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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.excel.in;
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import java.io.FileNotFoundException;
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import java.net.MalformedURLException;
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import java.net.URI;
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import java.util.ArrayList;
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import java.util.Calendar;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Scanner;
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import java.util.Set;
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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 org.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
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import eu.etaxonomy.cdm.common.ExcelUtils;
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import eu.etaxonomy.cdm.io.common.CdmImportBase;
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import eu.etaxonomy.cdm.io.common.ICdmIO;
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import eu.etaxonomy.cdm.io.specimen.UnitsGatheringArea;
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import eu.etaxonomy.cdm.io.specimen.UnitsGatheringEvent;
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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.agent.Team;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DefinedTermBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.name.ITaxonNameBase;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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import eu.etaxonomy.cdm.model.occurrence.Collection;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
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import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
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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.Classification;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
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/**
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* @author p.kelbert
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* @created 29.10.2008
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* @date 13 mars 2013
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*
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*/
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@Component
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public class SpecimenSythesysExcelImport extends CdmImportBase<SpecimenSynthesysExcelImportConfigurator, SpecimenSynthesysExcelImportState>
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implements ICdmIO<SpecimenSynthesysExcelImportState> {
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private static final Logger logger = Logger.getLogger(SpecimenSythesysExcelImport.class);
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protected String fullScientificNameString;
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protected String nomenclatureCode;
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protected String institutionCode;
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protected String collectionCode;
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protected String unitID;
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protected String recordBasis;
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protected String accessionNumber;
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protected String fieldNumber;
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protected Double longitude;
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protected Double latitude;
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protected String locality;
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protected String languageIso = null;
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protected String country;
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protected String isocountry;
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protected int depth;
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protected int altitude;
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protected String gatheringYear;
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protected String gatheringMonth;
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protected String gatheringDay;
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protected String gatheringDate;
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protected String gatheringTeam;
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protected String gatheringAgent;
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protected String originalsource;
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protected String identifier;
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protected String gatheringNotes;
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private DerivedUnit derivedUnitBase;
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private Reference ref = null;
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private TransactionStatus tx;
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private Classification classification = null;
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protected ArrayList<String> identificationList = new ArrayList<String>();
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protected ArrayList<String> multimediaObjects = new ArrayList<String>();
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private boolean keepAtomisedDate=true;
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private boolean useTDWGarea = true;
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boolean DEBUG =false;
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public SpecimenSythesysExcelImport() {
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super();
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}
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/**
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* private HashMap that handle null values (missing keys)
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* return empty string instead of null
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* */
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public class MyHashMap<K,V> extends HashMap<K,V> {
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/**
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*
