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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.app.wp6.palmae;
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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.openxml4j.exceptions.InvalidFormatException;
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import org.apache.poi.ss.usermodel.Cell;
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import org.apache.poi.ss.usermodel.Row;
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import org.apache.poi.ss.usermodel.Sheet;
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import org.apache.poi.ss.usermodel.Workbook;
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import org.apache.poi.ss.usermodel.WorkbookFactory;
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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.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.DefinedTerm;
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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.TermType;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.common.VerbatimTimePeriod;
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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.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.location.NamedArea;
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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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public class UseImport {
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public static final Logger logger = Logger.getLogger(UseImport.class);
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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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String cdmPWD = "root";
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return makeDestination(dbType, cdmServer, cdmDB, -1, cdmUserName, cdmPWD);
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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);
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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);
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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) throws InvalidFormatException {
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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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//
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// HSSFWorkbook workBook = new HSSFWorkbook(fileSystem);
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Workbook workBook = WorkbookFactory.create(inputStream);
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Sheet sheet = workBook.getSheetAt(0);
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Iterator<Row> 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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Row row = rows.next();
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System.out.println("Row No.: " + row.getRowNum());
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Iterator<Cell> cells = row.cellIterator();
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ArrayList<String> lstTaxon = new ArrayList<String>();
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while (cells.hasNext()) {
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Cell cell = 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.setAuthorship(authorTeam);
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citation.setTitle(lstUpdate.get(4));
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//citation.
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VerbatimTimePeriod year = VerbatimTimePeriod.NewVerbatimInstance(Integer.parseInt(lstUpdate.get(5)));
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citation.setDatePublished(year);
