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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.io.specimen;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.UUID;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.api.service.IAgentService;
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import eu.etaxonomy.cdm.api.service.ITermService;
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import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
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import eu.etaxonomy.cdm.io.specimen.abcd206.in.Abcd206ImportConfigurator;
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import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenSynthesysExcelImportConfigurator;
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import eu.etaxonomy.cdm.io.taxonx2013.TaxonXImportConfigurator;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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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.TimePeriod;
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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.ReferenceSystem;
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import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
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/**
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* @author p.kelbert
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* @created 20.10.2008
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* @version 1.0
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*/
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public class UnitsGatheringEvent {
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private static final Logger logger = Logger.getLogger(UnitsGatheringEvent.class);
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private static final boolean DEBUG = false;
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private final GatheringEvent gatheringEvent = GatheringEvent.NewInstance();
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/*
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* Constructor
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* Fill in the locality, coordinates and the collector(s) for the current GatheringEvent
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* @param app: the CDM Application Controller
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* @param locality
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* @param languageIso
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* @param longitude
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* @param latitude
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* @param collectorNames
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*/
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public UnitsGatheringEvent(ITermService termService, String locality, String languageIso, Double longitude,
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Double latitude, String collectorName, String team, SpecimenSynthesysExcelImportConfigurator config){
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this.setLocality(termService, locality, languageIso);
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this.setCoordinates(longitude, latitude);
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if (!collectorName.isEmpty()) {
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this.setCollector(collectorName, config);
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}
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if (!team.isEmpty()) {
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this.setTeam(team, config);
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}
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}
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//
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public UnitsGatheringEvent(ITermService termService, String locality, String collectorName, Double longitude,
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Double latitude, TaxonXImportConfigurator config,IAgentService agentService){
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if (!StringUtils.isEmpty(locality)) {
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this.setLocality(termService, locality, null);
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}
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this.setCoordinates(longitude, latitude);
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if (!StringUtils.isEmpty(collectorName)) {
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this.setCollector(collectorName, config, agentService);
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}
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// if (!team.isEmpty()) {
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// this.setTeam(team, config);
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// }
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}
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/*
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* Constructor
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* Fill in the locality, coordinates and the collector(s) for the current GatheringEvent
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* @param app: the CDM Application Controller
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* @param locality
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* @param languageIso
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* @param longitude
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* @param latitude
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* @param collectorNames
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*/
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public UnitsGatheringEvent(ITermService termService, String locality, String languageIso, Double longitude,
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Double latitude, String elevationText, String elevationMin, String elevationMax, String elevationUnit,
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String date, String gatheringNotes, String gatheringMethod, ReferenceSystem referenceSystem,
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Abcd206ImportConfigurator config) {
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this.setLocality(termService, locality, languageIso);
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this.setCoordinates(longitude, latitude, referenceSystem);
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this.setDate(date);
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this.setNotes(gatheringNotes);
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this.setElevation(elevationText, elevationMin, elevationMax, elevationUnit);
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this.setGatheringMethod(gatheringMethod);
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}
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/**
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* @param gatheringImages
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*/
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public void setGatheringImages(HashMap<String, Map<String, String>> gatheringImages) {
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}
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public GatheringEvent getGatheringEvent(){
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return this.gatheringEvent;
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}
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/**
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* Set the locality for the current GatheringEvent
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* @param locality
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* @param langageIso
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*/
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public void setLocality(ITermService termService, String locality, String languageIso){
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LanguageString loc = null;
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List<LanguageString> languages = termService.getAllLanguageStrings(0, 0);
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boolean locFound=false;
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if ((languageIso == null) || (termService.getLanguageByIso(languageIso) == null)){
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// if (languageIso != null && termService.getLanguageByIso(languageIso) == null ){
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// logger.info("unknown iso used for the locality: "+languageIso);
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// }
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for (LanguageString ls:languages){
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if (ls == null) {
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continue;
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}
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ls = HibernateProxyHelper.deproxy(ls, LanguageString.class);
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if (ls.getText() == null){
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continue;
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}
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if (ls.getText().equalsIgnoreCase(locality)){