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*/
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private static final long serialVersionUID = -6230407405666753405L;
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@SuppressWarnings("unchecked")
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@Override
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public V get(Object key) {
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Object a;
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if (containsKey(key)) {
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a= super.get(key);
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} else {
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a="";
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}
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if (a ==null || a.toString().equalsIgnoreCase("none")) {
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a="";
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}
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return (V) a;
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}
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}
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/**
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* getClassification : get the classification declared in the ImportState
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*
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* @param state
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* @return
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*/
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private void setClassification(SpecimenSynthesysExcelImportState state) {
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if (classification == null){
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boolean configreused=false;
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if (state.getConfig().getClassificationName()!=null && state.getConfig().getClassificationName().equalsIgnoreCase("Goosefoots")) {
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classification = getClassificationService().find(UUID.fromString("2c2dc41c-9891-42cd-9cd5-8b28dfdd1b8a"));
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if (classification ==null){
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String name = state.getConfig().getClassificationName();
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classification = Classification.NewInstance(name, ref, Language.DEFAULT());
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getClassificationService().saveOrUpdate(classification);
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}
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configreused=true;
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}
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if (state.getConfig().getClassificationName()!=null && state.getConfig().getClassificationName().equalsIgnoreCase("Ants")) {
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classification = getClassificationService().find(UUID.fromString("9b72d32f-2868-4f0d-81bd-ebc38ee8c645"));
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if (classification ==null){
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String name = state.getConfig().getClassificationName();
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classification = Classification.NewInstance(name, ref, Language.DEFAULT());
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getClassificationService().saveOrUpdate(classification);
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}
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configreused=true;
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}
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if (state.getConfig().getClassificationName()!=null && state.getConfig().getClassificationName().equalsIgnoreCase("Fungi")) {
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classification = getClassificationService().find(UUID.fromString("fe07274d-daff-4678-9f7d-2c3916948c3e"));
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if (classification ==null){
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String name = state.getConfig().getClassificationName();
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classification = Classification.NewInstance(name, ref, Language.DEFAULT());
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getClassificationService().saveOrUpdate(classification);
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}
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configreused=true;
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}
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if (state.getConfig().getClassificationName()!=null && state.getConfig().getClassificationName().equalsIgnoreCase("Campylopus")) {
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classification = getClassificationService().find(UUID.fromString("9dccbd11-eb0e-4cac-ae04-aa61ad82b8a6"));
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if (classification ==null){
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String name = state.getConfig().getClassificationName();
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classification = Classification.NewInstance(name, ref, Language.DEFAULT());
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getClassificationService().saveOrUpdate(classification);
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}
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configreused=true;
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}
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if (state.getConfig().getClassificationName()!=null && state.getConfig().getClassificationName().equalsIgnoreCase("Eupolybothrus")) {
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classification = getClassificationService().find(UUID.fromString("62ce65e0-e036-49aa-aae7-4d4d0f88966c"));
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if (classification ==null){
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String name = state.getConfig().getClassificationName();
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classification = Classification.NewInstance(name, ref, Language.DEFAULT());
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getClassificationService().saveOrUpdate(classification);
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}
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configreused=true;
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}
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if(!configreused){