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citation.setTitleCache(lstUpdate.get(6), true);
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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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Synonym synonym = CdmBase.deproxy(taxon, Synonym.class);
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Taxon acceptetdTaxon = synonym.getAcceptedTaxon();
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if(acceptetdTaxon != null){
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Set<TaxonDescription> taxonDescriptions = acceptetdTaxon.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: " + acceptetdTaxon.getName());
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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() throws InvalidFormatException {
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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//CDMLib-apps//cdmlib-apps//UseImport//src//main//resources//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//CDMLib-apps//cdmlib-apps//UseImport//src//main//resources//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<DefinedTerm> notAvailModPager = termService.findByTitle(DefinedTerm.class, "N/A", null, null, null, null, null, null);
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Pager<State> notAvailStatePager = termService.findByTitle(State.class, "N/A", null, null, null, null, null, null);
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DefinedTerm notAvailMod = notAvailModPager.getRecords().get(0);
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State notAvailState = 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.NewPrimarySourceInstance(useReference, null); //is type correct?
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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<State> 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 = useCategoryPager.getRecords().get(0);
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} else {
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useCategory = notAvailState;
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}
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322
|
StateData stateCatData = StateData.NewInstance(useCategory);
|
|
323
|
stateCatData.setState(useCategory);
|
|
324
|
stateCatData.putModifyingText(Language.ENGLISH(), "Use Category");
|
|
325
|
modifyingText += useCategory.toString() + ";";
|
|
326
|
useRecord.addStateData(stateCatData);
|
|
327
|
|
|
328
|
|
|
329
|
//useRecord.addState(stateData);
|
|
330
|
} else {
|
|
331
|
State useCategory = notAvailState;
|
|
332
|
StateData stateCatData = StateData.NewInstance(useCategory);
|
|
333
|
stateCatData.setState(useCategory);
|
|
334
|
stateCatData.putModifyingText(Language.ENGLISH(), "Use Category");
|
|
335
|
modifyingText += useCategory.toString() + ";";
|
|
336
|
useRecord.addStateData(stateCatData);
|
|
337
|
|
|
338
|
}
|
|
339
|
|
|
340
|
if(lstUseRecord.get(4) != null && lstUseRecord.get(4).length() > 0) {
|
|
341
|
Pager<State> useSubCategoryPager = termService.findByTitle(State.class, lstUseRecord.get(4), null, null, null, null, null, null);
|
|
342
|
State useSubCategory = null;
|
|
343
|
if(useSubCategoryPager.getCount() > 0) {
|
|
344
|
useSubCategory = useSubCategoryPager.getRecords().get(0);
|
|
345
|
|
|
346
|
} else {
|
|
347
|
useSubCategory = notAvailState;
|
|
348
|
}
|
|
349
|
StateData stateSubCatData = StateData.NewInstance(useSubCategory);
|
|
350
|
stateSubCatData.setState(useSubCategory);
|
|
351
|
stateSubCatData.putModifyingText(Language.ENGLISH(), "Use SubCategory");
|
|
352
|
modifyingText += useSubCategory.toString() + ";";
|
|
353
|
useRecord.addStateData(stateSubCatData);
|
|
354
|
|
|
355
|
}
|
|
356
|
else {
|
|
357
|
State useSubCategory = notAvailState;
|
|
358
|