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loc=ls;
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locFound=true;
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// System.out.println("REUSE LOCALITY");
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}
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}
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if (!locFound){
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loc = LanguageString.NewInstance(locality, Language.DEFAULT());
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termService.saveLanguageData(loc);
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languages.add(loc);
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}
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}else{
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for (LanguageString ls:languages){
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if (ls.getText().equalsIgnoreCase(locality) && ls.getLanguage().equals(termService.getLanguageByIso(languageIso))){
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loc=ls;
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locFound=true;
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// System.out.println("REUSE LOCALITY");
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}
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}
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if (!locFound) {
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loc = LanguageString.NewInstance(locality, termService.getLanguageByIso(languageIso));
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termService.saveLanguageData(loc);
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languages.add(loc);
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}
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}
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if (loc == null){logger.warn("PROBLEM LOCALITY");}
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this.gatheringEvent.setLocality(loc);
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}
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/*
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* return the locality associated to the GatheringEvent
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*/
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public LanguageString getLocality(){
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return this.gatheringEvent.getLocality();
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}
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/*
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* Set the coordinates for the current GatheringEvent
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* @param: longitude
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* @param: latitude
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*/
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public void setCoordinates(Double longitude, Double latitude){
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setCoordinates(longitude, latitude, null);
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}
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public void setCoordinates(Double longitude, Double latitude, ReferenceSystem referenceSystem){
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//create coordinates point
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if((longitude == null) || (latitude == null)){
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return;
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}
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Point coordinates = Point.NewInstance();
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//add coordinates
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if (longitude != 0.0) {
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coordinates.setLongitude(longitude);
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}
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if (latitude != 0.0) {
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coordinates.setLatitude(latitude);
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}
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coordinates.setReferenceSystem(referenceSystem);
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this.gatheringEvent.setExactLocation(coordinates);
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}
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public void setNotes(String gatheringNotes){
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this.gatheringEvent.addAnnotation(Annotation.NewDefaultLanguageInstance(gatheringNotes));
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}
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public void setDate(String date){
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TimePeriod timeperiod = this.gatheringEvent.getTimeperiod();
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if(timeperiod==null){
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timeperiod = TimePeriod.NewInstance();
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this.gatheringEvent.setTimeperiod(timeperiod);
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}
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timeperiod.setFreeText(date);
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}
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public void setElevation(String elevationText, String elevationMin, String elevationMax, String elevationUnit){
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if(elevationText!=null){
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this.gatheringEvent.setAbsoluteElevationText(elevationText);
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}
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else{
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//TODO check for unit at string end
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String pattern = "\\D";// regex for non-digits
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if(elevationMin!=null){
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Integer min = Integer.parseInt(elevationMin.replaceAll(pattern, ""));
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this.gatheringEvent.setAbsoluteElevation(min);
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}
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if(elevationMax!=null){
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Integer max = Integer.parseInt(elevationMax.replaceAll(pattern, ""));
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this.gatheringEvent.setAbsoluteElevationMax(max);
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}
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if(elevationUnit!=null){
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if(!elevationUnit.equals("m")){
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//TODO convert if necessary
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}
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}
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}
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}
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public void setHeight(String heightText, String heightMin, String heightMax, String heightUnit){
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if(heightText!=null){
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this.gatheringEvent.setAbsoluteElevationText(heightText);
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}
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else{
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//TODO check for unit at string end
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String pattern = "\\D";// regex for non-digits
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if(heightMin!=null){
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Double min = Double.parseDouble(heightMin.replaceAll(pattern, ""));
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this.gatheringEvent.setDistanceToGround(min);
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}
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if(heightMax!=null){
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Double max = Double.parseDouble(heightMax.replaceAll(pattern, ""));
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this.gatheringEvent.setDistanceToGroundMax(max);
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}
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if(heightUnit!=null){
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if (!heightUnit.equals("m")){
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logger.debug("The unit " + heightUnit + " of the distance to ground is not meter.");
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}
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}
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}
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}
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public void setGatheringDepth(String depthText, Double depthMin, Double depthMax, String depthUnit){
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if(depthText!=null){
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this.gatheringEvent.setDistanceToWaterSurfaceText(depthText);
