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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.text.ParseException;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.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 sun.security.util.DerEncoder;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType;
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import eu.etaxonomy.cdm.api.service.config.MatchingTaxonConfigurator;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.common.CdmImportBase.TermMatchMode;
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import eu.etaxonomy.cdm.io.common.ICdmIO;
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.io.excel.common.ExcelImporterBase;
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import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenRow.DeterminationLight;
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import eu.etaxonomy.cdm.io.specimen.excel.in.SpecimenRow.PostfixTerm;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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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.AnnotationType;
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import eu.etaxonomy.cdm.model.common.Extension;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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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.location.NamedAreaLevel;
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import eu.etaxonomy.cdm.model.location.NamedAreaType;
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import eu.etaxonomy.cdm.model.location.ReferenceSystem;
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import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
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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.DerivedUnitBase;
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import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
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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.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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/**
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* @author a.mueller
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* @created 10.05.2011
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* @version 1.0
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*/
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@Component
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public class SpecimenCdmExcelImport extends ExcelImporterBase<SpecimenCdmExcelImportState> implements ICdmIO<SpecimenCdmExcelImportState> {
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private static final Logger logger = Logger.getLogger(SpecimenCdmExcelImport.class);
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private static final String WORKSHEET_NAME = "Specimen";
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private static final String UUID_COLUMN = "(?i)(UUID)";
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private static final String BASIS_OF_RECORD_COLUMN = "(?i)(BasisOfRecord)";
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private static final String COUNTRY_COLUMN = "(?i)(Country)";
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private static final String AREA_COLUMN = "(?i)(Area)";
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private static final String ISO_COUNTRY_COLUMN = "(?i)(ISOCountry|CountryCode)";
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private static final String LOCALITY_COLUMN = "(?i)(Locality)";
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private static final String ALTITUDE_COLUMN = "(?i)(AbsoluteElevation|Altitude)";
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private static final String ALTITUDE_MAX_COLUMN = "(?i)(AbsoluteElevation|Altitude)Max(imum)?";
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private static final String COLLECTION_DATE_COLUMN = "(?i)(CollectionDate)";
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private static final String COLLECTION_DATE_END_COLUMN = "(?i)(CollectionDateEnd)";
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private static final String COLLECTOR_COLUMN = "(?i)(Collector)";
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private static final String LONGITUDE_COLUMN = "(?i)(Longitude)";
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private static final String LATITUDE_COLUMN = "(?i)(Latitude)";
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private static final String REFERENCE_SYSTEM_COLUMN = "(?i)(ReferenceSystem)";
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private static final String ERROR_RADIUS_COLUMN = "(?i)(ErrorRadius)";
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private static final String COLLECTORS_NUMBER_COLUMN = "(?i)((Collectors|Field)Number)";
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private static final String ECOLOGY_COLUMN = "(?i)(Ecology|Habitat)";
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private static final String PLANT_DESCRIPTION_COLUMN = "(?i)(PlantDescription)";
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private static final String FIELD_NOTES_COLUMN = "(?i)(FieldNotes)";
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private static final String SEX_COLUMN = "(?i)(Sex)";
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private static final String ACCESSION_NUMBER_COLUMN = "(?i)(AccessionNumber)";
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private static final String BARCODE_COLUMN = "(?i)(Barcode)";
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private static final String COLLECTION_CODE_COLUMN = "(?i)(CollectionCode)";
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private static final String COLLECTION_COLUMN = "(?i)(Collection)";
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private static final String UNIT_NOTES_COLUMN = "(?i)((Unit)?Notes)";
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private static final String TYPE_CATEGORY_COLUMN = "(?i)(TypeCategory)";
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private static final String TYPIFIED_NAME_COLUMN = "(?i)(TypifiedName|TypeOf)";
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private static final String SOURCE_COLUMN = "(?i)(Source)";
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private static final String ID_IN_SOURCE_COLUMN = "(?i)(IdInSource)";
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private static final String RANK_COLUMN = "(?i)(Rank)";
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private static final String FULL_NAME_COLUMN = "(?i)(FullName)";
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private static final String FAMILY_COLUMN = "(?i)(Family)";
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private static final String GENUS_COLUMN = "(?i)(Genus)";
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private static final String SPECIFIC_EPITHET_COLUMN = "(?i)(SpecificEpi(thet)?)";
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private static final String INFRASPECIFIC_EPITHET_COLUMN = "(?i)(InfraSpecificEpi(thet)?)";