StateData stateSubCatData = StateData.NewInstance(useSubCategory);
|
|
359
|
stateSubCatData.setState(useSubCategory);
|
|
360
|
stateSubCatData.putModifyingText(Language.ENGLISH(), "Use SubCategory");
|
|
361
|
modifyingText += useSubCategory.toString() + ";";
|
|
362
|
useRecord.addStateData(stateSubCatData);
|
|
363
|
|
|
364
|
}
|
|
365
|
if(lstUseRecord.get(5) != null && lstUseRecord.get(5).length() > 0) {
|
|
366
|
Pager<DefinedTerm> countryPager = termService.findByTitle(DefinedTerm.class, lstUseRecord.get(5), null, null, null, null, null, null);
|
|
367
|
DefinedTerm country = null;
|
|
368
|
if(countryPager.getCount() > 0) {
|
|
369
|
country = countryPager.getRecords().get(0);
|
|
370
|
} else {
|
|
371
|
country = notAvailMod;
|
|
372
|
}
|
|
373
|
modifyingText += country.toString() + ";";
|
|
374
|
useRecord.addModifier(country);
|
|
375
|
} else {
|
|
376
|
DefinedTerm country = notAvailMod;
|
|
377
|
modifyingText += country.toString() + ";";
|
|
378
|
useRecord.addModifier(country);
|
|
379
|
}
|
|
380
|
|
|
381
|
if(lstUseRecord.get(6) != null && lstUseRecord.get(6).length() > 0) {
|
|
382
|
Pager<DefinedTerm> plantPartPager = termService.findByTitle(DefinedTerm.class, lstUseRecord.get(6), null, null, null, null, null, null);
|
|
383
|
DefinedTerm plantPart = null;
|
|
384
|
if(plantPartPager.getCount() > 0) {
|
|
385
|
plantPart = plantPartPager.getRecords().get(0);
|
|
386
|
} else {
|
|
387
|
plantPart = notAvailMod;
|
|
388
|
}
|
|
389
|
modifyingText += plantPart.toString() + ";";
|
|
390
|
useRecord.addModifier(plantPart);
|
|
391
|
}else {
|
|
392
|
DefinedTerm plantPart = notAvailMod;
|
|
393
|
modifyingText += plantPart.toString() + ";";
|
|
394
|
useRecord.addModifier(plantPart);
|
|
395
|
}
|
|
396
|
if(lstUseRecord.get(7) != null && lstUseRecord.get(7).length() > 0) {
|
|
397
|
Pager<DefinedTerm> humanGroupPager = termService.findByTitle(DefinedTerm.class, lstUseRecord.get(7), null, null, null, null, null, null);
|
|
398
|
DefinedTerm humanGroup = null;
|
|
399
|
if(humanGroupPager.getCount() > 0) {
|
|
400
|
humanGroup = humanGroupPager.getRecords().get(0);
|
|
401
|
} else {
|
|
402
|
humanGroup = notAvailMod;
|
|
403
|
}
|
|
404
|
modifyingText += humanGroup.toString() + ";";
|
|
405
|
useRecord.addModifier(humanGroup);
|
|
406
|
} else {
|
|
407
|
DefinedTerm humanGroup = notAvailMod;
|
|
408
|
modifyingText += humanGroup.toString() + ";";
|
|
409
|
useRecord.addModifier(humanGroup);
|
|
410
|
}
|
|
411
|
if(lstUseRecord.get(8) != null && lstUseRecord.get(8).length() > 0) {
|
|
412
|
Pager<DefinedTerm> ethnicGroupPager = termService.findByTitle(DefinedTerm.class, lstUseRecord.get(8), null, null, null, null, null, null);
|
|
413
|
DefinedTerm ethnicGroup = null;
|
|
414
|
if(ethnicGroupPager.getCount() > 0) {
|
|
415
|
ethnicGroup = ethnicGroupPager.getRecords().get(0);
|
|
416
|
modifyingText += ethnicGroup.toString() + ";";
|
|
417
|
} else {
|
|
418
|
ethnicGroup = notAvailMod;
|
|
419
|
}
|
|
420
|
useRecord.addModifier(ethnicGroup);
|
|
421
|
}
|
|
422
|
else {
|
|
423
|
DefinedTerm ethnicGroup = notAvailMod;
|
|
424
|
modifyingText += ethnicGroup.toString() + ";";
|
|
425
|
useRecord.addModifier(ethnicGroup);
|
|
426
|
}
|
|
427
|
useRecord.putModifyingText(Language.ENGLISH(), modifyingText);
|
|
428
|
descService.saveDescriptionElement(useRecord);
|
|
429
|
newUseDescription.addElement(useRecord);
|
|
430
|
}
|
|
431
|
}
|
|
432
|
|
|
433
|
|
|
434
|
|
|
435
|
if (taxon.isInstanceOf(Synonym.class)){
|
|
436
|
Taxon bestCandidate = null;
|
|
437
|
Synonym synonym = CdmBase.deproxy(taxon, Synonym.class);
|
|
438
|
Taxon acceptedTaxon = synonym.getAcceptedTaxon();
|
|
439
|
if(acceptedTaxon != null){
|
|
440
|
acceptedTaxon.addDescription(newUseDescription);
|
|
441
|
taxonService.saveOrUpdate(bestCandidate);
|
|
442
|
conversation.commit();
|
|
443
|
}
|
|
444
|
} else {
|
|
445
|