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String name = state.getConfig().getClassificationName();
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classification = Classification.NewInstance(name, ref, Language.DEFAULT());
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if (state.getConfig().getClassificationUuid() != null) {
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classification.setUuid(state.getConfig().getClassificationUuid());
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}
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getClassificationService().saveOrUpdate(classification);
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}
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}
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}
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/**
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* refresh the hibernate transaction :
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* - commit the current queries
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* - get the reference and the classification and the derivedUnitBase back from the hibernate session
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* */
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private void refreshTransaction(){
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commitTransaction(tx);
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tx = startTransaction();
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ref = getReferenceService().find(ref.getUuid());
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classification = getClassificationService().find(classification.getUuid());
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try{
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derivedUnitBase = (DerivedUnit) getOccurrenceService().find(derivedUnitBase.getUuid());
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}catch(Exception e){
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//logger.warn("derivedunit up to date or not created yet");
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}
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}
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// /**
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// * refresh the hibernate transaction :
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// * - commit the current queries
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// * - get the reference and the classification and the derivedUnitBase back from the hibernate session
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// * */
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// private void refreshTransac(){
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// commitTransaction(tx);
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// tx = startTransaction();
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// }
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/*
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* Store the unit's properties into variables
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* @param unit: the hashmap containing the splitted Excel line (Key=column name, value=value)
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*/
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private void setUnitPropertiesExcel(MyHashMap<String,String> unit, String defaultAuthor){
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multimediaObjects = new ArrayList<String>();
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identificationList = new ArrayList<String>();
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gatheringTeam="";
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gatheringAgent="";
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String author = unit.get("author");
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if (author.isEmpty() && !defaultAuthor.isEmpty()) {
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author=defaultAuthor;
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}
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String taxonName = unit.get("taxonName");
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institutionCode = unit.get("institution");
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collectionCode = unit.get("collection");
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unitID = unit.get("unitID");
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recordBasis = unit.get("recordBasis");
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accessionNumber = null;
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try {longitude = Double.valueOf(unit.get("longitude"));
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} catch (Exception e) {longitude = 0.0;}
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try {latitude = Double.valueOf(unit.get("latitude"));
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} catch (Exception e) {latitude = 0.0;}
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country = unit.get("country");
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isocountry = unit.get("isoCountry");
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locality = unit.get("locality");
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String habitat = unit.get("habitat");
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String stateProvince = unit.get("stateProvince");
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if (!stateProvince.isEmpty()) {
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locality=stateProvince+", "+locality;
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}
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if (!habitat.isEmpty()){
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locality+=" (Habitat: "+habitat+")";
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}
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fieldNumber = unit.get("field number");
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String url =unit.get("url");
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if (!url.isEmpty()) {
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multimediaObjects.add(url);
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}
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String coll =unit.get("collector");
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if (!coll.isEmpty()) {
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if (coll.indexOf("& al.")!=-1 || coll.indexOf("et al.") != -1 || coll.indexOf(" al. ")!=-1 ||