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private static final String DETERMINATION_AUTHOR_COLUMN = "(?i)(Author)";
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private static final String DETERMINATION_MODIFIER_COLUMN = "(?i)(DeterminationModifier)";
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private static final String DETERMINED_BY_COLUMN = "(?i)(DeterminationBy)";
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private static final String DETERMINED_WHEN_COLUMN = "(?i)(DeterminationWhen)";
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private static final String DETERMINATION_NOTES_COLUMN = "(?i)(DeterminationNote)";
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private static final String EXTENSION_COLUMN = "(?i)(Ext(ension)?)";
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private static final String IGNORE_COLUMN = "(?i)(Ignore|Not)";
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public SpecimenCdmExcelImport() {
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super();
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}
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@Override
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protected boolean analyzeRecord(HashMap<String, String> record, SpecimenCdmExcelImportState state) {
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boolean success = true;
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Set<String> keys = record.keySet();
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SpecimenRow row = new SpecimenRow();
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state.setSpecimenRow(row);
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for (String originalKey: keys) {
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Integer index = 0;
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String postfix = null;
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String indexedKey = CdmUtils.removeDuplicateWhitespace(originalKey.trim()).toString();
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String[] split = indexedKey.split("_");
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String key = split[0];
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if (split.length > 1){
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for (int i = 1 ; i < split.length ; i++ ){
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String indexString = split[i];
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if (isInteger(indexString)){
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index = Integer.valueOf(indexString);
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}else{
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postfix = split[i];
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}
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}
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}
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String value = (String) record.get(indexedKey);
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if (! StringUtils.isBlank(value)) {
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if (logger.isDebugEnabled()) { logger.debug(key + ": " + value); }
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value = CdmUtils.removeDuplicateWhitespace(value.trim()).toString();
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}else{
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continue;
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}
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if (key.matches(UUID_COLUMN)) {
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row.setUuid(UUID.fromString(value)); //VALIDATE UUID
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} else if(key.matches(BASIS_OF_RECORD_COLUMN)) {
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row.setBasisOfRecord(value);
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} else if(key.matches(COUNTRY_COLUMN)) {
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row.setCountry(value);
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} else if(key.matches(ISO_COUNTRY_COLUMN)) {
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row.setIsoCountry(value);
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} else if(key.matches(LOCALITY_COLUMN)) {
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row.setLocality(value);
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} else if(key.matches(FIELD_NOTES_COLUMN)) {
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row.setLocality(value);
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} else if(key.matches(ALTITUDE_COLUMN)) {
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row.setAltitude(value);
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} else if(key.matches(ALTITUDE_MAX_COLUMN)) {
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row.setAltitudeMax(value);
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} else if(key.matches(COLLECTOR_COLUMN)) {
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row.putCollector(index, value);
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} else if(key.matches(ECOLOGY_COLUMN)) {
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row.setEcology(value);
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} else if(key.matches(PLANT_DESCRIPTION_COLUMN)) {
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row.setPlantDescription(value);
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} else if(key.matches(SEX_COLUMN)) {
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row.setSex(value);
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} else if(key.matches(COLLECTION_DATE_COLUMN)) {
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row.setCollectingDate(value);
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} else if(key.matches(COLLECTION_DATE_END_COLUMN)) {
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row.setCollectingDateEnd(value);
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} else if(key.matches(COLLECTOR_COLUMN)) {
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row.putCollector(index, value);
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} else if(key.matches(COLLECTORS_NUMBER_COLUMN)) {
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row.setCollectorsNumber(value);
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} else if(key.matches(LONGITUDE_COLUMN)) {
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row.setLongitude(value);
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} else if(key.matches(LATITUDE_COLUMN)) {
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row.setLatitude(value);
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} else if(key.matches(REFERENCE_SYSTEM_COLUMN)) {
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row.setReferenceSystem(value);
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} else if(key.matches(ERROR_RADIUS_COLUMN)) {
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row.setErrorRadius(value);
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} else if(key.matches(AREA_COLUMN)) {
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if (postfix != null){