Taxon taxonAccepted = (Taxon) taxon;
|
|
446
|
taxonAccepted.addDescription(newUseDescription);
|
|
447
|
taxonService.saveOrUpdate(taxonAccepted);
|
|
448
|
conversation.commit();
|
|
449
|
}
|
|
450
|
}
|
|
451
|
else {
|
|
452
|
System.out.println("Processing UseSummary#: " + i + " ID:" + lstUseSummary.get(0));
|
|
453
|
}
|
|
454
|
}
|
|
455
|
|
|
456
|
conversation.close();
|
|
457
|
applicationController.close();
|
|
458
|
|
|
459
|
} catch (Exception e) {
|
|
460
|
success = false;
|
|
461
|
e.printStackTrace();
|
|
462
|
}
|
|
463
|
return success;
|
|
464
|
|
|
465
|
}
|
|
466
|
|
|
467
|
//Completed and tested!
|
|
468
|
private boolean loadTerms() throws InvalidFormatException {
|
|
469
|
boolean success = true;
|
|
470
|
|
|
471
|
//String xslPathString = "C://workspace//terms.xls";
|
|
472
|
String xslPathString = "//Users//alextheys//Projects//CDM_Trunk//Palm_Use_Data_Extension//CDMLib-apps//cdmlib-apps//UseImport//src//main//resources//terms.xls";
|
|
473
|
|
|
474
|
CdmApplicationController applicationController = CdmApplicationController.NewInstance(dataSource());
|
|
475
|
ConversationHolder conversation = applicationController.NewConversation();
|
|
476
|
conversation.startTransaction();
|
|
477
|
|
|
478
|
ITaxonService service = applicationController.getTaxonService();
|
|
479
|
ITermService termService = applicationController.getTermService();
|
|
480
|
IVocabularyService vocabularyService = applicationController.getVocabularyService();
|
|
481
|
IReferenceService referenceService = applicationController.getReferenceService();
|
|
482
|
|
|
483
|
TermVocabulary<State> stateVocabulary = vocabularyService.find(UUID.fromString("67430d7c-fd43-4e9d-af5e-d0dca3f74931"));
|
|
484
|
TermVocabulary<DefinedTermBase<?>> countryVocabulary = vocabularyService.find(UUID.fromString("116c51f1-e63a-46f7-a258-e1149a42868b"));
|
|
485
|
TermVocabulary<DefinedTerm> plantPartVocabulary = vocabularyService.find(UUID.fromString("369914fe-d54b-4063-99ce-abc81d30ad35"));
|
|
486
|
TermVocabulary<DefinedTerm> humanGroupVocabulary = vocabularyService.find(UUID.fromString("ca46cea5-bdf7-438d-9cd8-e2793d2178dc"));
|
|
487
|
|
|
488
|
IDescriptionService descService = applicationController.getDescriptionService();
|
|
489
|
InputStream inputStream = null;
|
|
490
|
|
|
491
|
try {
|
|
492
|
inputStream = new FileInputStream(xslPathString);
|
|
493
|
|
|
494
|
} catch (FileNotFoundException e) {
|
|
495
|
success = false;
|
|
496
|
System.out.println("File not found in the specified path.");
|
|
497
|
e.printStackTrace();
|
|
498
|
}
|
|
499
|
|
|
500
|
|
|
501
|
try {
|
|
502
|
// POIFSFileSystem fileSystem = new POIFSFileSystem(inputStream);
|
|
503
|
// HSSFWorkbook workBook = new HSSFWorkbook(fileSystem);
|
|
504
|
|
|
505
|
Workbook workBook = WorkbookFactory.create(inputStream);
|
|
506
|
|
|
507
|
|
|
508
|
Sheet sheet = workBook.getSheetAt(0);
|
|
509
|
Iterator<Row> rows = sheet.rowIterator();
|
|
510
|
|
|
511
|
ArrayList<ArrayList<String>> lstUpdates = new ArrayList<ArrayList<String>>();
|
|
512
|
|
|
513
|
while (rows.hasNext()) {
|
|
514
|
|
|
515
|
Row row = rows.next();
|
|
516
|
System.out.println("Row No.: " + row.getRowNum());
|
|
517
|
Iterator<Cell> cells = row.cellIterator();
|
|
518
|
ArrayList<String> lstTerms = new ArrayList<String>();
|
|
519
|
while (cells.hasNext()) {
|
|
520
|
Cell cell = cells.next();
|
|
521
|
|
|
522
|
int intCellType = cell.getCellType();
|
|
523
|
switch (intCellType) {
|
|
524
|
case 0:
|
|
525
|
int cellValue = (int) cell.getNumericCellValue();
|
|
526
|
lstTerms.add(Integer.toString(cellValue));
|
|
527
|
break;
|
|
528
|
case 1:
|
|
529
|
lstTerms.add(cell.getStringCellValue());
|
|
530
|
break;
|
|
531
|
}
|
|
532
|
}
|
|
533
|
lstUpdates.add(lstTerms);
|
|
534
|
//lstTaxonIDs.add(Integer.parseInt(lstTaxon.get(0)));
|
|
535
|
}
|
|
536
|
for (ArrayList<String> lstUpdate : lstUpdates) {