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coll.indexOf("&") != -1 || coll.indexOf(" et ") != -1 || coll.indexOf(";")!=-1) {
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gatheringTeam = coll;
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} else{
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//single
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gatheringAgent = coll;
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}
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}
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if(!taxonName.contains(author)) {
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identificationList.add(taxonName+" "+author);
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} else {
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identificationList.add(taxonName);
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}
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gatheringYear = unit.get("year");
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gatheringMonth = unit.get("month");
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gatheringDay = unit.get("day");
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gatheringDate = unit.get("date");
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gatheringNotes = unit.get("eventRemarks");
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originalsource = unit.get("originalsource");
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identifier = unit.get("identifier");
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}
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private Institution getInstitution(SpecimenSynthesysExcelImportConfigurator config){
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Institution institution;
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List<Institution> institutions;
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try{
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institutions= getAgentService().searchInstitutionByCode(institutionCode);
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}catch(Exception e){
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institutions=new ArrayList<Institution>();
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}
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if (institutions.size() ==0 || !config.getReUseExistingMetadata()){
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logger.debug("Institution (agent) unknown or not allowed to reuse existing metadata");
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//create institution
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institution = Institution.NewInstance();
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institution.setCode(institutionCode);
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getAgentService().saveOrUpdate(institution);
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}
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else{
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logger.debug("Institution (agent) already in the db");
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institution = institutions.get(0);
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}
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return CdmBase.deproxy(institution, Institution.class);
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}
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/*
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* Look if the Collection does already exists
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* @param collectionCode: a string
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* @param institution: the current Institution
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* @param app
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* @return the Collection (existing or new)
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*/
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private Collection getCollection(Institution institution, SpecimenSynthesysExcelImportConfigurator config){
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Collection collection =null;
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List<Collection> collections;
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try{
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collections = getCollectionService().searchByCode(collectionCode);
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}catch(Exception e){
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collections=new ArrayList<Collection>();
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}
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359
|
if (collections.size() ==0 || !config.getReUseExistingMetadata()){
|
|
360
|
logger.debug("Collection not found or do not reuse existing metadata "+collectionCode);
|
|
361
|
//create new collection
|
|
362
|
collection= Collection.NewInstance();
|
|
363
|
collection.setCode(collectionCode);
|
|
364
|
collection.setCodeStandard("GBIF");
|
|
365
|
collection.setInstitute(institution);
|
|
366
|
}
|
|
367
|
else{
|
|
368
|
boolean collectionFound=false;
|
|
369
|
for (int i=0; i<collections.size(); i++){
|
|
370
|
collection = collections.get(i);
|
|
371
|
try {
|
|
372
|
if (collection.getInstitute().getCode().equalsIgnoreCase(institution.getCode())){
|
|
373
|
//found a collection with the same code and the same institution
|
|
374
|
collectionFound=true;
|
|
375
|
}
|
|
376
|
} catch (NullPointerException e) {}
|
|
377
|
}
|
|
378
|
if (!collectionFound){
|
|
379
|
collection= Collection.NewInstance();
|
|
380
|
collection.setCode(collectionCode);
|
|
381
|
collection.setCodeStandard("GBIF");
|
|
382
|
collection.setInstitute(institution);
|
|
383
|
}
|
|
384
|
|
|
385
|
}
|
|
386
|
return collection;
|
|
387
|
}
|
|
388
|
|
|
389
|
/*
|
|
390
|
*
|
|
391
|
* @param app
|
|
392
|
* @param derivedThing
|
|
393
|
* @param sec
|
|
394
|
*/
|
|
395
|
private void setTaxonName(SpecimenSynthesysExcelImportConfigurator config){
|
|
396
|
ITaxonNameBase taxonName = null;
|
|
397
|
Taxon taxon = null;
|
|
398
|
|
|
399
|
String scientificName="";
|
|
400
|
boolean preferredFlag=false;
|
|
401
|
|
|
402
|
for (int i = 0; i < identificationList.size(); i++) {
|
|
403
|
String fullScientificNameString = identificationList.get(i);
|
|
404
|
fullScientificNameString = fullScientificNameString.replaceAll(" et ", " & ");
|
|
405
|
if (fullScientificNameString.indexOf("_preferred_") != -1){
|
|
406
|
scientificName = fullScientificNameString.split("_preferred_")[0].trim();
|
|
407
|
