697 |
e.printStackTrace();
|
|
698 |
}
|
|
699 |
return lstUpdates;
|
|
700 |
}
|
|
701 |
|
|
702 |
|
|
703 |
private boolean setupNecessaryItems() {
|
|
704 |
boolean success = false;
|
|
705 |
CdmApplicationController applicationController = CdmApplicationController.NewInstance(dataSource());
|
|
706 |
ConversationHolder conversation = applicationController.NewConversation();
|
|
707 |
|
|
708 |
|
|
709 |
ITaxonService service = applicationController.getTaxonService();
|
|
710 |
ITermService termService = applicationController.getTermService();
|
|
711 |
IVocabularyService vocabularyService = applicationController.getVocabularyService();
|
|
712 |
IFeatureTreeService featureTreeService = applicationController.getFeatureTreeService();
|
|
713 |
|
|
714 |
MarkerType existingMarkertype = (MarkerType)termService.find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
|
|
715 |
Feature featureUseRecord = (Feature) termService.find(UUID.fromString("8125a59d-b4d5-4485-89ea-67306297b599"));
|
|
716 |
Feature featureUseSummary = (Feature) termService.find(UUID.fromString("6acb0348-c070-4512-a37c-67bcac016279"));
|
|
717 |
TermVocabulary<State> stateVocabulary = (TermVocabulary<State>) vocabularyService.find(UUID.fromString("67430d7c-fd43-4e9d-af5e-d0dca3f74931"));
|
|
718 |
TermVocabulary<Modifier> countryVocabulary = (TermVocabulary<Modifier>) vocabularyService.find(UUID.fromString("116c51f1-e63a-46f7-a258-e1149a42868b"));
|
|
719 |
TermVocabulary<Modifier> plantPartVocabulary = (TermVocabulary<Modifier>) vocabularyService.find(UUID.fromString("369914fe-d54b-4063-99ce-abc81d30ad35"));
|
|
720 |
TermVocabulary<Modifier> humanGroupVocabulary = (TermVocabulary<Modifier>) vocabularyService.find(UUID.fromString("ca46cea5-bdf7-438d-9cd8-e2793d2178dc"));
|
|
721 |
Pager<DefinedTermBase> notAvailModPager = (Pager<DefinedTermBase> ) termService.findByTitle(Modifier.class, "N/A", null, null, null, null, null, null);
|
|
722 |
Pager<DefinedTermBase> notAvailStatePager = (Pager<DefinedTermBase> ) termService.findByTitle(State.class, "N/A", null, null, null, null, null, null);
|
|
723 |
|
|
724 |
conversation.startTransaction();
|
|
725 |
if (existingMarkertype == null) {
|
|
726 |
existingMarkertype = MarkerType.NewInstance("use", "use", null);
|
|
727 |
existingMarkertype.setUuid( UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
|
|
728 |
TermVocabulary<MarkerType> markerTypeVocabulary = (TermVocabulary<MarkerType>)vocabularyService.find((UUID.fromString("19dffff7-e142-429c-a420-5d28e4ebe305")));
|
|
729 |
markerTypeVocabulary.addTerm(existingMarkertype);
|
|
730 |
vocabularyService.saveOrUpdate(markerTypeVocabulary);
|
|
731 |
conversation.commit(true);
|
|
732 |
}
|
|
733 |
if (stateVocabulary == null) {
|
|
734 |
|
|
735 |
URI termSourceUri = null;
|
|
736 |
try {
|
|
737 |
termSourceUri = new URI("eu.etaxonomy.cdm.model.description.State");
|
|
738 |
} catch (URISyntaxException e) {
|
|
739 |
e.printStackTrace();
|
|
740 |
}
|
|
741 |
stateVocabulary = TermVocabulary.NewInstance("Use Category", "Use Category", null, termSourceUri);
|
|
742 |
stateVocabulary.setUuid(UUID.fromString("67430d7c-fd43-4e9d-af5e-d0dca3f74931"));
|
|
743 |
vocabularyService.saveOrUpdate(stateVocabulary);
|
|
744 |
conversation.commit(true);
|
|
745 |
}
|
|
746 |
if (countryVocabulary == null) {
|
|
747 |
URI termSourceUri = null;
|
|
748 |
try {
|
|
749 |