|
|
537
|
int termType = Integer.parseInt(lstUpdate.get(0));
|
|
538
|
switch (termType) {
|
|
539
|
//Case 0 = UseCategory
|
|
540
|
case 0:
|
|
541
|
Pager<State> useCategoryPager = termService.findByRepresentationText(lstUpdate.get(1), State.class, null, null);
|
|
542
|
State useCategory = null;
|
|
543
|
State useSubCat = null;
|
|
544
|
if (useCategoryPager.getCount()>0) {
|
|
545
|
useCategory = useCategoryPager.getRecords().get(0);
|
|
546
|
}
|
|
547
|
if(useCategory == null) {
|
|
548
|
useCategory = State.NewInstance(lstUpdate.get(1), lstUpdate.get(1), null);
|
|
549
|
}
|
|
550
|
//State useCategory = (State) termService.
|
|
551
|
if(lstUpdate.size() > 2) {
|
|
552
|
useSubCat = State.NewInstance(lstUpdate.get(2), lstUpdate.get(2), null);
|
|
553
|
useCategory.addIncludes(useSubCat);
|
|
554
|
}
|
|
555
|
stateVocabulary.addTerm(useCategory);
|
|
556
|
vocabularyService.saveOrUpdate(stateVocabulary);
|
|
557
|
conversation.commit(true);
|
|
558
|
break;
|
|
559
|
|
|
560
|
//case 1: = HumanGroup
|
|
561
|
case 1:
|
|
562
|
Pager<DefinedTerm> humanGroupPager = termService.findByRepresentationText(lstUpdate.get(1), DefinedTerm.class, null, null);
|
|
563
|
|
|
564
|
DefinedTerm humanGroup = null;
|
|
565
|
DefinedTerm ethnicGroup = null;
|
|
566
|
if(humanGroupPager.getCount()>0) {
|
|
567
|
humanGroup = humanGroupPager.getRecords().get(0);
|
|
568
|
}
|
|
569
|
|
|
570
|
if(humanGroup == null) {
|
|
571
|
humanGroup = DefinedTerm.NewModifierInstance(lstUpdate.get(1), lstUpdate.get(1), null);
|
|
572
|
}
|
|
573
|
|
|
574
|
if(lstUpdate.size() >2) {
|
|
575
|
ethnicGroup = DefinedTerm.NewModifierInstance(lstUpdate.get(2), lstUpdate.get(2), null);
|
|
576
|
humanGroup.addIncludes(ethnicGroup);
|
|
577
|
}
|
|
578
|
humanGroupVocabulary.addTerm(humanGroup);
|
|
579
|
vocabularyService.saveOrUpdate(humanGroupVocabulary);
|
|
580
|
conversation.commit(true);
|
|
581
|
break;
|
|
582
|
|
|
583
|
//case 2: = Country
|
|
584
|
case 2:
|
|
585
|
Pager<DefinedTerm> countryPager = termService.findByRepresentationText(lstUpdate.get(1), DefinedTerm.class, null, null);
|
|
586
|
DefinedTermBase country = null;
|
|
587
|
|
|
588
|
if(countryPager.getCount()>0) {
|
|
589
|
country = countryPager.getRecords().get(0);
|
|
590
|
}
|
|
591
|
|
|
592
|
if(country == null) {
|
|
593
|
country = NamedArea.NewInstance(lstUpdate.get(1), lstUpdate.get(1), null);
|
|
594
|
countryVocabulary.addTerm(country);
|
|
595
|
vocabularyService.saveOrUpdate(countryVocabulary);
|
|
596
|
}
|
|
597
|
conversation.commit(true);
|
|
598
|
break;
|
|
599
|
|
|
600
|
//case 3: //plantPart
|
|
601
|
case 3:
|
|
602
|
Pager<DefinedTerm> plantPartPager = termService.findByRepresentationText(lstUpdate.get(1), DefinedTerm.class, null, null);
|
|
603
|
DefinedTerm plantPart = null;
|
|
604
|
|
|
605
|
if(plantPartPager.getCount()>0) {
|
|
606
|
plantPart = plantPartPager.getRecords().get(0);
|
|
607
|
}
|
|
608
|
|
|
609
|
if(plantPart == null) {
|
|
610
|
plantPart = DefinedTerm.NewModifierInstance(lstUpdate.get(1), lstUpdate.get(1), null);
|
|
611
|
plantPartVocabulary.addTerm(plantPart);
|
|
612
|
vocabularyService.saveOrUpdate(plantPartVocabulary);
|
|
613
|
}
|
|
614
|
conversation.commit(true);
|
|
615
|
break;
|
|
616
|
|
|
617
|
}
|
|
618
|
}
|
|
619
|
conversation.close();
|
|
620
|
applicationController.close();
|
|
621
|
|
|
622
|
} catch (IOException e) {
|
|
623
|
success = false;
|
|
624
|
e.printStackTrace();
|
|
625
|
}
|
|
626
|
return success;
|
|
627
|
|
|
628
|
}
|
|
629
|
|
|
630
|
private ArrayList<ArrayList<String>> loadSpreadsheet(String xslPathString) throws InvalidFormatException {
|
|
631
|
ArrayList<ArrayList<String>> lstUpdates = new ArrayList<ArrayList<String>>();
|
|
632
|
InputStream inputStream = null;
|
|
633
|
|
|
634
|
try {
|
|
635
|
inputStream = new FileInputStream(xslPathString);
|
|
636
|
|
|
637
|