String pTmp = fullScientificNameString.split("_preferred_")[1].split("_code_")[0];
|
|
408
|
if (pTmp == "1" || pTmp.toLowerCase().indexOf("true") != -1) {
|
|
409
|
preferredFlag=true;
|
|
410
|
} else {
|
|
411
|
preferredFlag=false;
|
|
412
|
}
|
|
413
|
}else {
|
|
414
|
scientificName = fullScientificNameString.trim();
|
|
415
|
}
|
|
416
|
|
|
417
|
if (fullScientificNameString.indexOf("_code_") != -1){
|
|
418
|
nomenclatureCode = fullScientificNameString.split("_code_")[1].trim();
|
|
419
|
}
|
|
420
|
|
|
421
|
if (config.getDoReUseTaxon()){
|
|
422
|
List<TaxonBase> c = null;
|
|
423
|
try {
|
|
424
|
Taxon cc= getTaxonService().findBestMatchingTaxon(scientificName);
|
|
425
|
if (cc != null){
|
|
426
|
if ((cc.getSec() == null || cc.getSec().toString().isEmpty()) || (cc.getSec() != null &&
|
|
427
|
cc.getSec().getTitleCache().equalsIgnoreCase(ref.getTitleCache()))) {
|
|
428
|
if(cc.getSec() == null || cc.getSec().toString().isEmpty()){
|
|
429
|
cc.setSec(ref);
|
|
430
|
getTaxonService().saveOrUpdate(cc);
|
|
431
|
}
|
|
432
|
taxon=cc;
|
|
433
|
}
|
|
434
|
}
|
|
435
|
else{
|
|
436
|
c = getTaxonService().searchTaxaByName(scientificName, ref);
|
|
437
|
for (TaxonBase<?> b : c) {
|
|
438
|
taxon = (Taxon) b;
|
|
439
|
}
|
|
440
|
}
|
|
441
|
} catch (Exception e) {
|
|
442
|
logger.info("Searchtaxabyname failed" + e);
|
|
443
|
taxon = null;
|
|
444
|
}
|
|
445
|
|
|
446
|
}
|
|
447
|
if (!config.getDoReUseTaxon() || taxon == null){
|
|
448
|
if (DEBUG) {
|
|
449
|
logger.info("create new taxonName instance");
|
|
450
|
}
|
|
451
|
if (config.getDoAutomaticParsing()){
|
|
452
|
taxonName = parseScientificName(scientificName);
|
|
453
|
}
|
|
454
|
else{
|
|
455
|
taxonName = TaxonNameFactory.NewNonViralInstance(null);
|
|
456
|
taxonName.setTitleCache(scientificName, true);
|
|
457
|
}
|
|
458
|
getNameService().save((TaxonName<?,?>)taxonName);
|
|
459
|
taxon = Taxon.NewInstance(taxonName, ref); //sec set null
|
|
460
|
getTaxonService().save(taxon);
|
|
461
|
// refreshTransaction();
|
|
462
|
taxon = (Taxon) getTaxonService().find(taxon.getUuid());
|
|
463
|
taxon = addTaxonNode(taxon, config);
|
|
464
|
}
|
|
465
|
|
|
466
|
|
|
467
|
|
|
468
|
DeterminationEvent determinationEvent = DeterminationEvent.NewInstance();
|
|
469
|
determinationEvent.setTaxon(getTaxonService().find(taxon.getUuid()));
|
|
470
|
determinationEvent.setPreferredFlag(preferredFlag);
|
|
471
|
|
|
472
|
determinationEvent.setIdentifiedUnit(derivedUnitBase);
|
|
473
|
if (!identifier.isEmpty()){
|
|
474
|
Person p = Person.NewInstance();
|
|
475
|
p.setTitleCache(identifier, true);
|
|
476
|
determinationEvent.setActor(p);
|
|
477
|
}
|
|
478
|
derivedUnitBase.addDetermination(determinationEvent);
|
|
479
|
|
|
480
|
makeIndividualsAssociation(taxon,determinationEvent,config);
|
|
481
|
|
|
482
|
getOccurrenceService().saveOrUpdate(derivedUnitBase);
|
|
483
|
}
|
|
484
|
|
|
485
|
}
|
|
486
|
|
|
487
|
/**
|
|
488
|
* @param taxon
|
|
489
|
* @param taxonName
|
|
490
|
* @param config
|
|
491
|
* @return
|
|
492
|
*/
|
|
493
|
private Taxon addTaxonNode(Taxon taxon, SpecimenSynthesysExcelImportConfigurator config) {
|
|
494
|
if (DEBUG) {
|
|
495
|
logger.info("link taxon to a taxonNode");
|
|
496
|
}
|
|
497
|
boolean exist = false;
|
|
498
|
for (TaxonNode p : classification.getAllNodes()){
|
|
499
|
if(p.getTaxon().equals(taxon)) {
|
|
500
|
exist =true;
|
|
501
|
}
|
|
502
|
}
|
|
503
|
if (!exist){
|
|
504
|
taxon = (Taxon) getTaxonService().find(taxon.getUuid());
|
|
505
|
classification.addChildTaxon(taxon, ref, null);
|
|
506
|
getClassificationService().saveOrUpdate(classification);
|
|
507
|
// refreshTransaction();
|
|
508
|
}
|
|
509
|
return (Taxon) getTaxonService().find(taxon.getUuid());
|
|
510
|
}
|
|
511
|
|
|
512
|
private ITaxonNameBase parseScientificName(String scientificName){
|
|
513
|
if (DEBUG) {
|
|
514
|
logger.debug("in parseScientificName");
|
|
515
|
}
|
|
516
|
NonViralNameParserImpl nvnpi = NonViralNameParserImpl.NewInstance();
|
|
517
|
ITaxonNameBase taxonName = null;
|
|
518
|
boolean problem=false;
|
|
519
|
|
|
520
|
if (DEBUG) {
|
|
521
|
logger.debug("nomenclature: "+nomenclatureCode);
|
|
522
|
}
|
|
523
|
|
|
524
|
if(nomenclatureCode == null){
|
|
525
|
taxonName = TaxonNameFactory.NewNonViralInstance(null);
|
|
526
|
taxonName.setTitleCache(scientificName, true);
|
|
527
|
return taxonName;
|
|
528
|
}
|
|
529
|
|
|
530
|
if (nomenclatureCode.toString().equals("Zoological")){
|
|
531
|
taxonName = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICZN,null);
|
|
532
|
if (taxonName.hasProblem()) {
|
|
533
|
problem=true;
|
|
534
|
}
|
|
535
|
}
|
|
536
|
if (nomenclatureCode.toString().equals("Botanical")){
|
|
537
|
taxonName = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICNAFP,null);
|
|
538
|
if (taxonName.hasProblem()) {
|
|
539
|
problem=true;
|
|
540
|
}}
|
|
541
|
if (nomenclatureCode.toString().equals("Bacterial")){
|
|
542
|
taxonName = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICNB, null);
|
|
543
|
if (taxonName.hasProblem()) {
|
|
544
|
problem=true;
|
|
545
|
}
|
|
546
|
}
|
|
547
|
if (nomenclatureCode.toString().equals("Cultivar")){
|
|
548
|
taxonName = nvnpi.parseFullName(scientificName,NomenclaturalCode.ICNCP, null);
|
|
549
|
if (taxonName.hasProblem()) {
|
|
550
|
problem=true;
|
|
551
|
}
|
|
552
|
}
|
|
553
|
// if (nomenclatureCode.toString().equals("Viral")){
|
|
554
|
// ViralName taxonName = (ViralName)nvnpi.parseFullName(scientificName,NomenclaturalCode.ICVCN(), null);
|
|
555
|
// if (taxonName.hasProblem())
|
|
556
|
// System.out.println("pb ICVCN");
|
|
557
|
// }
|
|
558
|
//TODO: parsing of ViralNames?
|
|
559
|
if(problem){
|
|
560
|
taxonName = TaxonNameFactory.NewNonViralInstance(null);
|
|
561
|
taxonName.setTitleCache(scientificName, true);
|
|
562
|
}
|
|
563
|
return taxonName;
|
|
564
|
|
|
565
|
}
|
|
566
|
|
|
567
|
private DerivedUnitFacade getFacade() {
|
|
568
|
// logger.info("GETFACADE");
|
|
569
|
/**
|
|
570
|
* SPECIMEN OR OBSERVATION OR LIVING
|
|
571
|
*/
|
|
572
|
// DerivedUnit derivedThing = null;
|
|
573
|
SpecimenOrObservationType type = null;
|
|
574
|
|
|
575
|
// create specimen
|
|
576
|
if (recordBasis != null) {
|
|
577
|
String rec = recordBasis.toLowerCase();
|
|
578
|
if (rec.contains("specimen") || rec.startsWith("s")) {// specimen
|
|
579
|
type = SpecimenOrObservationType.PreservedSpecimen;
|
|
580
|
}
|
|
581
|
if (rec.contains("observat") || rec.startsWith("o")) {
|
|
582
|
type = SpecimenOrObservationType.Observation;
|
|
583
|
}
|
|
584
|
if (rec.contains("fossil") || rec.startsWith("f") ){
|
|
585
|
type = SpecimenOrObservationType.Fossil;
|
|
586
|
}
|
|
587
|
|
|
588
|