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row.addLeveledArea(postfix, value);
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}else{
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logger.warn("Not yet implemented");
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}
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} else if(key.matches(ACCESSION_NUMBER_COLUMN)) {
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row.setLocality(value);
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} else if(key.matches(BARCODE_COLUMN)) {
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row.setBarcode(value);
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} else if(key.matches(UNIT_NOTES_COLUMN)) {
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row.putUnitNote(index, value);
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} else if(key.matches(FAMILY_COLUMN)) {
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row.putDeterminationFamily(index, value);
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} else if(key.matches(GENUS_COLUMN)) {
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row.putDeterminationGenus(index, value);
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} else if(key.matches(SPECIFIC_EPITHET_COLUMN)) {
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row.putDeterminationSpeciesEpi(index, value);
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} else if(key.matches(INFRASPECIFIC_EPITHET_COLUMN)) {
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row.putDeterminationInfraSpeciesEpi(index, value);
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} else if(key.matches(RANK_COLUMN)) {
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row.putDeterminationRank(index, value);
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} else if(key.matches(FULL_NAME_COLUMN)) {
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row.putDeterminationFullName(index, value);
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} else if(key.matches(DETERMINATION_AUTHOR_COLUMN)) {
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row.putDeterminationAuthor(index, value);
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} else if(key.matches(DETERMINATION_MODIFIER_COLUMN)) {
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row.putDeterminationDeterminationModifier(index, value);
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} else if(key.matches(DETERMINATION_NOTES_COLUMN)) {
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row.putDeterminationDeterminationNotes(index, value);
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} else if(key.matches(DETERMINED_BY_COLUMN)) {
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row.putDeterminationDeterminedBy(index, value);
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} else if(key.matches(DETERMINED_WHEN_COLUMN)) {
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row.putDeterminationDeterminedWhen(index, value);
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} else if(key.matches(COLLECTION_CODE_COLUMN)) {
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row.setCollectionCode(value);
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} else if(key.matches(COLLECTION_COLUMN)) {
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row.setCollection(value);
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} else if(key.matches(TYPE_CATEGORY_COLUMN)) {
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row.putTypeCategory(index, getSpecimenTypeStatus(state, value));
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} else if(key.matches(TYPIFIED_NAME_COLUMN)) {
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row.putTypifiedName(index, getTaxonName(state, value));
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} else if(key.matches(SOURCE_COLUMN)) {
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row.putSourceReference(index, getOrMakeReference(state, value));
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} else if(key.matches(ID_IN_SOURCE_COLUMN)) {
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row.putIdInSource(index, value);
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} else if(key.matches(EXTENSION_COLUMN)) {
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if (postfix != null){
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row.addExtension(postfix, value);
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}else{
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logger.warn("Extension without postfix not yet implemented");
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}
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} else if(key.matches(IGNORE_COLUMN)) {
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logger.debug("Ignored column" + originalKey);
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}else {
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success = false;
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logger.error("Unexpected column header " + originalKey);
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}
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}
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return success;
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}
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@Override
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protected boolean firstPass(SpecimenCdmExcelImportState state) {
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SpecimenRow row = state.getSpecimenRow();
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//basis of record
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DerivedUnitType type = DerivedUnitType.valueOf2(row.getBasisOfRecord());
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if (type == null){
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String message = "%s is not a valid BasisOfRecord. 'Unknown' is used instead.";
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message = String.format(message, row.getBasisOfRecord());
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logger.warn(message);
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type = DerivedUnitType.DerivedUnit;
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}
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DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(type);
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//country
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handleCountry(facade, row, state);
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handleAreas(facade,row, state);
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facade.setGatheringPeriod(getTimePeriod(row.getCollectingDate(), row.getCollectingDateEnd()));
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facade.setLocality(row.getLocality());
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facade.setFieldNotes(row.getFieldNotes());
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facade.setFieldNumber(row.getCollectorsNumber());
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facade.setEcology(row.getEcology());
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facade.setPlantDescription(row.getPlantDescription());
