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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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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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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.abcdImport;
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import java.io.FileInputStream;
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import java.util.ArrayList;
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import java.util.Hashtable;
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import java.util.List;
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import java.util.ListIterator;
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import java.io.File;
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import java.net.URI;
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import java.net.URISyntaxException;
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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 org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.api.application.CdmApplicationController;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.app.common.CdmDestinations;
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import eu.etaxonomy.cdm.database.DbSchemaValidation;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.agent.Institution;
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import eu.etaxonomy.cdm.model.agent.Person;
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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.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.Point;
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import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.occurrence.Collection;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;
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import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
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import eu.etaxonomy.cdm.model.occurrence.FieldObservation;
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import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
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import eu.etaxonomy.cdm.model.occurrence.LivingBeing;
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import eu.etaxonomy.cdm.model.occurrence.Observation;
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import eu.etaxonomy.cdm.model.occurrence.Specimen;
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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.Taxon;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
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import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenSynthesysExcelImportConfigurator;
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... | ... | |
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* @version 1.0
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*/
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public class SynthesysCacheActivator {
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private static final Logger logger = Logger.getLogger(SynthesysCacheActivator.class);
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protected String fullScientificNameString = null;
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protected String institutionCode = null;
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protected String collectionCode = null;
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protected String unitID = null;
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protected String recordBasis = null;
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protected String accessionNumber = null;
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protected String collectorsNumber = null;
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protected String fieldNumber = null;
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protected Double longitude = null;
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protected Double latitude = null;
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protected String locality = null;
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protected String country = null;
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protected String isocountry = null;
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protected ArrayList<String> gatheringAgentList = new ArrayList<String>();
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protected ArrayList<String> identificationList = new ArrayList<String>();
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static DbSchemaValidation hbm2dll = DbSchemaValidation.UPDATE;
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protected HSSFWorkbook hssfworkbook = null;
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private ArrayList<Hashtable<String, String>> parseXLS() {
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String filename = "/home/patricia/Desktop/CDMtabular9c04a474e2_23_09_08.xls";
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// String filename = "/home/patricia/Desktop/synthesys.xls";
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ArrayList<Hashtable<String, String>> units = new ArrayList<Hashtable<String,String>>();
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try {
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POIFSFileSystem fs = new POIFSFileSystem(new FileInputStream(filename));
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HSSFWorkbook wb = new HSSFWorkbook(fs);
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HSSFSheet sheet = wb.getSheetAt(0);
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HSSFRow row;
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HSSFCell cell;
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int rows; // No of rows
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rows = sheet.getPhysicalNumberOfRows();
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int cols = 0; // No of columns
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int tmp = 0;
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// This trick ensures that we get the data properly even if it doesn't start from first few rows
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for(int i = 0; i < 10 || i < rows; i++) {
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row = sheet.getRow(i);
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if(row != null) {
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tmp = sheet.getRow(i).getPhysicalNumberOfCells();
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if(tmp > cols) cols = tmp;
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}
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}
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Hashtable<String, String> headers = null;
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ArrayList<String> columns = new ArrayList<String>();
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row = sheet.getRow(0);
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for (int c =0; c<cols; c++){
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cell = row.getCell(c);
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columns.add(cell.toString());
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}
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for(int r = 1; r < rows; r++) {
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row = sheet.getRow(r);
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headers = new Hashtable<String, String>();
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if(row != null) {
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for(int c = 0; c < cols; c++) {
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cell = row.getCell((short)c);
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if(cell != null) {
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headers.put(columns.get(c),cell.toString());
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}
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}
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}
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units.add(headers);
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}
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System.out.println("units: "+units);
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} catch(Exception ioe) {
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ioe.printStackTrace();
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}
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return units;
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}
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public void saveUnit(Hashtable<String,String> unit){
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String author = unit.get("author");
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author=author.replaceAll("None","");
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String taxonName = unit.get("taxonName");
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taxonName = taxonName.replaceAll("None", "");
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try {
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this.institutionCode = unit.get("institution").replaceAll("None", null);
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} catch (Exception e) {
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}
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try {this.collectionCode = unit.get("collection").replaceAll("None", null);
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} catch (Exception e) {
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}
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try {this.unitID = unit.get("unitID").replaceAll("None", null);
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} catch (Exception e) {
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}
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try {this.recordBasis = unit.get("recordBasis").replaceAll("None", null);