if (rec.contains("living") || rec.startsWith("l")) {
|
|
589
|
type = SpecimenOrObservationType.LivingSpecimen;
|
|
590
|
}
|
|
591
|
if (type == null) {
|
|
592
|
if(DEBUG) {
|
|
593
|
logger.info("The basis of record does not seem to be known: " + recordBasis);
|
|
594
|
}
|
|
595
|
type = SpecimenOrObservationType.DerivedUnit;
|
|
596
|
}
|
|
597
|
} else {
|
|
598
|
logger.info("The basis of record is null");
|
|
599
|
type = SpecimenOrObservationType.DerivedUnit;
|
|
600
|
}
|
|
601
|
DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(type);
|
|
602
|
return derivedUnitFacade;
|
|
603
|
}
|
|
604
|
|
|
605
|
/*
|
|
606
|
* Store the unit with it's Gathering informations in the CDM
|
|
607
|
*/
|
|
608
|
public boolean start(SpecimenSynthesysExcelImportConfigurator config){
|
|
609
|
boolean result = true;
|
|
610
|
|
|
611
|
// refreshTransaction();
|
|
612
|
try {
|
|
613
|
|
|
614
|
/**
|
|
615
|
* SPECIMEN OR OBSERVATION OR LIVING
|
|
616
|
*/
|
|
617
|
DerivedUnitFacade derivedUnitFacade = getFacade();
|
|
618
|
derivedUnitBase = derivedUnitFacade.innerDerivedUnit();
|
|
619
|
|
|
620
|
//set catalogue number (unitID)
|
|
621
|
derivedUnitFacade.setCatalogNumber(unitID);
|
|
622
|
derivedUnitFacade.setAccessionNumber(accessionNumber);
|
|
623
|
|
|
624
|
if (!originalsource.isEmpty()){
|
|
625
|
Reference reference = ReferenceFactory.newGeneric();
|
|
626
|
reference.setTitleCache(originalsource, true);
|
|
627
|
derivedUnitBase.addSource(OriginalSourceType.Import, originalsource, "", reference, "");
|
|
628
|
}else{
|
|
629
|
derivedUnitBase.addSource(OriginalSourceType.Import, unitID,"",ref,ref.getCitation());
|
|
630
|
}
|
|
631
|
/**
|
|
632
|
* INSTITUTION & COLLECTION
|
|
633
|
*/
|
|
634
|
//manage institution
|
|
635
|
if (!institutionCode.isEmpty()){
|
|
636
|
Institution institution = getInstitution(config);
|
|
637
|
//manage collection
|
|
638
|
if (!collectionCode.isEmpty()){
|
|
639
|
Collection collection = getCollection(institution, config);
|
|
640
|
//link specimen & collection
|
|
641
|
derivedUnitFacade.setCollection(collection);
|
|
642
|
}
|
|
643
|
}
|
|
644
|
|
|
645
|
/**
|
|
646
|
* GATHERING EVENT
|
|
647
|
*/
|
|
648
|
// gathering event
|
|
649
|
UnitsGatheringEvent unitsGatheringEvent = new UnitsGatheringEvent(getTermService(), locality, languageIso,
|
|
650
|
longitude, latitude, gatheringAgent, gatheringTeam,config);
|
|
651
|
// country
|
|
652
|
UnitsGatheringArea unitsGatheringArea = new UnitsGatheringArea();
|
|
653
|
unitsGatheringArea.useTDWGareas(this.useTDWGarea);
|
|
654
|
// unitsGatheringArea.setConfig(config, getOccurrenceService(),getTermService());
|
|
655
|
unitsGatheringArea.setParams(isocountry, country, config, getTermService(), getOccurrenceService());
|
|
656
|
DefinedTermBase areaCountry =unitsGatheringArea.getCountry();
|
|
657
|
|
|
658
|
|
|
659
|
|
|
660
|
// copy gathering event to facade
|
|
661
|
GatheringEvent gatheringEvent = unitsGatheringEvent.getGatheringEvent();
|
|
662
|
//join gatheringEvent to fieldObservation
|
|
663
|
derivedUnitFacade.setGatheringEvent(gatheringEvent);
|
|
664
|
|
|
665
|
derivedUnitFacade.setLocality(gatheringEvent.getLocality());
|
|
666
|
derivedUnitFacade.setExactLocation(gatheringEvent.getExactLocation());
|
|
667
|
//derivedUnitFacade.setCollector(gatheringEvent.getCollector());
|
|
668
|
derivedUnitFacade.setCountry((NamedArea)areaCountry);
|
|
669
|
for(DefinedTermBase<?> area:unitsGatheringArea.getAreas()){
|
|
670
|
derivedUnitFacade.addCollectingArea((NamedArea) area);
|
|
671
|
}
|
|
672
|
if (gatheringNotes != null && !gatheringNotes.isEmpty()) {
|
|
673
|
derivedUnitFacade.setFieldNotes(gatheringNotes);
|
|
674
|
}
|
|
675
|
|
|
676
|
|
|
677
|
/*
|
|
678
|
* merge AND STORE DATA
|
|
679
|
*/
|
|
680
|
// getTermService().saveOrUpdate(areaCountry);// TODO save area sooner
|
|
681
|
getTermService().saveLanguageData(unitsGatheringEvent.getLocality());
|
|
682
|
|
|
683
|
|
|
684
|
|
|
685
|
//add gathering date
|
|
686
|
if (keepAtomisedDate && (!gatheringYear.isEmpty() || !gatheringMonth.isEmpty() || !gatheringDay.isEmpty())){
|
|
687
|
Calendar calendar = Calendar.getInstance();
|
|
688
|
if (!gatheringYear.isEmpty()) {
|
|
689
|
TimePeriod tp = TimePeriod.NewInstance(Integer.parseInt(gatheringYear));
|
|
690
|
if (!gatheringMonth.isEmpty()) {
|
|
691
|
tp.setStartMonth(Integer.parseInt(gatheringMonth));
|
|
692
|
if (!gatheringDay.isEmpty()) {
|
|
693
|
tp.setStartDay(Integer.parseInt(gatheringDay));
|
|
694
|
}
|
|
695
|
}
|
|
696
|
unitsGatheringEvent.setGatheringDate(tp);
|
|
697
|
}
|
|
698
|
|
|
699
|
}else{
|
|
700
|
if (!gatheringDate.isEmpty()){
|
|
701
|
TimePeriod tp = TimePeriodParser.parseString(gatheringDate);
|
|
702
|
unitsGatheringEvent.setGatheringDate(tp);
|
|
703
|
}
|
|
704
|
}
|
|
705
|
|
|
706
|
|
|
707
|
//add fieldNumber
|
|
708
|
derivedUnitFacade.setFieldNumber(fieldNumber);
|
|
709
|
|
|
710
|
//add Multimedia URLs
|
|
711
|
if(multimediaObjects.size()>0){
|
|
712
|
for (String multimediaObject : multimediaObjects) {
|
|
713
|
Media media;
|
|
714
|
try {
|
|
715
|
media = getImageMedia(multimediaObject, READ_MEDIA_DATA);
|
|
716
|
derivedUnitFacade.addDerivedUnitMedia(media);
|
|
717
|
} catch (MalformedURLException e) {
|
|
718
|
// TODO Auto-generated catch block
|
|
719
|
e.printStackTrace();
|
|
720
|
}
|
|
721
|
}
|
|
722
|
}
|
|
723
|
|
|
724
|
getOccurrenceService().saveOrUpdate(derivedUnitBase);
|
|
725
|
|
|
726
|
setTaxonName(config);
|
|
727
|
|
|
728
|
// refreshTransaction();
|
|
729
|
if (DEBUG) {
|
|
730
|
logger.info("saved new specimen ...");
|
|
731
|
}
|
|
732
|
|
|
733
|
} catch (Exception e) {
|
|
734
|
logger.warn("Error when reading record!!");
|
|
735
|
e.printStackTrace();
|
|
736
|
result = false;
|
|
737
|
}
|
|
738
|
if (DEBUG) {
|
|
739
|
logger.info("commit done");
|
|
740
|
}
|
|
741
|
//app.close();
|
|
742
|
return result;
|
|
743
|
}
|
|
744
|
|
|
745
|
/*
|
|
746
|
* Store the unit with it's Gathering informations in the CDM
|
|
747
|
*/
|
|
748
|
public boolean resetCollectionInstitution(SpecimenSynthesysExcelImportConfigurator config,List<SpecimenOrObservationBase> specimenOrObs){
|
|
749
|
boolean result = true;
|
|
750
|
|
|
751
|
|
|
752
|
for (SpecimenOrObservationBase<?> specimen:specimenOrObs){
|
|
753
|
DerivedUnit derivedUnit=null;
|
|
754
|
if (specimen.isInstanceOf(GatheringEvent.class)){
|
|
755
|
System.out.println("gathering");
|
|
756
|
GatheringEvent gath = CdmBase.deproxy(specimen, GatheringEvent.class);
|
|
757
|
}
|
|
758
|
if (specimen.isInstanceOf(DerivedUnit.class)){
|
|
759
|
derivedUnit = CdmBase.deproxy(specimen, DerivedUnit.class);
|
|
760
|
String unitIDDB = derivedUnit.getCatalogNumber();
|
|
761