termSourceUri = new URI("eu.etaxonomy.cdm.model.description.Modifier");
|
|
750 |
} catch (URISyntaxException e) {
|
|
751 |
e.printStackTrace();
|
|
752 |
}
|
|
753 |
countryVocabulary = TermVocabulary.NewInstance("Country", "Country", null, termSourceUri);
|
|
754 |
countryVocabulary.setUuid(UUID.fromString("116c51f1-e63a-46f7-a258-e1149a42868b"));
|
|
755 |
|
|
756 |
vocabularyService.saveOrUpdate(countryVocabulary);
|
|
757 |
conversation.commit(true);
|
|
758 |
}
|
|
759 |
if (plantPartVocabulary == null) {
|
|
760 |
URI termSourceUri = null;
|
|
761 |
try {
|
|
762 |
termSourceUri = new URI("eu.etaxonomy.cdm.model.description.Modifier");
|
|
763 |
} catch (URISyntaxException e) {
|
|
764 |
e.printStackTrace();
|
|
765 |
}
|
|
766 |
plantPartVocabulary = TermVocabulary.NewInstance("Plant Part", "Plant Part", null, termSourceUri);
|
|
767 |
plantPartVocabulary.setUuid(UUID.fromString("369914fe-d54b-4063-99ce-abc81d30ad35"));
|
|
768 |
vocabularyService.saveOrUpdate(plantPartVocabulary);
|
|
769 |
conversation.commit(true);
|
|
770 |
}
|
|
771 |
if (humanGroupVocabulary == null) {
|
|
772 |
URI termSourceUri = null;
|
|
773 |
try {
|
|
774 |
termSourceUri = new URI("eu.etaxonomy.cdm.model.description.Modifier");
|
|
775 |
} catch (URISyntaxException e) {
|
|
776 |
e.printStackTrace();
|
|
777 |
}
|
|
778 |
humanGroupVocabulary = TermVocabulary.NewInstance("Human Group", "Human Group", null, termSourceUri);
|
|
779 |
humanGroupVocabulary.setUuid(UUID.fromString("ca46cea5-bdf7-438d-9cd8-e2793d2178dc"));
|
|
780 |
vocabularyService.saveOrUpdate(humanGroupVocabulary);
|
|
781 |
conversation.commit(true);
|
|
782 |
}
|
|
783 |
if(featureUseRecord == null|| featureUseSummary == null) {
|
|
784 |
TermVocabulary<Feature> featureVocabulary = (TermVocabulary<Feature>)vocabularyService.find((UUID.fromString("b187d555-f06f-4d65-9e53-da7c93f8eaa8")));
|
|
785 |
FeatureTree palmWebFeatureTree = featureTreeService.find(UUID.fromString("72ccce05-7cc8-4dab-8e47-bf3f5fd848a0"));
|
|
786 |
//List<FeatureTree> featureTrees = CdmStore.getService(IFeatureTreeService.class).list(FeatureTree.class, null, null, null, null);
|
|
787 |
|
|
788 |
if (featureUseRecord == null ) {
|
|
789 |
featureUseRecord = Feature.NewInstance("Use Record", "Use Record", null);
|
|
790 |
featureUseRecord.setUuid(UUID.fromString("8125a59d-b4d5-4485-89ea-67306297b599"));
|
|
791 |
featureUseRecord.isSupportsCategoricalData();
|
|
792 |
featureUseRecord.setSupportsCategoricalData(true);
|
|
793 |
featureVocabulary.addTerm(featureUseRecord);
|
|
794 |
FeatureNode useRecFeatureNode = FeatureNode.NewInstance(featureUseRecord);
|
|
795 |
palmWebFeatureTree.getRoot().addChild(useRecFeatureNode);
|
|
796 |
}
|
|
797 |
if (featureUseSummary == null) {
|
|
798 |
featureUseSummary = Feature.NewInstance("Use", "Use", null);
|
|
799 |
featureUseSummary.setUuid(UUID.fromString("6acb0348-c070-4512-a37c-67bcac016279"));
|
|
800 |
featureUseSummary.isSupportsTextData();
|
|
801 |
featureUseSummary.setSupportsTextData(true);
|
|
802 |
//TermVocabulary<Feature> featureVocabulary = (TermVocabulary<Feature>)CdmStore.getService(IVocabularyService.class).find((UUID.fromString("b187d555-f06f-4d65-9e53-da7c93f8eaa8")));
|
|
803 |
featureVocabulary.addTerm(featureUseSummary);
|
|
804 |
FeatureNode useSumFeatureNode = FeatureNode.NewInstance(featureUseSummary);
|
|
805 |
palmWebFeatureTree.getRoot().addChild(useSumFeatureNode);