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} catch (Exception e) {
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}
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try {this.accessionNumber = null;
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} catch (Exception e) {
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}
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try {this.locality = unit.get("locality").replaceAll("None", null);
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} catch (Exception e) {
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}
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try {this.longitude = Double.valueOf(unit.get("longitude"));
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} catch (Exception e) {
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}
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try {this.latitude = Double.valueOf(unit.get("latitude"));
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} catch (Exception e) {
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}
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try {this.country = unit.get("country").replaceAll("None", null);
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} catch (Exception e) {
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}
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try {this.isocountry = unit.get("isoCountry").replaceAll("None", null);
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} catch (Exception e) {
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}
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try {this.fieldNumber = unit.get("field number").replaceAll("None", null);
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} catch (Exception e) {
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}
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try {this.collectorsNumber = unit.get("collector number").replaceAll("None", null);
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} catch (Exception e) {
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}
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try {String coll =unit.get("collector");
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coll=coll.replaceAll("None", null);
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this.gatheringAgentList.add(coll);
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} catch (Exception e) {
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}
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try {this.identificationList.add(taxonName+" "+author);
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} catch (Exception e) {System.out.println(e);
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}
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}
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@SuppressWarnings("unchecked")
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public boolean invoke(){
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boolean result = true;
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boolean withCdm = true;
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CdmApplicationController app = null;
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TransactionStatus tx = null;
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app = CdmApplicationController.NewInstance(CdmDestinations.localH2(), hbm2dll);
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tx = app.startTransaction();
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try {
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ReferenceFactory refFactory = ReferenceFactory.newInstance();
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Reference sec = refFactory.newDatabase();
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sec.setTitleCache("SYNTHESYS CACHE DATA", true);
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/**
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* SPECIMEN OR OBSERVATION OR LIVING
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*/
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DerivedUnitBase derivedThing = null;
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//create specimen
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if (this.recordBasis != null){
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if (this.recordBasis.toLowerCase().startsWith("s")) {//specimen
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derivedThing = Specimen.NewInstance();
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}
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else if (this.recordBasis.toLowerCase().startsWith("o")) {//observation
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derivedThing = Observation.NewInstance();
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}
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else if (this.recordBasis.toLowerCase().startsWith("l")) {//living -> fossil, herbarium sheet....???
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derivedThing = LivingBeing.NewInstance();
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}
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}
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if (derivedThing == null) derivedThing = Observation.NewInstance();
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TaxonNameBase taxonName = null;
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Taxon taxon = null;
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DeterminationEvent determinationEvent = null;
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List<TaxonNameBase> names = null;
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NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
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String scientificName="";
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boolean preferredFlag=false;
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System.out.println(this.identificationList);
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for (int i = 0; i < this.identificationList.size(); i++) {
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this.fullScientificNameString = this.identificationList.get(i);
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this.fullScientificNameString = this.fullScientificNameString.replaceAll(" et ", " & ");
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if (this.fullScientificNameString.indexOf("_preferred_") != -1){
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scientificName = this.fullScientificNameString.split("_preferred_")[0];
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String pTmp = this.fullScientificNameString.split("_preferred_")[1];
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if (pTmp == "1" || pTmp.toLowerCase().indexOf("true") != -1)
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preferredFlag=true;
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else
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preferredFlag=false;
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}
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else scientificName = this.fullScientificNameString;
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// taxonName = nvnpi.parseFullName(this.fullScientificNameString,NomenclaturalCode.ICZN(),null);
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// if (taxonName.hasProblem()){
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// System.out.println("pb ICZN");
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// taxonName = nvnpi.parseFullName(this.fullScientificNameString,NomenclaturalCode.ICBN(),null);
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// if (taxonName.hasProblem()){
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// System.out.println("pb ICBN");
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// taxonName = nvnpi.parseFullName(this.fullScientificNameString,NomenclaturalCode.ICNB(), null);
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// if (taxonName.hasProblem()){
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// System.out.println("pb ICNB");
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// taxonName = nvnpi.parseFullName(this.fullScientificNameString,NomenclaturalCode.ICNCP(), null);
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// if (taxonName.hasProblem()){
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// System.out.println("pb ICNCP");
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// }
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// }
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// }
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// }
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taxonName = nvnpi.parseFullName(scientificName);
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if (withCdm){
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names = app.getNameService().getNamesByName(scientificName);
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if (names.size() == 0){
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System.out.println("Name not found: " + scientificName);
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}else{
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if (names.size() > 1){
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System.out.println("More then 1 name found: " + scientificName);
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}
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System.out.println("Name found");
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taxonName = names.get(0);
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}
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}
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// tx = app.startTransaction();
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app.getNameService().saveOrUpdate(taxonName);
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taxon = Taxon.NewInstance(taxonName, sec); //TODO use real reference for sec