|
if (unitIDDB !=null) {
|
|
762
|
if(unitIDDB.equalsIgnoreCase(this.unitID)){
|
|
763
|
System.out.println("unitID found");
|
|
764
|
|
|
765
|
Institution institution = getInstitution(config);
|
|
766
|
|
|
767
|
Collection col = getCollection(institution, config);
|
|
768
|
getCollectionService().saveOrUpdate(col);
|
|
769
|
derivedUnit.setCollection(col);
|
|
770
|
getOccurrenceService().saveOrUpdate(derivedUnit);
|
|
771
|
return result;
|
|
772
|
}
|
|
773
|
}
|
|
774
|
}
|
|
775
|
if(specimen.isInstanceOf(IndividualsAssociation.class)) {
|
|
776
|
System.out.println("Indivi assoc");
|
|
777
|
}
|
|
778
|
}
|
|
779
|
return result;
|
|
780
|
}
|
|
781
|
|
|
782
|
|
|
783
|
private Feature makeFeature(SpecimenOrObservationBase<?> unit) {
|
|
784
|
if (unit == null){
|
|
785
|
return null;
|
|
786
|
}
|
|
787
|
SpecimenOrObservationType type = unit.getRecordBasis();
|
|
788
|
|
|
789
|
if (type.isFeatureObservation()){
|
|
790
|
return Feature.OBSERVATION();
|
|
791
|
}else if (type.isPreservedSpecimen() ||
|
|
792
|
type == SpecimenOrObservationType.LivingSpecimen ||
|
|
793
|
type == SpecimenOrObservationType.OtherSpecimen
|
|
794
|
){
|
|
795
|
return Feature.SPECIMEN();
|
|
796
|
}else if (type == SpecimenOrObservationType.Unknown ||
|
|
797
|
type == SpecimenOrObservationType.DerivedUnit
|
|
798
|
) {
|
|
799
|
return Feature.INDIVIDUALS_ASSOCIATION();
|
|
800
|
}
|
|
801
|
if (DEBUG) {
|
|
802
|
logger.warn("No feature defined for derived unit class: "
|
|
803
|
+ unit.getClass().getSimpleName());
|
|
804
|
}
|
|
805
|
return null;
|
|
806
|
}
|
|
807
|
|
|
808
|
private void makeIndividualsAssociation(Taxon taxon, DeterminationEvent determinationEvent, SpecimenSynthesysExcelImportConfigurator config) {
|
|
809
|
// try{
|
|
810
|
// taxon = (Taxon) getTaxonService().find(taxon.getUuid());
|
|
811
|
// }
|
|
812
|
// catch(Exception e){
|
|
813
|
// //logger.info("taxon uptodate");
|
|
814
|
// }
|
|
815
|
|
|
816
|
TaxonDescription taxonDescription=null;
|
|
817
|
if (taxon.getTitleCache().contains("Chenopodium vulvaria L.")) {
|
|
818
|
taxonDescription = (TaxonDescription) getDescriptionService().find(UUID.fromString("a60074e7-979b-41fd-ad4d-d391db474ac4"));
|
|
819
|
}
|
|
820
|
if(!taxon.getTitleCache().contains("Chenopodium vulvaria L.") || taxonDescription ==null) {
|
|
821
|
taxonDescription = getTaxonDescription(taxon, ref, false, true);
|
|
822
|
taxonDescription.setTitleCache(ref.getTitleCache(), true);
|
|
823
|
}
|
|
824
|
|
|
825
|
|
|
826
|
taxon.addDescription(taxonDescription);
|
|
827
|
|
|
828
|
IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();
|
|
829
|
Feature feature = makeFeature(derivedUnitBase);
|
|
830
|
indAssociation.setAssociatedSpecimenOrObservation(derivedUnitBase);
|
|
831
|
indAssociation.setFeature(feature);
|
|
832
|
|
|
833
|
for (Reference citation : determinationEvent.getReferences()) {
|
|
834
|
indAssociation.addSource(DescriptionElementSource.NewInstance(OriginalSourceType.Import, null, null, citation, null));
|
|
835
|
}
|
|
836
|
indAssociation.addSource(OriginalSourceType.Import, null,null,config.getDataReference(),null);
|
|
837
|
|
|
838
|
taxonDescription.addElement(indAssociation);
|
|
839
|
|
|
840
|
getDescriptionService().saveOrUpdate(taxonDescription);
|
|
841
|
getTaxonService().saveOrUpdate(taxon);
|
|
842
|
}
|
|
843
|
|
|
844
|
@Override
|
|
845
|
protected boolean isIgnore(SpecimenSynthesysExcelImportState state) {
|
|
846
|
return false;
|
|
847
|
}
|
|
848
|
|
|
849
|
@Override
|
|
850
|
protected void doInvoke(SpecimenSynthesysExcelImportState state) {
|
|
851
|
boolean success = true;
|
|
852
|
if (state.getConfig().doAskForDate()) {
|
|
853
|
keepAtomisedDate = askQuestion("Gathering dates can be stored in either atomised fieds (day month year) or in a concatenated field."+
|
|
854
|
"\nWhich value do you want to store?\nPress 1 for the atomised, press 2 for the concatenated field, and then press enter.");
|
|
855
|
useTDWGarea = askQuestion("Use TDWG area or Country/namedarea?\n Press 1 for TDWG areas\n Press 2 for classics Country.");
|
|
856
|
}
|
|
857
|
|
|
858
|
tx = startTransaction();
|
|
859
|
|
|
860
|
ref = state.getConfig().getTaxonReference();
|
|
861
|
if (ref == null){
|
|
862
|
ref = state.getConfig().getSourceReference();
|
|
863
|
}
|
|
864
|
AgentBase<?> agent= ref.getAuthorship();
|
|
865
|
if (agent != null){
|
|
866
|
if (agent.getClass().equals(Team.class)){
|
|
867
|
for (Person p : ((Team) agent).getTeamMembers()){
|
|
868
|
getAgentService().saveOrUpdate(p);
|
|
869
|
}
|
|
870
|
}
|
|
871
|
if (agent.getClass().equals(Person.class)){
|
|
872
|
getAgentService().saveOrUpdate(agent);
|
|
873
|
}
|
|
874
|
}
|
|
875
|
getReferenceService().saveOrUpdate(ref);
|
|
876
|
setClassification(state);
|
|
877
|
|
|
878
|
refreshTransaction();
|
|
879
|
|
|
880
|
URI source = state.getConfig().getSource();
|
|
881
|
ArrayList<HashMap<String,String>> unitsList = null;
|
|
882
|
try{
|
|
883
|
unitsList = ExcelUtils.parseXLS(source);
|
|
884
|
logger.info("unitslist : "+unitsList.size());
|
|
885
|
} catch(FileNotFoundException e){
|
|
886
|
String message = "File not found: " + source;
|
|
887
|
warnProgress(state, message, e);
|
|
888
|
logger.error(message);
|
|
889
|
}
|
|
890
|
|
|
891
|
if (unitsList != null){
|
|
892
|
//load collectors in the database
|
|
893
|
if (!state.getConfig().isDebugInstitutionOnly()) {
|
|
894
|
prepareCollectors(unitsList,state);
|
|
895
|
}
|
|
896
|
|
|
897
|
List<SpecimenOrObservationBase> specimenOrObs = null;
|
|
898
|
if (state.getConfig().isDebugInstitutionOnly()){
|
|
899
|
//DEBUG CHENOPODIUM VULVARIA
|
|
900
|
UUID uuid = UUID.fromString("85234ff5-8e40-4813-8f06-44ab960a905a");
|
|
901
|
Taxon taxon = (Taxon)getTaxonService().find(uuid);
|
|
902
|
|
|
903
|
specimenOrObs = getOccurrenceService().listByAssociatedTaxon(null, null, taxon, null, null, null, null, null);
|
|
904
|
}
|
|
905
|
HashMap<String,String> unit=null;
|
|
906
|
MyHashMap<String,String> myunit;
|
|
907
|
for (int i=0; i<unitsList.size();i++){
|
|
908
|
// for (int i=0; i<10;i++){
|
|
909
|
if (i%20==0) {
|
|
910
|
logger.info("NbUnit prepared: "+i);
|
|
911
|
refreshTransaction();
|
|
912
|
}
|
|
913
|
unit = unitsList.get(i);
|
|
914
|
myunit=new MyHashMap<String, String>();
|
|
915
|
for (String key :unit.keySet()) {
|
|
916
|
myunit.put(key, unit.get(key));
|
|
917
|
}
|
|
918
|
System.out.println(myunit.toString());
|
|
919
|
//FIXME do this via state
|
|
920
|
setUnitPropertiesExcel(myunit, state.getConfig().getDefaultAuthor());//and then invoke
|
|
921
|
if (state.getConfig().isDebugInstitutionOnly()){
|
|
922
|
success &= resetCollectionInstitution(state.getConfig(),specimenOrObs);