|
|
806 |
}
|
|
807 |
|
|
808 |
vocabularyService.saveOrUpdate(featureVocabulary);
|
|
809 |
featureTreeService.saveOrUpdate(palmWebFeatureTree);
|
|
810 |
conversation.commit(true);
|
|
811 |
|
|
812 |
}
|
|
813 |
if(notAvailModPager.getCount() == 0) {
|
|
814 |
Modifier notAvailMod = Modifier.NewInstance("N/A", "N/A", null);
|
|
815 |
termService.saveOrUpdate(notAvailMod);
|
|
816 |
conversation.commit(true);
|
|
817 |
}
|
|
818 |
|
|
819 |
if(notAvailStatePager.getCount() == 0) {
|
|
820 |
State notAvailState = State.NewInstance("N/A", "N/A", null);
|
|
821 |
termService.saveOrUpdate(notAvailState);
|
|
822 |
conversation.commit(true);
|
|
823 |
}
|
|
824 |
/*if(featureUseRecord == null) {
|
|
825 |
featureUseRecord = Feature.NewInstance("Use Record", "Use Record", null);
|
|
826 |
featureUseRecord.setUuid(UUID.fromString("8125a59d-b4d5-4485-89ea-67306297b599"));
|
|
827 |
featureUseRecord.isSupportsCategoricalData();
|
|
828 |
featureUseRecord.setSupportsCategoricalData(true);
|
|
829 |
//TermVocabulary<Feature> featureVocabulary = (TermVocabulary<Feature>)vocabularyService.find((UUID.fromString("b187d555-f06f-4d65-9e53-da7c93f8eaa8")));
|
|
830 |
featureVocabulary.addTerm(featureUseRecord);
|
|
831 |
FeatureTree palmWebFeatureTree = featureTreeService.find(UUID.fromString("72ccce05-7cc8-4dab-8e47-bf3f5fd848a0"));
|
|
832 |
FeatureNode useRecFeatureNode = FeatureNode.NewInstance(featureUseRecord);
|
|
833 |
palmWebFeatureTree.getRoot().addChild(useRecFeatureNode);
|
|
834 |
vocabularyService.saveOrUpdate(featureVocabulary);
|
|
835 |
featureTreeService.saveOrUpdate(palmWebFeatureTree);
|
|
836 |
conversation.commit(true);
|
|
837 |
|
|
838 |
}
|
|
839 |
if(featureUseSummary == null) {
|
|
840 |
featureUseSummary = Feature.NewInstance("Use Summary", "Use Summary", null);
|
|
841 |
featureUseSummary.setUuid(UUID.fromString("6acb0348-c070-4512-a37c-67bcac016279"));
|
|
842 |
featureUseSummary.isSupportsTextData();
|
|
843 |
featureUseSummary.setSupportsTextData(true);
|
|
844 |
//TermVocabulary<Feature> featureVocabulary = (TermVocabulary<Feature>)vocabularyService.find((UUID.fromString("b187d555-f06f-4d65-9e53-da7c93f8eaa8")));
|
|
845 |
featureVocabulary.addTerm(featureUseSummary);
|
|
846 |
FeatureTree palmWebFeatureTree = featureTreeService.find(UUID.fromString("72ccce05-7cc8-4dab-8e47-bf3f5fd848a0"));
|
|
847 |
FeatureNode useRecFeatureNode = FeatureNode.NewInstance(featureUseSummary);
|
|
848 |
palmWebFeatureTree.getRoot().addChild(useRecFeatureNode);
|
|
849 |
vocabularyService.saveOrUpdate(featureVocabulary);
|
|
850 |
featureTreeService.saveOrUpdate(palmWebFeatureTree);
|
|
851 |
conversation.commit(true);
|
|
852 |
}*/
|
|
853 |
|
|
854 |
conversation.close();
|
|
855 |
applicationController.close();
|
|
856 |
|
|
857 |
return success;
|
|
858 |
}
|
|
859 |
|
|
860 |
public static void main(String[] args) {
|
|
861 |
UseImport uiImport = new UseImport();
|
|
862 |
// String xlsPath = ".//toload.xlsx";
|
|
863 |
//String xlsPath = "C://workspace//CDM Trunk//UseImport//src//main//java//eu//etaxonomy//cdm//toLoad2.xls";
|
|
864 |
|
|
865 |
uiImport.setupNecessaryItems();
|
|
866 |
uiImport.loadTerms();
|
|
867 |
uiImport.loadUses();
|
|
868 |
//String xlsPath = "C://workspace//toLoad3.xls";
|
|
869 |
//uiImport.importFromExcelSS(xlsPath);
|
|
870 |
|
|
871 |
}
|
|
872 |
}
|
AT: couldn't branch this folder so I am committing to trunk