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// facade.setSex(row.get)
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handleExactLocation(facade, row, state);
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312
|
facade.setCollector(getOrMakeAgent(state, row.getCollectors()));
|
|
313
|
handleAbsoluteElevation(facade, row, state);
|
|
314
|
|
|
315
|
|
|
316
|
//derivedUnit
|
|
317
|
facade.setBarcode(row.getBarcode());
|
|
318
|
facade.setAccessionNumber(row.getAccessionNumber());
|
|
319
|
facade.setCollection(getOrMakeCollection(state, row.getCollectionCode(), row.getCollection()));
|
|
320
|
for (IdentifiableSource source : row.getSources()){
|
|
321
|
facade.addSource(source);
|
|
322
|
}
|
|
323
|
for (SpecimenTypeDesignation designation : row.getTypeDesignations()){
|
|
324
|
//FIXME
|
|
325
|
// facade.innerDerivedUnit().addSpecimenTypeDesignation(designation);
|
|
326
|
}
|
|
327
|
handleDeterminations(state, row, facade);
|
|
328
|
handleExtensions(facade,row, state);
|
|
329
|
for (String note : row.getUnitNotes()){
|
|
330
|
Annotation annotation = Annotation.NewInstance(note, AnnotationType.EDITORIAL(), Language.DEFAULT());
|
|
331
|
facade.addAnnotation(annotation);
|
|
332
|
}
|
|
333
|
|
|
334
|
//save
|
|
335
|
getOccurrenceService().save(facade.innerDerivedUnit());
|
|
336
|
return true;
|
|
337
|
}
|
|
338
|
|
|
339
|
private void handleAbsoluteElevation(DerivedUnitFacade facade, SpecimenRow row, SpecimenCdmExcelImportState state) {
|
|
340
|
//altitude
|
|
341
|
|
|
342
|
try {
|
|
343
|
String altitude = row.getAltitude();
|
|
344
|
if (StringUtils.isBlank(altitude)){
|
|
345
|
return;
|
|
346
|
}
|
|
347
|
// if (altitude.endsWith(".0")){
|
|
348
|
// altitude = altitude.substring(0, altitude.length() -2);
|
|
349
|
// }
|
|
350
|
int value = Integer.valueOf(altitude);
|
|
351
|
facade.setAbsoluteElevation(value);
|
|
352
|
} catch (NumberFormatException e) {
|
|
353
|
String message = "Absolute elevation / Altitude '%s' is not an integer number in line %d";
|
|
354
|
message = String.format(message, row.getAltitude(), state.getCurrentLine());
|
|
355
|
logger.warn(message);
|
|
356
|
return;
|
|
357
|
}
|
|
358
|
|
|
359
|
//max
|
|
360
|
|
|
361
|
try {
|
|
362
|
String max = row.getAltitudeMax();
|
|
363
|
if (StringUtils.isBlank(max)){
|
|
364
|
return;
|
|
365
|
}
|
|
366
|
// if (max.endsWith(".0")){
|
|
367
|
// max = max.substring(0, max.length() -2);
|
|
368
|
// }
|
|
369
|
int value = Integer.valueOf(max);
|
|
370
|
//TODO avoid unequal distance
|
|
371
|
int min = facade.getAbsoluteElevation();
|
|
372
|
if ( (value - min) % 2 == 1 ){
|
|
373
|
String message = "Altitude min-max difference ist not equal. Max reduced by 1 in line %d";
|
|
374
|
message = String.format(message, state.getCurrentLine());
|
|
375
|
logger.warn(message);
|
|
376
|
value--;
|
|
377
|
}
|
|
378
|
facade.setAbsoluteElevationRange(min, value);
|
|
379
|
} catch (NumberFormatException e) {
|
|
380
|
String message = "Absolute elevation / Altitude maximum '%s' is not an integer number in line %d";
|
|
381
|
message = String.format(message, row.getAltitudeMax(), state.getCurrentLine());
|
|
382
|
logger.warn(message);
|
|
383
|
return;
|
|
384
|
}catch (Exception e){
|
|
385
|
String message = "Error occurred when trying to write Absolute elevation / Altitude maximum '%s' in line %d";
|
|
386
|
message = String.format(message, row.getAltitudeMax(), state.getCurrentLine());
|
|
387
|
logger.warn(message);
|
|
388
|
return;
|
|
389
|
|
|
390
|
}
|
|
391
|
|
|
392
|
|
|
393
|
}
|
|
394
|
|
|
395
|
|
|
396
|
private void handleExtensions(DerivedUnitFacade facade, SpecimenRow row, SpecimenCdmExcelImportState state) {
|
|
397
|
List<PostfixTerm> extensions = row.getExtensions();
|
|
398
|
|
|
399
|
for (PostfixTerm exType : extensions){
|
|
400
|
ExtensionType extensionType = state.getPostfixExtensionType(exType.postfix);
|
|
401
|
|
|
402
|
Extension extension = Extension.NewInstance();
|
|
403
|
extension.setType(extensionType);
|
|
404
|
extension.setValue(exType.term);
|
|
405
|
facade.innerDerivedUnit().addExtension(extension);
|
|
406
|
}
|
|
407
|
|
|
408
|
}
|
|
409
|
|
|
410
|
|
|
411
|
private void handleAreas(DerivedUnitFacade facade, SpecimenRow row, SpecimenCdmExcelImportState state) {
|
|
412
|
List<PostfixTerm> areas = row.getLeveledAreas();
|
|
413
|
|
|
414
|
for (PostfixTerm lArea : areas){
|
|
415
|
String description = lArea.term;
|
|
416
|
String abbrev = lArea.term;
|
|
417
|
NamedAreaType type = null;
|
|
418
|
String key = lArea.postfix + "_" + lArea.term;
|
|
419
|
UUID areaUuid = state.getArea(key);
|
|
420
|
NamedAreaLevel level = state.getPostfixLevel(lArea.postfix);
|
|
421
|
|
|
422
|
TermMatchMode matchMode = state.getConfig().getAreaMatchMode();
|
|
423
|
NamedArea area = getNamedArea(state, areaUuid, lArea.term, description, abbrev, type, level, null, matchMode);
|
|
424
|
facade.addCollectingArea(area);
|
|
425
|
if (areaUuid == null){
|
|
426
|
state.putArea(key, area.getUuid());
|
|
427
|
}
|
|
428
|
}
|
|
429
|
}
|
|
430
|
|
|
431
|
|
|
432
|
/**
|
|
433
|
* @param state
|
|
434
|
* @param row
|
|
435
|
* @param facade
|
|
436
|
*/
|
|
437
|
private void handleDeterminations(SpecimenCdmExcelImportState state,SpecimenRow row, DerivedUnitFacade facade) {
|
|
438
|
boolean isFirstDetermination = true;
|
|
439
|
for (DeterminationLight determinationLight : row.getDetermination()){
|
|
440
|
Taxon taxon = findBestMatchingTaxon(state, determinationLight, state.getConfig().isCreateTaxonIfNotExists());
|
|
441
|
TaxonNameBase<?,?> name = findBestMatchingName(state, determinationLight);
|
|
442
|
if (taxon != null){
|
|
443
|
getTaxonService().saveOrUpdate(taxon);
|
|
444
|
if (state.getConfig().isMakeIndividualAssociations() && taxon != null){
|
|
445
|
IndividualsAssociation indivAssociciation = IndividualsAssociation.NewInstance();
|
|
446
|
DerivedUnitBase<?> du = facade.innerDerivedUnit();
|
|
447
|
indivAssociciation.setAssociatedSpecimenOrObservation(du);
|
|
448
|
getTaxonDescription(taxon).addElement(indivAssociciation);
|
|
449
|
Feature feature = Feature.INDIVIDUALS_ASSOCIATION();
|
|
450
|
if (facade.getType().equals(DerivedUnitType.Specimen)){
|
|
451
|
feature = Feature.SPECIMEN();
|
|
452
|
}else if (facade.getType().equals(DerivedUnitType.Observation)){
|
|
453
|
feature = Feature.OBSERVATION();
|
|
454
|
}
|
|
455
|
if (state.getConfig().isUseMaterialsExaminedForIndividualsAssociations()){
|
|
456
|
feature = Feature.MATERIALS_EXAMINED();
|
|
457
|
}
|
|
458
|
|
|
459
|
indivAssociciation.setFeature(feature);
|
|
460
|
}
|
|
461
|
if (state.getConfig().isDeterminationsAreDeterminationEvent()){
|
|
462
|
DeterminationEvent detEvent = makeDeterminationEvent(state, determinationLight, taxon);
|
|
463
|
detEvent.setPreferredFlag(isFirstDetermination);
|
|
464
|
facade.addDetermination(detEvent);
|
|
465
|
}
|
|
466
|
}
|
|
467
|
if (name != null){
|
|
468
|
if (isFirstDetermination && state.getConfig().isFirstDeterminationIsStoredUnder()){
|
|
469
|
facade.setStoredUnder(name);
|
|
470
|
}
|
|
471
|
}
|
|
472
|
isFirstDetermination = false;
|
|
473
|
}
|
|
474
|
}
|
|
475
|
|
|
476
|
/**
|
|
477
|
* This method tries to find the best matching taxon depending on the import configuration,
|
|
478
|
* the taxon name information and the concept information available.