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// app.commitTransaction(tx);
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determinationEvent = DeterminationEvent.NewInstance();
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determinationEvent.setTaxon(taxon);
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determinationEvent.setPreferredFlag(preferredFlag);
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derivedThing.addDetermination(determinationEvent);
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}
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//set catalogue number (unitID)
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derivedThing.setCatalogNumber(this.unitID);
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derivedThing.setAccessionNumber(this.accessionNumber);
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derivedThing.setCollectorsNumber(this.collectorsNumber);
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/**
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* INSTITUTION & COLLECTION
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*/
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//manage institution
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Institution institution;
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List<Institution> institutions;
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try{
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System.out.println(this.institutionCode);
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institutions= app.getAgentService().searchInstitutionByCode(this.institutionCode);
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}catch(Exception e){
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System.out.println("BLI "+e);
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institutions=new ArrayList<Institution>();
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}
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318 |
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if (institutions.size() ==0){
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System.out.println("Institution (agent) unknown");
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//create institution
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institution = Institution.NewInstance();
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institution.setCode(this.institutionCode);
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}
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else{
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System.out.println("Institution (agent) already in the db");
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institution = institutions.get(0);
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}
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//manage collection
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Collection collection = Collection.NewInstance();
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List<Collection> collections;
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try{
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collections = app.getCollectionService().searchByCode(this.collectionCode);
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}catch(Exception e){
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System.out.println("BLA"+e);
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collections=new ArrayList<Collection>();
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337 |
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}
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338 |
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if (collections.size() ==0){
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System.out.println("Collection not found "+this.collectionCode);
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//create new collection
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collection.setCode(this.collectionCode);
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collection.setCodeStandard("GBIF");
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collection.setInstitute(institution);
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}
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else{
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346 |
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boolean collectionFound=false;
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347 |
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for (int i=0; i<collections.size(); i++){
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collection = collections.get(i);
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349 |
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try {
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350 |
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if (collection.getInstitute().getCode().equalsIgnoreCase(institution.getCode())){
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//found a collection with the same code and the same institution
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collectionFound=true;
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}
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} catch (NullPointerException e) {}
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355 |
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}
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System.out.println("a trouvé la collection avec la meme institution? "+collectionFound);
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357 |
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if (!collectionFound){ //need to add a new collection with the pre-configured institution
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collection.setCode(this.collectionCode);
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collection.setCodeStandard("GBIF");
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collection.setInstitute(institution);
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361 |
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}
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362 |
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363 |
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}
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364 |
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System.out.println("collection inserted");
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//link specimen & collection
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derivedThing.setCollection(collection);
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367 |
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368 |
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/**
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* GATHERING EVENT
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370 |
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*/
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371 |
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//create gathering event
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372 |
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GatheringEvent gatheringEvent = GatheringEvent.NewInstance();
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373 |
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//add locality
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374 |
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Language language = Language.DEFAULT();
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LanguageString loc = LanguageString.NewInstance(this.locality,language);
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gatheringEvent.setLocality(loc);
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377 |
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//create coordinates point
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379 |
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Point coordinates = Point.NewInstance();
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380 |
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//add coordinates
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381 |
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coordinates.setLatitude(this.latitude);
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382 |
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coordinates.setLongitude(this.longitude);
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383 |
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gatheringEvent.setExactLocation(coordinates);
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384 |
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|
385 |
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NamedArea area = NamedArea.NewInstance();
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386 |
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|
387 |
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|
388 |
|
WaterbodyOrCountry country = null;
|
389 |
|
// System.out.println("isocountry "+this.isocountry);
|
390 |
|
if (this.isocountry != null)
|
391 |
|
country = app.getOccurrenceService().getCountryByIso(this.isocountry);
|
392 |
|
|
393 |
|
// System.out.println(country.getLabel());
|
394 |
|
// Set<Continent> cont = country.getContinents();
|
395 |
|
//
|
396 |
|
// System.out.println(cont.size());
|
397 |
|
// Iterator<Continent> iter = cont.iterator();
|
398 |
|
// while (iter.hasNext())
|
399 |
|
// System.out.println(iter.next().toString());
|
400 |
|
|
401 |
|
if (country != null){
|
402 |
|
area.addWaterbodyOrCountry(country);
|
403 |
|
System.out.println("country not null!");
|
404 |
|
}
|
405 |
|
// else{
|
406 |
|
// if (this.country != null){
|
407 |
|
// List<WaterbodyOrCountry>countries = app.getOccurrenceService().getWaterbodyOrCountryByName(this.country);
|
408 |
|
// if (countries.size() >0)
|
409 |
|
// area.addWaterbodyOrCountry(countries.get(0));
|
410 |
|
// else
|
411 |
|
// System.out.println("NO COUNTRY");//TODO need to add a new country!