|
|
923
|
} else {
|
|
924
|
success &= start(state.getConfig());
|
|
925
|
}
|
|
926
|
}
|
|
927
|
}
|
|
928
|
if (success == false){
|
|
929
|
state.setUnsuccessfull();
|
|
930
|
}
|
|
931
|
commitTransaction(tx);
|
|
932
|
return;
|
|
933
|
}
|
|
934
|
|
|
935
|
|
|
936
|
/**
|
|
937
|
* @param unitsList
|
|
938
|
* @param state
|
|
939
|
*/
|
|
940
|
private void prepareCollectors(ArrayList<HashMap<String, String>> unitsList, SpecimenSynthesysExcelImportState state) {
|
|
941
|
System.out.println("PREPARE COLLECTORS");
|
|
942
|
List<String> collectors = new ArrayList<String>();
|
|
943
|
List<String> teams = new ArrayList<String>();
|
|
944
|
List<List<String>> collectorinteams = new ArrayList<List<String>>();
|
|
945
|
String tmp;
|
|
946
|
for (HashMap<String,String> unit : unitsList){
|
|
947
|
tmp=null;
|
|
948
|
tmp = unit.get("collector");
|
|
949
|
if (tmp != null && !tmp.isEmpty()) {
|
|
950
|
if (tmp.indexOf("et al.") != -1 || tmp.indexOf(" al. ")!=-1 || tmp.indexOf("& al.")!=-1 ) {
|
|
951
|
if (!tmp.trim().isEmpty()) {
|
|
952
|
teams.add(tmp.trim());
|
|
953
|
}
|
|
954
|
} else{
|
|
955
|
if(tmp.indexOf(" et ")!=-1 || tmp.indexOf("&")!=-1 || tmp.indexOf(";") !=-1){
|
|
956
|
List<String> collteam = new ArrayList<String>();
|
|
957
|
String[] tmp1 = tmp.split(" et ");
|
|
958
|
for (String elt:tmp1){
|
|
959
|
String tmp2[] = elt.split("&");
|
|
960
|
for (String elt2:tmp2) {
|
|
961
|
if (!elt2.trim().isEmpty()) {
|
|
962
|
String tmp3[] = elt.split(";");
|
|
963
|
for (String elt3:tmp3) {
|
|
964
|
if (!elt3.isEmpty()){
|
|
965
|
collectors.add(elt3.trim());
|
|
966
|
collteam.add(elt3.trim());
|
|
967
|
}
|
|
968
|
}
|
|
969
|
}
|
|
970
|
}
|
|
971
|
}
|
|
972
|
if (collteam.size()>0) {
|
|
973
|
collectorinteams.add(new ArrayList<String>(new HashSet<String>(collteam)));
|
|
974
|
}
|
|
975
|
}
|
|
976
|
else
|
|
977
|
if (!tmp.trim().isEmpty() && !tmp.toString().trim().equalsIgnoreCase("none")) {
|
|
978
|
collectors.add(tmp.trim());
|
|
979
|
}
|
|
980
|
}
|
|
981
|
}
|
|
982
|
}
|
|
983
|
|
|
984
|
List<String> collectorsU = new ArrayList<String>(new HashSet<String>(collectors));
|
|
985
|
List<String> teamsU = new ArrayList<String>(new HashSet<String>(teams));
|
|
986
|
|
|
987
|
|
|
988
|
//existing teams in DB
|
|
989
|
Map<String,Team> titleCacheTeam = new HashMap<String, Team>();
|
|
990
|
List<UuidAndTitleCache<Team>> hiberTeam = getAgentService().getTeamUuidAndTitleCache();
|
|
991
|
|
|
992
|
Set<UUID> uuids = new HashSet<UUID>();
|
|
993
|
for (UuidAndTitleCache<Team> hibernateT:hiberTeam){
|
|
994
|
uuids.add(hibernateT.getUuid());
|
|
995
|
}
|
|
996
|
if (!uuids.isEmpty()){
|
|
997
|
List<AgentBase> existingTeams = getAgentService().find(uuids);
|
|
998
|
for (AgentBase<?> existingP:existingTeams){
|
|
999
|
titleCacheTeam.put(existingP.getTitleCache(),(Team) existingP);
|
|
1000
|
}
|
|
1001
|
}
|
|
1002
|
|
|
1003
|
|
|
1004
|
Map<String,UUID> teamMap = new HashMap<String, UUID>();
|
|
1005
|
for (UuidAndTitleCache<Team> uuidt:hiberTeam){
|
|
1006
|
teamMap.put(uuidt.getTitleCache(), uuidt.getUuid());
|
|
1007
|
}
|
|
1008
|
|
|
1009
|
//existing persons in DB
|
|
1010
|
List<UuidAndTitleCache<Person>> hiberPersons = getAgentService().getPersonUuidAndTitleCache();
|
|
1011
|
Map<String,Person> titleCachePerson = new HashMap<String, Person>();
|
|
1012
|
uuids = new HashSet<UUID>();
|
|
1013
|
for (UuidAndTitleCache<Person> hibernateP:hiberPersons){
|
|
1014
|
uuids.add(hibernateP.getUuid());
|
|
1015
|
}
|
|
1016
|
|
|
1017
|
if (!uuids.isEmpty()){
|
|
1018
|
List<AgentBase> existingPersons = getAgentService().find(uuids);
|
|
1019
|
for (AgentBase<?> existingP:existingPersons){
|
|
1020
|
titleCachePerson.put(existingP.getTitleCache(),CdmBase.deproxy(existingP, Person.class));
|
|
1021
|
}
|
|
1022
|
}
|
|
1023
|
|
|
1024
|
Map<String,UUID> personMap = new HashMap<String, UUID>();
|
|
1025
|
for (UuidAndTitleCache<Person> person:hiberPersons){
|
|
1026
|
personMap.put(person.getTitleCache(), person.getUuid());
|
|
1027
|
}
|
|
1028
|
|
|
1029
|
java.util.Collection<AgentBase> personsToAdd = new ArrayList<AgentBase>();
|
|
1030
|
java.util.Collection<AgentBase> teamsToAdd = new ArrayList<AgentBase>();
|
|
1031
|
|
|
1032
|
for (String collector:collectorsU){
|
|
1033
|
Person p = Person.NewInstance();
|
|
1034
|
p.setTitleCache(collector,true);
|
|
1035
|
if (!personMap.containsKey(p.getTitleCache())){
|
|
1036
|
personsToAdd.add(p);
|
|
1037
|
}
|
|
1038
|
}
|
|
1039
|
for (String team:teamsU){
|
|
1040
|
Team p = Team.NewInstance();
|
|
1041
|
p.setTitleCache(team,true);
|
|
1042
|
if (!teamMap.containsKey(p.getTitleCache())){
|
|
1043
|
teamsToAdd.add(p);
|
|
1044
|
}
|
|
1045
|
}
|
|
1046
|
Map<UUID, AgentBase> uuuidPerson = getAgentService().save(personsToAdd);
|
|
1047
|
for (UUID u:uuuidPerson.keySet()){
|
|
1048
|
titleCachePerson.put(uuuidPerson.get(u).getTitleCache(),CdmBase.deproxy(uuuidPerson.get(u), Person.class) );
|
|
1049
|
}
|
|
1050
|
|
|
1051
|
|
|
1052
|
Person ptmp ;
|
|
1053
|
Map <String,Integer>teamdone = new HashMap<String, Integer>();
|
|
1054
|
for (List<String> collteam: collectorinteams){
|
|
1055
|
if (!teamdone.containsKey(StringUtils.join(collteam.toArray(),"-"))){
|
|
1056
|
Team team = new Team();
|
|
1057
|
boolean em =true;
|
|
1058
|
for (String collector:collteam){
|
|
1059
|
ptmp = Person.NewInstance();
|
|
1060
|
ptmp.setTitleCache(collector,true);
|
|
1061
|
Person p2 = titleCachePerson.get(ptmp.getTitleCache());
|
|
1062
|
team.addTeamMember(p2);
|
|
1063
|
em=false;
|
|
1064
|
}
|
|
1065
|
if (!em) {
|
|
1066
|
teamsToAdd.add(team);
|
|
1067
|
}
|
|
1068
|
teamdone.put(StringUtils.join(collteam.toArray(),"-"),0);
|
|
1069
|
}
|
|
1070
|
}
|
|
1071
|
|
|
1072
|
|
|
1073
|
Map<UUID, AgentBase> uuuidTeam = getAgentService().save(teamsToAdd);
|
|
1074
|
|
|
1075
|
for (UUID u:uuuidTeam.keySet()){
|
|
1076
|
titleCacheTeam.put(uuuidTeam.get(u).getTitleCache(), (Team) uuuidTeam.get(u) );
|
|
1077
|
}
|
|
1078
|
|
|
1079
|
state.getConfig().setTeams(titleCacheTeam);
|
|
1080
|
state.getConfig().setPersons(titleCachePerson);
|
|
1081
|
}
|
|
1082
|
|
|
1083
|
private boolean askQuestion(String question){
|
|
1084
|
Scanner scan = new Scanner(System.in);
|
|
1085
|
System.out.println(question);
|
|
1086
|
int index = scan.nextInt();
|
|
1087
|
if (index == 1) {
|
|
1088
|
return true;
|
|
1089
|
} else {
|
|
1090
|
return false;
|
|
1091
|
}
|
|
1092
|
}
|
|
1093
|
|
|
1094
|
|
|
1095
|
@Override
|
|
1096
|
protected boolean doCheck(SpecimenSynthesysExcelImportState state) {
|
|
1097
|
logger.warn("Validation not yet implemented for " + getClass().getSimpleName());
|
|
1098
|
return true;
|
|
1099
|
}
|
|
1100
|
}
|