|
|
479
|
*
|
|
480
|
*
|
|
481
|
* @param state
|
|
482
|
* @param determinationLight
|
|
483
|
* @param createIfNotExists
|
|
484
|
* @return
|
|
485
|
*/
|
|
486
|
private Taxon findBestMatchingTaxon(SpecimenCdmExcelImportState state, DeterminationLight determinationLight, boolean createIfNotExists) {
|
|
487
|
NonViralName<?> name = makeTaxonName(state, determinationLight);
|
|
488
|
|
|
489
|
String titleCache = makeSearchNameTitleCache(state, determinationLight, name);
|
|
490
|
|
|
491
|
if (! StringUtils.isBlank(titleCache)){
|
|
492
|
MatchingTaxonConfigurator matchConfigurator = MatchingTaxonConfigurator.NewInstance();
|
|
493
|
matchConfigurator.setTaxonNameTitle(titleCache);
|
|
494
|
matchConfigurator.setIncludeSynonyms(false);
|
|
495
|
Taxon taxon = getTaxonService().findBestMatchingTaxon(matchConfigurator);
|
|
496
|
|
|
497
|
if(taxon == null && createIfNotExists){
|
|
498
|
logger.info("creating new Taxon from TaxonName '" + titleCache+"'");
|
|
499
|
UUID secUuid = null; //TODO
|
|
500
|
Reference<?> sec = null;
|
|
501
|
if (secUuid != null){
|
|
502
|
sec = getReferenceService().find(secUuid);
|
|
503
|
}
|
|
504
|
taxon = Taxon.NewInstance(name, sec);
|
|
505
|
}else if (taxon == null){
|
|
506
|
String message = "Taxon '%s' not found in line %d";
|
|
507
|
message = String.format(message, titleCache, state.getCurrentLine());
|
|
508
|
logger.warn(message);
|
|
509
|
}
|
|
510
|
return taxon;
|
|
511
|
}else {
|
|
512
|
return null;
|
|
513
|
}
|
|
514
|
}
|
|
515
|
|
|
516
|
/**
|
|
517
|
* @param state
|
|
518
|
* @param determinationLight
|
|
519
|
* @param name
|
|
520
|
* @return
|
|
521
|
*/
|
|
522
|
private String makeSearchNameTitleCache(SpecimenCdmExcelImportState state, DeterminationLight determinationLight,
|
|
523
|
NonViralName name) {
|
|
524
|
String titleCache = determinationLight.fullName;
|
|
525
|
if (! state.getConfig().isPreferNameCache() || StringUtils.isBlank(titleCache) ){
|
|
526
|
String computedTitleCache = name.getTitleCache();
|
|
527
|
if (StringUtils.isNotBlank(computedTitleCache)){
|
|
528
|
titleCache = computedTitleCache;
|
|
529
|
}
|
|
530
|
|
|
531
|
}
|
|
532
|
return titleCache;
|
|
533
|
}
|
|
534
|
|
|
535
|
/**
|
|
536
|
* @param state
|
|
537
|
* @param determinationLight
|
|
538
|
* @return
|
|
539
|
*/
|
|
540
|
private NonViralName makeTaxonName(SpecimenCdmExcelImportState state, DeterminationLight determinationLight) {
|
|
541
|
//TODO correct type by config.nc
|
|
542
|
NonViralName name =NonViralName.NewInstance(null);
|
|
543
|
name.setGenusOrUninomial(determinationLight.genus);
|
|
544
|
name.setSpecificEpithet(determinationLight.speciesEpi);
|
|
545
|
name.setInfraSpecificEpithet(determinationLight.infraSpeciesEpi);
|
|
546
|
|
|
547
|
//FIXME bracketAuthors and teams not yet implemented!!!