|
412 |
|
// }
|
413 |
|
// }
|
414 |
|
// app.getTermService().saveTerm(area);
|
415 |
|
gatheringEvent.addCollectingArea(area);
|
416 |
|
|
417 |
|
//create collector
|
418 |
|
AgentBase collector;
|
419 |
|
ListIterator<String> collectors = this.gatheringAgentList.listIterator();
|
420 |
|
//add the collectors
|
421 |
|
String collName;
|
422 |
|
while (collectors.hasNext()){
|
423 |
|
collName = collectors.next();
|
424 |
|
/*check if the collector does already exist*/
|
425 |
|
try{
|
426 |
|
Pager<AgentBase> col = app.getAgentService().findByTitle(null, collName, null, null, null, null, null, null);
|
427 |
|
collector=col.getRecords().get(0);
|
428 |
|
System.out.println("a trouve l'agent");
|
429 |
|
}catch (Exception e) {
|
430 |
|
collector = Person.NewInstance();
|
431 |
|
collector.setTitleCache(collName, true);
|
432 |
|
}
|
433 |
|
gatheringEvent.setCollector(collector);
|
434 |
|
}
|
435 |
|
|
436 |
|
//create field/observation
|
437 |
|
FieldObservation fieldObservation = FieldObservation.NewInstance();
|
438 |
|
//add fieldNumber
|
439 |
|
fieldObservation.setFieldNumber(this.fieldNumber);
|
440 |
|
|
441 |
|
//join gatheringEvent to fieldObservation
|
442 |
|
fieldObservation.setGatheringEvent(gatheringEvent);
|
443 |
|
|
444 |
|
|
445 |
|
// //link fieldObservation and specimen
|
446 |
|
DerivationEvent derivationEvent = DerivationEvent.NewInstance();
|
447 |
|
derivationEvent.addOriginal(fieldObservation);
|
448 |
|
derivedThing.addDerivationEvent(derivationEvent);
|
449 |
|
// derivationEvent.addDerivative(derivedThing);
|
450 |
|
|
451 |
|
/**
|
452 |
|
* SAVE AND STORE DATA
|
453 |
|
*/
|
454 |
|
//save the specimen data
|
455 |
|
// app.getOccurrenceService().saveSpecimenOrObservationBase(fieldObservation);
|
456 |
|
try {
|
457 |
|
// tx = app.startTransaction();
|
458 |
|
app.getTermService().saveOrUpdate(area);//save it sooner
|
459 |
|
app.getOccurrenceService().saveOrUpdate(derivedThing);
|
460 |
|
// app.commitTransaction(tx);
|
461 |
|
// app.close();
|
462 |
|
} catch (Exception e) {
|
463 |
|
// TODO Auto-generated catch block
|
464 |
|
System.out.println("PATATE "+e);
|
465 |
|
}
|
466 |
|
|
467 |
|
|
468 |
|
logger.info("saved new specimen ...");
|
469 |
|
|
470 |
|
|
471 |
|
|
472 |
|
} catch (Exception e) {
|
473 |
|
logger.warn("Error when reading record!!");
|
474 |
|
e.printStackTrace();
|
475 |
|
result = false;
|
476 |
|
}
|
477 |
|
//
|
478 |
|
app.commitTransaction(tx);
|
479 |
|
System.out.println("commit done");
|
480 |
|
app.close();
|
481 |
|
|
482 |
|
return result;
|
483 |
|
}
|
484 |
|
|
485 |
|
|
486 |
|
|
487 |
|
private DeterminationEvent getDetermination(Taxon taxon, String actor){
|
488 |
|
logger.info("Create determination event");
|
489 |
|
DeterminationEvent determinationEvent = DeterminationEvent.NewInstance();
|
490 |
|
determinationEvent.setTaxon(taxon);
|
491 |
|
Person person = Person.NewTitledInstance(actor);
|
492 |
|
determinationEvent.setActor(person);
|
493 |
|
return determinationEvent;
|
494 |
|
}
|
495 |
|
|
496 |
|
|
497 |
|
|
498 |
|
/**
|
499 |
|
* @param args
|
500 |
|
*/
|
501 |
|
public static void main(String[] args) {
|
502 |
|
logger.info("main method");
|
503 |
|
SynthesysCacheActivator abcdAct = new SynthesysCacheActivator();
|
504 |
|
ArrayList<Hashtable<String,String>> units = abcdAct.parseXLS();
|
505 |
|
Hashtable<String,String> unit=null;
|
506 |
|
for (int i=0; i<units.size();i++){
|
507 |
|
unit = units.get(i);
|
508 |
|
System.out.println(unit);
|
509 |
|
abcdAct.saveUnit(unit);//and then invoke
|
510 |
|
abcdAct.invoke();
|
511 |
|
|
512 |
|
}
|
513 |
|
}
|
514 |
|
|
|
34 |
@SuppressWarnings("unused")
|
|
35 |
private static Logger logger = Logger.getLogger(SynthesysCacheActivator.class);
|
|
36 |
|
|
37 |
//database validation status (create, update, validate ...)