} catch (FileNotFoundException e) {
|
|
638
|
System.out.println("File not found in the specified path.");
|
|
639
|
e.printStackTrace();
|
|
640
|
}
|
|
641
|
|
|
642
|
try {
|
|
643
|
// POIFSFileSystem fileSystem = new POIFSFileSystem(inputStream);
|
|
644
|
// HSSFWorkbook workBook = new HSSFWorkbook(fileSystem);
|
|
645
|
|
|
646
|
Workbook workBook = WorkbookFactory.create(inputStream);
|
|
647
|
|
|
648
|
|
|
649
|
Sheet sheet = workBook.getSheetAt(0);
|
|
650
|
Iterator<Row> rows = sheet.rowIterator();
|
|
651
|
// Iterator rows = sheet.rowIterator();
|
|
652
|
//Set<Integer> lstTaxonIDs;
|
|
653
|
|
|
654
|
|
|
655
|
while (rows.hasNext()) {
|
|
656
|
|
|
657
|
Row row = rows.next();
|
|
658
|
System.out.println("Row No.: " + row.getRowNum());
|
|
659
|
Iterator<Cell> cells = row.cellIterator();
|
|
660
|
ArrayList<String> lstTerms = new ArrayList<String>();
|
|
661
|
while (cells.hasNext()) {
|
|
662
|
Cell cell = cells.next();
|
|
663
|
|
|
664
|
int intCellType = cell.getCellType();
|
|
665
|
switch (intCellType) {
|
|
666
|
case 0:
|
|
667
|
int cellValue = (int) cell.getNumericCellValue();
|
|
668
|
lstTerms.add(Integer.toString(cellValue));
|
|
669
|
break;
|
|
670
|
case 1:
|
|
671
|
lstTerms.add(cell.getStringCellValue());
|
|
672
|
break;
|
|
673
|
}
|
|
674
|
}
|
|
675
|
lstUpdates.add(lstTerms);
|
|
676
|
//lstTaxonIDs.add(Integer.parseInt(lstTaxon.get(0)));
|
|
677
|
}
|
|
678
|
} catch (IOException e) {
|
|
679
|
e.printStackTrace();
|
|
680
|
}
|
|
681
|
return lstUpdates;
|
|
682
|
}
|
|
683
|
|
|
684
|
|
|
685
|
private boolean setupNecessaryItems() {
|
|
686
|
boolean success = false;
|
|
687
|
CdmApplicationController applicationController = CdmApplicationController.NewInstance(dataSource());
|
|
688
|
ConversationHolder conversation = applicationController.NewConversation();
|
|
689
|
|
|
690
|
|
|
691
|
ITaxonService service = applicationController.getTaxonService();
|
|
692
|
ITermService termService = applicationController.getTermService();
|
|
693
|
IVocabularyService vocabularyService = applicationController.getVocabularyService();
|
|
694
|
IFeatureTreeService featureTreeService = applicationController.getFeatureTreeService();
|
|
695
|
|
|
696
|
MarkerType existingMarkertype = (MarkerType)termService.find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
|
|
697
|
Feature featureUseRecord = (Feature) termService.find(UUID.fromString("8125a59d-b4d5-4485-89ea-67306297b599"));
|
|
698
|
Feature featureUseSummary = (Feature) termService.find(UUID.fromString("6acb0348-c070-4512-a37c-67bcac016279"));
|
|
699
|
TermVocabulary<State> stateVocabulary = vocabularyService.find(UUID.fromString("67430d7c-fd43-4e9d-af5e-d0dca3f74931"));
|
|
700
|
TermVocabulary<DefinedTerm> countryVocabulary = vocabularyService.find(UUID.fromString("116c51f1-e63a-46f7-a258-e1149a42868b"));
|
|
701
|
TermVocabulary<DefinedTerm> plantPartVocabulary = vocabularyService.find(UUID.fromString("369914fe-d54b-4063-99ce-abc81d30ad35"));
|
|
702
|
TermVocabulary<DefinedTerm> humanGroupVocabulary = vocabularyService.find(UUID.fromString("ca46cea5-bdf7-438d-9cd8-e2793d2178dc"));
|
|
703
|
Pager<DefinedTerm> notAvailModPager = termService.findByTitle(DefinedTerm.class, "N/A", null, null, null, null, null, null);
|
|
704
|
Pager<State> notAvailStatePager = termService.findByTitle(State.class, "N/A", null, null, null, null, null, null);
|
|
705
|
|
|
706
|
conversation.startTransaction();
|
|
707
|
if (existingMarkertype == null) {
|
|
708
|
existingMarkertype = MarkerType.NewInstance("use", "use", null);
|
|
709
|
existingMarkertype.setUuid( UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));
|
|
710
|
TermVocabulary<MarkerType> markerTypeVocabulary = vocabularyService.find((UUID.fromString("19dffff7-e142-429c-a420-5d28e4ebe305")));
|
|
711
|
markerTypeVocabulary.addTerm(existingMarkertype);
|
|
712
|