|
|
548
|
List<String> authors = new ArrayList<String>();
|
|
549
|
if (StringUtils.isNotBlank(determinationLight.author)){
|
|
550
|
authors.add(determinationLight.author);
|
|
551
|
}
|
|
552
|
TeamOrPersonBase agent = (TeamOrPersonBase)getOrMakeAgent(state, authors);
|
|
553
|
name.setCombinationAuthorTeam(agent);
|
|
554
|
|
|
555
|
NomenclaturalCode nc = state.getConfig().getNomenclaturalCode();
|
|
556
|
try {
|
|
557
|
if (StringUtils.isNotBlank(determinationLight.rank) ){
|
|
558
|
name.setRank(Rank.getRankByNameOrAbbreviation(determinationLight.rank, nc, true));
|
|
559
|
}
|
|
560
|
} catch (UnknownCdmTypeException e) {
|
|
561
|
String message = "Rank not found: %s: ";
|
|
562
|
message = String.format(message, determinationLight.rank);
|
|
563
|
logger.warn(message);
|
|
564
|
}
|
|
565
|
if (StringUtils.isBlank(name.getInfraSpecificEpithet()) && StringUtils.isNotBlank(name.getSpecificEpithet() )){
|
|
566
|
name.setRank(Rank.SPECIES());
|
|
567
|
}
|
|
568
|
if (StringUtils.isBlank(name.getSpecificEpithet()) && StringUtils.isNotBlank(name.getGenusOrUninomial() )){
|
|
569
|
name.setRank(Rank.SPECIES());
|
|
570
|
}
|
|
571
|
if (StringUtils.isBlank(name.getTitleCache())){
|
|
572
|
//TODO test
|
|
573
|
name.setTitleCache(determinationLight.fullName, true);
|
|
574
|
}
|
|
575
|
return name;
|
|
576
|
}
|
|
577
|
|
|
578
|
private TaxonNameBase findBestMatchingName(SpecimenCdmExcelImportState state, DeterminationLight determinationLight) {
|
|
579
|
|
|
580
|
NonViralName name = makeTaxonName(state, determinationLight);
|
|
581
|
String titleCache = makeSearchNameTitleCache(state, determinationLight, name);
|
|
582
|
|
|
583
|
//TODO
|
|
584
|
List<TaxonNameBase> matchingNames = getNameService().findByName(null, titleCache, MatchMode.EXACT, null, null, null, null, null).getRecords();
|
|
585
|
if (matchingNames.size() > 0){
|
|
586
|
return matchingNames.get(0);
|
|
587
|
} else if (matchingNames.size() > 0){
|
|
588
|
logger.warn("Get best matching taxon name not yet fully implemeted for specimen import");
|
|
589
|
return matchingNames.get(0);
|
|
590
|
}else{
|
|
591
|
return null;
|
|
592
|
}
|
|
593
|
|
|
594
|
}
|
|
595
|
|
|
596
|
|
|
597
|
private DeterminationEvent makeDeterminationEvent(SpecimenCdmExcelImportState state, DeterminationLight determination, Taxon taxon) {
|
|
598
|
DeterminationEvent event = DeterminationEvent.NewInstance();
|
|
599
|
//taxon
|
|
600
|
event.setTaxon(taxon);
|
|
601
|
|
|
602
|
//date
|
|
603
|
TimePeriod date = TimePeriod.parseString(determination.determinedWhen);
|
|
604
|
event.setTimeperiod(date);
|
|
605
|
//by
|
|
606
|
//FIXME bracketAuthors and teams not yet implemented!!!
|
|
607
|
List<String> authors = new ArrayList<String>();
|
|
608
|
if (StringUtils.isNotBlank(determination.determinedBy)){
|
|
609
|
authors.add(determination.determinedBy);
|
|
610
|
}
|
|
611
|
AgentBase actor = getOrMakeAgent(state, authors);
|
|
612
|
event.setActor(actor);
|
|
613
|
|
|
614
|
//TODO
|
|
615
|
if (StringUtils.isNotBlank(determination.modifier)){
|
|
616
|
logger.warn("DeterminationModifiers not yet implemented for specimen import");
|
|
617
|
}
|
|
618
|
// DeterminationModifier modifier = DeterminationModifier.NewInstance(term, label, labelAbbrev);
|
|
619
|
// determination.modifier;
|
|
620
|
//notes
|
|
621
|
Annotation annotation = Annotation.NewInstance(determination.notes, AnnotationType.EDITORIAL(), Language.DEFAULT());
|
|
622
|
event.addAnnotation(annotation);
|
|
623
|
|
|
624
|
return event;
|
|
625
|
}
|
|
626
|
|
|
627
|
private TaxonDescription getTaxonDescription(Taxon taxon) {
|
|
628
|
TaxonDescription desc = this.getTaxonDescription(taxon, ! IMAGE_GALLERY, CREATE);
|
|
629
|
return desc;
|
|
630
|
}
|
|
631
|
|
|
632
|
private AgentBase<?> getOrMakeAgent(SpecimenCdmExcelImportState state, List<String> agents) {
|
|
633
|
if (agents.size() == 0){
|
|
634
|
return null;
|
|
635
|
}else if (agents.size() == 1){
|
|
636
|
return getOrMakePerson(state, agents.get(0));
|
|
637
|
}else{
|
|
638
|
return getOrMakeTeam(state, agents);
|
|
639
|
}
|
|
640
|
}
|
|
641
|
|
|
642
|