|
|
38 |
|
|
39 |
// final static String xmlSource = "/home/pkelbert/workspace/proibiosphere/cdmlib-io/target/test-classes/eu/etaxonomy/cdm/io/specimen/excel/in/ExcelImportConfiguratorTest-input.xls";
|
|
40 |
final static String xmlSource = "/home/pkelbert/Documents/Proibiosphere/ChenopodiumQuentin/GBIF data etc.xls";
|
|
41 |
|
|
42 |
|
|
43 |
// static final ICdmDataSource cdmDestination = CdmDestinations.mon_cdm();
|
|
44 |
// static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
|
|
45 |
static final ICdmDataSource cdmDestination = CdmDestinations.proibiosphere_local();
|
|
46 |
static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
|
|
47 |
static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
|
|
48 |
|
|
49 |
/**
|
|
50 |
* @param args
|
|
51 |
*/
|
|
52 |
public static void main(String[] args) {
|
|
53 |
URI source;
|
|
54 |
try {
|
|
55 |
URI uri = new File(xmlSource).toURI();
|
|
56 |
source = new URI(uri.toString());
|
|
57 |
System.out.println(source.toString());
|
|
58 |
System.out.println("Start import from Excel Specimen data("+ source.toString() + ") ...");
|
|
59 |
|
|
60 |
ICdmDataSource destination = cdmDestination;
|
|
61 |
SpecimenSynthesysExcelImportConfigurator specimenImportConfigurator = SpecimenSynthesysExcelImportConfigurator.NewInstance(source, destination);
|
|
62 |
|
|
63 |
specimenImportConfigurator.setSourceSecId("specimen");
|
|
64 |
specimenImportConfigurator.setCheck(check);
|
|
65 |
specimenImportConfigurator.setDbSchemaValidation(hbm2dll);
|
|
66 |
specimenImportConfigurator.setDoAutomaticParsing(true);
|
|
67 |
specimenImportConfigurator.setReUseExistingMetadata(true);
|
|
68 |
specimenImportConfigurator.setAskForDate(true);
|
|
69 |
specimenImportConfigurator.setDefaultAuthor("L.");
|
|
70 |
specimenImportConfigurator.setClassificationName("Chenopodium");
|
|
71 |
|
|
72 |
specimenImportConfigurator.setReUseTaxon(true);
|
|
73 |
|
|
74 |
specimenImportConfigurator.setSourceReference(null);
|
|
75 |
specimenImportConfigurator.setTaxonReference(null);
|
|
76 |
|
|
77 |
// invoke import
|
|
78 |
CdmDefaultImport<SpecimenSynthesysExcelImportConfigurator> specimenImport = new CdmDefaultImport<SpecimenSynthesysExcelImportConfigurator>();
|
|
79 |
//new Test().invoke(tcsImportConfigurator);
|
|
80 |
specimenImport.invoke(specimenImportConfigurator);
|
|
81 |
System.out.println("End import from SpecimenData ("+ source.toString() + ")...");
|
|
82 |
} catch (URISyntaxException e) {
|
|
83 |
e.printStackTrace();
|
|
84 |
}
|
|
85 |
|
|
86 |
}
|
515 |
87 |
|
516 |
88 |
|
517 |
89 |
}
|
copy main method for abcd and synthesys excel import testing