vocabularyService.saveOrUpdate(markerTypeVocabulary);
|
|
713
|
conversation.commit(true);
|
|
714
|
}
|
|
715
|
if (stateVocabulary == null) {
|
|
716
|
|
|
717
|
URI termSourceUri = null;
|
|
718
|
try {
|
|
719
|
termSourceUri = new URI("eu.etaxonomy.cdm.model.description.State");
|
|
720
|
} catch (URISyntaxException e) {
|
|
721
|
e.printStackTrace();
|
|
722
|
}
|
|
723
|
stateVocabulary = TermVocabulary.NewInstance(TermType.State, "Use Category", "Use Category", null, termSourceUri);
|
|
724
|
stateVocabulary.setUuid(UUID.fromString("67430d7c-fd43-4e9d-af5e-d0dca3f74931"));
|
|
725
|
vocabularyService.saveOrUpdate(stateVocabulary);
|
|
726
|
conversation.commit(true);
|
|
727
|
}
|
|
728
|
if (countryVocabulary == null) {
|
|
729
|
URI termSourceUri = null;
|
|
730
|
try {
|
|
731
|
termSourceUri = new URI("eu.etaxonomy.cdm.model.description.DefinedTerm");
|
|
732
|
} catch (URISyntaxException e) {
|
|
733
|
e.printStackTrace();
|
|
734
|
}
|
|
735
|
countryVocabulary = TermVocabulary.NewInstance(TermType.NamedArea, "Country", "Country", null, termSourceUri);
|
|
736
|
countryVocabulary.setUuid(UUID.fromString("116c51f1-e63a-46f7-a258-e1149a42868b"));
|
|
737
|
|
|
738
|
vocabularyService.saveOrUpdate(countryVocabulary);
|
|
739
|
conversation.commit(true);
|
|
740
|
}
|
|
741
|
if (plantPartVocabulary == null) {
|
|
742
|
URI termSourceUri = null;
|
|
743
|
try {
|
|
744
|
termSourceUri = new URI("eu.etaxonomy.cdm.model.description.DefinedTerm");
|
|
745
|
} catch (URISyntaxException e) {
|
|
746
|
e.printStackTrace();
|
|
747
|
}
|
|
748
|
plantPartVocabulary = TermVocabulary.NewInstance(TermType.Modifier, "Plant Part", "Plant Part", null, termSourceUri);
|
|
749
|
plantPartVocabulary.setUuid(UUID.fromString("369914fe-d54b-4063-99ce-abc81d30ad35"));
|
|
750
|
vocabularyService.saveOrUpdate(plantPartVocabulary);
|
|
751
|
conversation.commit(true);
|
|
752
|
}
|
|
753
|
if (humanGroupVocabulary == null) {
|
|
754
|
URI termSourceUri = null;
|
|
755
|
try {
|
|
756
|
termSourceUri = new URI("eu.etaxonomy.cdm.model.description.DefinedTerm");
|
|
757
|
} catch (URISyntaxException e) {
|
|
758
|
e.printStackTrace();
|
|
759
|
}
|
|
760
|
humanGroupVocabulary = TermVocabulary.NewInstance(TermType.Modifier, "Human Group", "Human Group", null, termSourceUri);
|
|
761
|
humanGroupVocabulary.setUuid(UUID.fromString("ca46cea5-bdf7-438d-9cd8-e2793d2178dc"));
|
|
762
|
vocabularyService.saveOrUpdate(humanGroupVocabulary);
|
|
763
|
conversation.commit(true);
|
|
764
|
}
|
|
765
|
if(featureUseRecord == null|| featureUseSummary == null) {
|
|
766
|
TermVocabulary<Feature> featureVocabulary = vocabularyService.find((UUID.fromString("b187d555-f06f-4d65-9e53-da7c93f8eaa8")));
|
|
767
|
FeatureTree palmWebFeatureTree = featureTreeService.find(UUID.fromString("72ccce05-7cc8-4dab-8e47-bf3f5fd848a0"));
|
|
768
|
//List<FeatureTree> featureTrees = CdmStore.getService(IFeatureTreeService.class).list(FeatureTree.class, null, null, null, null);
|
|
769
|
|
|
770
|
if (featureUseRecord == null ) {
|
|
771
|
featureUseRecord = Feature.NewInstance("Use Record", "Use Record", null);
|
|
772
|
featureUseRecord.setUuid(UUID.fromString("8125a59d-b4d5-4485-89ea-67306297b599"));
|
|
773
|
featureUseRecord.isSupportsCategoricalData();
|
|
774
|
featureUseRecord.setSupportsCategoricalData(true);
|
|
775
|
featureVocabulary.addTerm(featureUseRecord);
|
|
776
|
FeatureNode useRecFeatureNode = FeatureNode.NewInstance(featureUseRecord);
|
|
777
|
palmWebFeatureTree.getRoot().addChild(useRecFeatureNode);
|
|
778
|
}
|
|
779
|
if (featureUseSummary == null) {
|
|
780
|
featureUseSummary = Feature.NewInstance("Use", "Use", null);
|
|
781
|
featureUseSummary.setUuid(UUID.fromString("6acb0348-c070-4512-a37c-67bcac016279"));
|
|
782
|
featureUseSummary.isSupportsTextData();
|
|
783
|
featureUseSummary.setSupportsTextData(true);
|
|
784
|