private Team getOrMakeTeam(SpecimenCdmExcelImportState state, List<String> agents) {
|
|
643
|
String key = CdmUtils.concat("_", agents.toArray(new String[0]));
|
|
644
|
|
|
645
|
Team result = state.getTeam(key);
|
|
646
|
if (result == null){
|
|
647
|
result = Team.NewInstance();
|
|
648
|
for (String member : agents){
|
|
649
|
Person person = getOrMakePerson(state, member);
|
|
650
|
result.addTeamMember(person);
|
|
651
|
}
|
|
652
|
state.putTeam(key, result);
|
|
653
|
}
|
|
654
|
return result;
|
|
655
|
}
|
|
656
|
|
|
657
|
private Person getOrMakePerson(SpecimenCdmExcelImportState state, String value) {
|
|
658
|
Person result = state.getPerson(value);
|
|
659
|
if (result == null){
|
|
660
|
result = Person.NewInstance();
|
|
661
|
result.setTitleCache(value, true);
|
|
662
|
state.putPerson(value, result);
|
|
663
|
}
|
|
664
|
return result;
|
|
665
|
}
|
|
666
|
|
|
667
|
private Reference<?> getOrMakeReference(SpecimenCdmExcelImportState state, String value) {
|
|
668
|
Reference<?> result = state.getReference(value);
|
|
669
|
if (result == null){
|
|
670
|
result = ReferenceFactory.newGeneric();
|
|
671
|
result.setTitleCache(value, true);
|
|
672
|
state.putReference(value, result);
|
|
673
|
}
|
|
674
|
return result;
|
|
675
|
}
|
|
676
|
|
|
677
|
|
|
678
|
|
|
679
|
private Collection getOrMakeCollection(SpecimenCdmExcelImportState state, String collectionCode, String collectionString) {
|
|
680
|
Collection result = state.getCollection(collectionCode);
|
|
681
|
if (result == null){
|
|
682
|
result = Collection.NewInstance();
|
|
683
|
result.setCode(collectionCode);
|
|
684
|
result.setName(collectionString);
|
|
685
|
state.putCollection(collectionCode, result);
|
|
686
|
}
|
|
687
|
return result;
|
|
688
|
}
|
|
689
|
|
|
690
|
|
|
691
|
private TaxonNameBase<?, ?> getTaxonName(SpecimenCdmExcelImportState state, String name) {
|
|
692
|
TaxonNameBase<?,?> result = null;
|
|
693
|
result = state.getName(name);
|
|
694
|
if (result != null){
|
|
695
|
return result;
|
|
696
|
}
|
|
697
|
List<TaxonNameBase<?,?>> list = getNameService().findNamesByTitle(name);
|
|
698
|
//TODO better strategy to find best name, e.g. depending on the classification it is used in
|
|
699
|
if (! list.isEmpty()){
|
|
700
|
result = list.get(0);
|
|
701
|
}
|
|
702
|
if (result == null){
|
|
703
|
NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
|
|
704
|
NomenclaturalCode code = state.getConfig().getNomenclaturalCode();
|
|
705
|
result = parser.parseFullName(name, code, null);
|
|
706
|
|
|
707
|
}
|
|
708
|
if (result != null){
|
|
709
|
state.putName(name, result);
|
|
710
|
}
|
|
711
|
return result;
|
|
712
|
}
|
|
713
|
|
|
714
|
private SpecimenTypeDesignationStatus getSpecimenTypeStatus(SpecimenCdmExcelImportState state, String key) {
|
|
715
|
SpecimenTypeDesignationStatus result = null;
|
|
716
|
try {
|
|
717
|
result = state.getTransformer().getSpecimenTypeDesignationStatusByKey(key);
|
|
718
|
if (result == null){
|
|
719
|
String message = "Type status not recognized for %s in line %d";
|
|
720
|
message = String.format(message, key, state.getCurrentLine());
|
|
721
|
logger.warn(message);
|
|
722
|
}
|
|
723
|
return result;
|
|
724
|
} catch (UndefinedTransformerMethodException e) {
|
|
725
|
throw new RuntimeException("getSpecimenTypeDesignationStatusByKey not yet implemented");
|
|
726
|
}
|
|
727
|
|
|
728
|
|
|
729
|
}
|
|
730
|
|
|
731
|
|
|
732
|
private void handleExactLocation(DerivedUnitFacade facade, SpecimenRow row, SpecimenCdmExcelImportState state) {
|
|
733
|
|
|
734
|
//reference system
|
|
735
|
ReferenceSystem refSys = null;
|
|
736
|
if (StringUtils.isNotBlank(row.getReferenceSystem())){
|
|
737
|
String strRefSys = row.getReferenceSystem().trim().replaceAll("\\s", "");
|
|
738
|
UUID refUuid;
|
|
739
|
try {
|
|
740
|
refSys = state.getTransformer().getReferenceSystemByKey(strRefSys);
|
|
741
|
if (refSys == null){
|
|
742
|
refUuid = state.getTransformer().getReferenceSystemUuid(strRefSys);
|
|
743
|
if (refUuid == null){
|
|
744
|
String message = "Unknown reference system %s in line %d";
|
|
745
|
message = String.format(message, strRefSys, state.getCurrentLine());