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}
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else{
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if(depthMin!=null){
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this.gatheringEvent.setDistanceToWaterSurface(depthMin);
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}
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if(depthMax!=null){
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this.gatheringEvent.setDistanceToWaterSurfaceMax(depthMax);
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}
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if(depthUnit!=null){
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if (!depthUnit.equals("m")){
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logger.debug("The unit " + depthUnit + " of the distance to ground is not meter.");
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}
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}
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}
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}
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/*
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* Add a NamedArea to the GatheringEvent
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* @param area: the NamedArea to add
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*/
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public void addArea(DefinedTermBase area){
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if (area.isInstanceOf(NamedArea.class)) {
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this.gatheringEvent.addCollectingArea((NamedArea) area);
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} else {
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logger.info("OUPPPPSS :"+area.getClass());
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}
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}
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/*
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* Create a new collector or collector's team
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* @param: collectorNames: the list of names to add as collector/collectorTeam
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* USED - create each time a new Collector
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*/
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public void setCollector(String collectorName, SpecimenSynthesysExcelImportConfigurator config){
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// System.out.println("collectors : "+collectorNames.toString());
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Person collector;
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collector = Person.NewInstance();
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collector.setTitleCache(collectorName, true);
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if (DEBUG) {
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System.out.println("getcoll:"+config.getPersons().get(collector.getTitleCache()));
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}
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this.gatheringEvent.setCollector(config.getPersons().get(collector.getTitleCache()));
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}
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/*
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* Create a new collector or collector's team
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* @param: collectorNames: the list of names to add as collector/collectorTeam
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* USED - create each time a new Collector
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*/
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public void setCollector(String collectorName, TaxonXImportConfigurator config, IAgentService agentService){
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// System.out.println("collectors : "+collectorNames.toString());
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Person collector;
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collector = Person.NewInstance();
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collector.setTitleCache(collectorName, true);
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Person collector_db = config.getPersons().get(collector.getTitleCache());
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if (collector_db == null) {
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UUID uuid = agentService.saveOrUpdate(collector);
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collector_db=(Person) agentService.find(uuid);
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}
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this.gatheringEvent.setCollector(collector_db);
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}
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/*
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* Create a new collector or collector's team
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* @param: collectorNames: the list of names to add as collector/collectorTeam
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* USED - create each time a new Collector
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*/
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public void setCollector(TeamOrPersonBase collector, Abcd206ImportConfigurator config){
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// System.out.println("collectors : "+collectorNames.toString());
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if (DEBUG) {
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System.out.println("getcoll:"+config.getPersons().get(collector.getTitleCache()));
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}
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this.gatheringEvent.setCollector(collector);
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}
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/**
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* @param tp
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*/
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public void setGatheringDate(TimePeriod tp) {
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this.gatheringEvent.setTimeperiod(tp);
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}
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/**
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* @param tp
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*/
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public void setGatheringMethod(String gatheringMethod) {
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this.gatheringEvent.setCollectingMethod(gatheringMethod);
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}
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public String getGatheringMethod(){
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return this.gatheringEvent.getCollectingMethod();
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}
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/**
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* @param gatheringTeam
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*/
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public void setTeam(String gatheringTeam, SpecimenSynthesysExcelImportConfigurator config) {
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Team t = new Team();
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if ((gatheringTeam != null) && !gatheringTeam.isEmpty()) {
|
|
378
|
if ((gatheringTeam.indexOf("et al.") != -1) || (gatheringTeam.indexOf("& al.") != -1) || (gatheringTeam.indexOf(" al.") != -1)){
|
|
379
|
t.setTitleCache(gatheringTeam);
|
|
380
|
} else{
|
|
381
|
String[] tmp1 = gatheringTeam.split(" et ");
|
|
382
|
for (String elt:tmp1){
|
|
383
|
String tmp2[] = elt.split("&");
|
|
384
|
for (String elt2:tmp2) {
|
|
385
|
if (!elt2.trim().isEmpty()) {
|
|
386
|
Person p = Person.NewInstance();
|
|
387
|
p.setTitleCache(elt2);
|
|
388
|
t.addTeamMember(p);
|
|
389
|
}
|
|
390
|
}
|
|
391
|
}
|
|
392
|
}
|
|
393
|
}
|
|
394
|
if (DEBUG) {
|
|
395
|
System.out.println("getteam:"+config.getTeams().get(t.getTitleCache()));
|
|
396
|
}
|
|
397
|
this.gatheringEvent.setCollector(config.getTeams().get(t.getTitleCache()));
|
|
398
|
}
|
|
399
|
|
|
400
|
/**
|
|
401
|
* @param gatheringTeam
|
|
402
|
*/
|
|
403
|
public void setTeam(String gatheringTeam, Abcd206ImportConfigurator config) {
|
|
404
|
Team t = new Team();
|
|
405
|
if ((gatheringTeam != null) && !gatheringTeam.isEmpty()) {
|
|
406
|
if ((gatheringTeam.indexOf("et al.") != -1) || (gatheringTeam.indexOf("& al.") != -1) || (gatheringTeam.indexOf(" al.") != -1)){
|
|
407
|
t.setTitleCache(gatheringTeam);
|
|
408
|
} else{
|
|
409
|
String[] tmp1 = gatheringTeam.split(" et ");
|
|
410
|
for (String elt:tmp1){
|
|
411
|
String tmp2[] = elt.split("&");
|
|
412
|
for (String elt2:tmp2) {
|
|
413
|
if (!elt2.trim().isEmpty()) {
|
|
414
|
Person p = Person.NewInstance();
|
|
415
|
p.setTitleCache(elt2);
|
|
416
|
t.addTeamMember(p);
|
|
417
|
}
|
|
418
|
}
|
|
419
|
}
|
|
420
|
}
|
|
421
|
}
|
|
422
|
if (DEBUG) {
|
|
423
|
System.out.println("getteam:"+config.getTeams().get(t.getTitleCache()));
|
|
424
|
}
|
|
425
|
//this.gatheringEvent.setCollector(config.getTeams().get(t.getTitleCache()));
|
|
426
|
}
|
|
427
|
|
|
428
|
|
|
429
|
}
|