//TermVocabulary<Feature> featureVocabulary = (TermVocabulary<Feature>)CdmStore.getService(IVocabularyService.class).find((UUID.fromString("b187d555-f06f-4d65-9e53-da7c93f8eaa8")));
|
|
785
|
featureVocabulary.addTerm(featureUseSummary);
|
|
786
|
FeatureNode useSumFeatureNode = FeatureNode.NewInstance(featureUseSummary);
|
|
787
|
palmWebFeatureTree.getRoot().addChild(useSumFeatureNode);
|
|
788
|
}
|
|
789
|
|
|
790
|
vocabularyService.saveOrUpdate(featureVocabulary);
|
|
791
|
featureTreeService.saveOrUpdate(palmWebFeatureTree);
|
|
792
|
conversation.commit(true);
|
|
793
|
|
|
794
|
}
|
|
795
|
if(notAvailModPager.getCount() == 0) {
|
|
796
|
DefinedTerm notAvailMod = DefinedTerm.NewInstance(TermType.Modifier, "N/A", "N/A", null);
|
|
797
|
termService.saveOrUpdate(notAvailMod);
|
|
798
|
conversation.commit(true);
|
|
799
|
}
|
|
800
|
|
|
801
|
if(notAvailStatePager.getCount() == 0) {
|
|
802
|
State notAvailState = State.NewInstance("N/A", "N/A", null);
|
|
803
|
termService.saveOrUpdate(notAvailState);
|
|
804
|
conversation.commit(true);
|
|
805
|
}
|
|
806
|
/*if(featureUseRecord == null) {
|
|
807
|
featureUseRecord = Feature.NewInstance("Use Record", "Use Record", null);
|
|
808
|
featureUseRecord.setUuid(UUID.fromString("8125a59d-b4d5-4485-89ea-67306297b599"));
|
|
809
|
featureUseRecord.isSupportsCategoricalData();
|
|
810
|
featureUseRecord.setSupportsCategoricalData(true);
|
|
811
|
//TermVocabulary<Feature> featureVocabulary = (TermVocabulary<Feature>)vocabularyService.find((UUID.fromString("b187d555-f06f-4d65-9e53-da7c93f8eaa8")));
|
|
812
|
featureVocabulary.addTerm(featureUseRecord);
|
|
813
|
FeatureTree palmWebFeatureTree = featureTreeService.find(UUID.fromString("72ccce05-7cc8-4dab-8e47-bf3f5fd848a0"));
|
|
814
|
FeatureNode useRecFeatureNode = FeatureNode.NewInstance(featureUseRecord);
|
|
815
|
palmWebFeatureTree.getRoot().addChild(useRecFeatureNode);
|
|
816
|
vocabularyService.saveOrUpdate(featureVocabulary);
|
|
817
|
featureTreeService.saveOrUpdate(palmWebFeatureTree);
|
|
818
|
conversation.commit(true);
|
|
819
|
|
|
820
|
}
|
|
821
|
if(featureUseSummary == null) {
|
|
822
|
featureUseSummary = Feature.NewInstance("Use Summary", "Use Summary", null);
|
|
823
|
featureUseSummary.setUuid(UUID.fromString("6acb0348-c070-4512-a37c-67bcac016279"));
|
|
824
|
featureUseSummary.isSupportsTextData();
|
|
825
|
featureUseSummary.setSupportsTextData(true);
|
|
826
|
//TermVocabulary<Feature> featureVocabulary = (TermVocabulary<Feature>)vocabularyService.find((UUID.fromString("b187d555-f06f-4d65-9e53-da7c93f8eaa8")));
|
|
827
|
featureVocabulary.addTerm(featureUseSummary);
|
|
828
|
FeatureTree palmWebFeatureTree = featureTreeService.find(UUID.fromString("72ccce05-7cc8-4dab-8e47-bf3f5fd848a0"));
|
|
829
|
FeatureNode useRecFeatureNode = FeatureNode.NewInstance(featureUseSummary);
|
|
830
|
palmWebFeatureTree.getRoot().addChild(useRecFeatureNode);
|
|
831
|
vocabularyService.saveOrUpdate(featureVocabulary);
|
|
832
|
featureTreeService.saveOrUpdate(palmWebFeatureTree);
|
|
833
|
conversation.commit(true);
|
|
834
|
}*/
|
|
835
|
|
|
836
|
conversation.close();
|
|
837
|
applicationController.close();
|
|
838
|
|
|
839
|
return success;
|
|
840
|
}
|
|
841
|
|
|
842
|
public static void main(String[] args) {
|
|
843
|
UseImport uiImport = new UseImport();
|
|
844
|
// String xlsPath = ".//toload.xlsx";
|
|
845
|
//String xlsPath = "C://workspace//CDM Trunk//UseImport//src//main//java//eu//etaxonomy//cdm//toLoad2.xls";
|
|
846
|
|
|
847
|
uiImport.setupNecessaryItems();
|
|
848
|
try {
|
|
849
|
uiImport.loadTerms();
|
|
850
|
uiImport.loadUses();
|
|
851
|
} catch (InvalidFormatException e) {
|
|
852
|
// TODO Auto-generated catch block
|
|
853
|
e.printStackTrace();
|
|
854
|
}
|
|
855
|
//String xlsPath = "C://workspace//toLoad3.xls";
|
|
856
|
//uiImport.importFromExcelSS(xlsPath);
|
|
857
|
|
|
858
|
}
|
|
859
|
}
|