|
|
746
|
logger.warn(message);
|
|
747
|
}
|
|
748
|
refSys = getReferenceSystem(state, refUuid, strRefSys, strRefSys, strRefSys, null);
|
|
749
|
}
|
|
750
|
|
|
751
|
} catch (UndefinedTransformerMethodException e) {
|
|
752
|
throw new RuntimeException(e);
|
|
753
|
}
|
|
754
|
}
|
|
755
|
|
|
756
|
|
|
757
|
|
|
758
|
// lat/ long /error
|
|
759
|
try {
|
|
760
|
String longitude = row.getLongitude();
|
|
761
|
String latitude = row.getLatitude();
|
|
762
|
Integer errorRadius = null;
|
|
763
|
if (StringUtils.isNotBlank(row.getErrorRadius())){
|
|
764
|
try {
|
|
765
|
errorRadius = Integer.valueOf(row.getErrorRadius());
|
|
766
|
} catch (NumberFormatException e) {
|
|
767
|
String message = "Error radius %s could not be transformed to Integer in line %d";
|
|
768
|
message = String.format(message, row.getErrorRadius(), state.getCurrentLine());
|
|
769
|
logger.warn(message);
|
|
770
|
}
|
|
771
|
}
|
|
772
|
//all
|
|
773
|
facade.setExactLocationByParsing(longitude, latitude, refSys, errorRadius);
|
|
774
|
} catch (ParseException e) {
|
|
775
|
String message = "Problems when parsing exact location for line %d";
|
|
776
|
message = String.format(message, state.getCurrentLine());
|
|
777
|
logger.warn(message);
|
|
778
|
|
|
779
|
}
|
|
780
|
|
|
781
|
|
|
782
|
|
|
783
|
}
|
|
784
|
|
|
785
|
|
|
786
|
/*
|
|
787
|
* Set the current Country
|
|
788
|
* Search in the DB if the isoCode is known
|
|
789
|
* If not, search if the country name is in the DB
|
|
790
|
* If not, create a new Label with the Level Country
|
|
791
|
* @param iso: the country iso code
|
|
792
|
* @param fullName: the country's full name
|
|
793
|
* @param app: the CDM application controller
|
|
794
|
*/
|
|
795
|
private void handleCountry(DerivedUnitFacade facade, SpecimenRow row, SpecimenCdmExcelImportState state) {
|
|
796
|
|
|
797
|
if (StringUtils.isNotBlank(row.getIsoCountry())){
|
|
798
|
NamedArea country = getOccurrenceService().getCountryByIso(row.getIsoCountry());
|
|
799
|
if (country != null){
|
|
800
|
facade.setCountry(country);
|
|
801
|
return;
|
|
802
|
}
|
|
803
|
}
|
|
804
|
if (StringUtils.isNotBlank(row.getCountry())){
|
|
805
|
List<WaterbodyOrCountry> countries = getOccurrenceService().getWaterbodyOrCountryByName(row.getCountry());
|
|
806
|
if (countries.size() >0){
|
|
807
|
facade.setCountry(countries.get(0));
|
|
808
|
}else{
|
|
809
|
UUID uuid = UUID.randomUUID();
|
|
810
|
String label = row.getCountry();
|
|
811
|
String text = row.getCountry();
|
|
812
|
String labelAbbrev = null;
|
|
813
|
NamedAreaType areaType = NamedAreaType.ADMINISTRATION_AREA();
|
|
814
|
NamedAreaLevel level = NamedAreaLevel.COUNTRY();
|
|
815
|
NamedArea newCountry = this.getNamedArea(state, uuid, label, text, labelAbbrev, areaType, level);
|
|
816
|
facade.setCountry(newCountry);
|
|
817
|
}
|
|
818
|
}
|
|
819
|
}
|
|
820
|
|
|
821
|
|
|
822
|
|
|
823
|
|
|
824
|
protected boolean isInteger(String value){
|
|
825
|
try {
|
|
826
|
Integer.valueOf(value);
|
|
827
|
return true;
|
|
828
|
} catch (NumberFormatException e) {
|
|
829
|
return false;
|
|
830
|
}
|
|
831
|
}
|
|
832
|
|
|
833
|
@Override
|
|
834
|
protected boolean secondPass(SpecimenCdmExcelImportState state) {
|
|
835
|
//no second path defined yet
|
|
836
|
return true;
|
|
837
|
}
|
|
838
|
|
|
839
|
|
|
840
|
@Override
|
|
841
|
protected String getWorksheetName() {
|
|
842
|
return WORKSHEET_NAME;
|
|
843
|
}
|
|
844
|
|
|
845
|
@Override
|
|
846
|
protected boolean needsNomenclaturalCode() {
|
|
847
|
return false;
|
|
848
|
}
|
|
849
|
|
|
850
|
|
|
851
|
/* (non-Javadoc)
|
|
852
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
|
|
853
|
*/
|
|
854
|
@Override
|
|
855
|
protected boolean doCheck(SpecimenCdmExcelImportState state) {
|
|
856
|
logger.warn("Validation not yet implemented for " + this.getClass().getSimpleName());
|
|
857
|
return true;
|
|
858
|
}
|
|
859
|
|
|
860
|
|
|
861
|
|
|
862
|
@Override
|
|
863
|
protected boolean isIgnore(SpecimenCdmExcelImportState state) {
|
|
864
|
return !state.getConfig().isDoSpecimen();
|
|
865
|
}
|
|
866
|
|
|
867
|
|
|
868
|
}
|