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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.algaterra;
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import java.net.URI;
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import java.sql.Date;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Map;
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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.api.facade.DerivedUnitFacade.DerivedUnitType;
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import eu.etaxonomy.cdm.io.algaterra.validation.AlgaTerraSpecimenImportValidator;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonImport;
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import eu.etaxonomy.cdm.io.common.IOValidator;
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
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import eu.etaxonomy.cdm.io.common.Source;
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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.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.description.CategoricalData;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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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.SpecimenDescription;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.Point;
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import eu.etaxonomy.cdm.model.location.ReferenceSystem;
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import eu.etaxonomy.cdm.model.location.TdwgArea;
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import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.occurrence.FieldObservation;
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import eu.etaxonomy.cdm.model.reference.Reference;
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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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/**
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* @author a.mueller
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* @created 20.03.2008
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* @version 1.0
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*/
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@Component
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public class AlgaTerraSpecimenImport extends BerlinModelImportBase {
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private static final Logger logger = Logger.getLogger(AlgaTerraSpecimenImport.class);
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public static final String FIELD_OBSERVATION_NAMESPACE = "FieldObservation";
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public static final String TERMS_NAMESPACE = "ALGA_TERRA_TERMS";
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//move to transformrer
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final static UUID uuidMarkerAlkalinity = UUID.fromString("e52d0ea2-0c1f-4d95-ae6d-e21ab317c594");
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final static UUID uuidRefSystemGps = UUID.fromString("c23e4928-c137-4e4a-b6ab-b430da3d0b94");
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final static UUID uuidFeatureSpecimenCommunity = UUID.fromString("3ff5b1ab-3999-4b5a-b8f7-01fd2f6c12c7");
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final static UUID uuidFeatureAdditionalData = UUID.fromString("0ac82ab8-2c2b-4953-98eb-a9f718eb9c57");
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final static UUID uuidVocAlgaTerraClimate = UUID.fromString("b0a677c6-8bb6-43f4-b1b8-fc377a10feb5");
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final static UUID uuidVocAlgaTerraHabitat = UUID.fromString("06f30114-e19c-4e7d-a8e5-5488c41fcbc5");
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final static UUID uuidVocAlgaTerraLifeForm = UUID.fromString("3c0b194e-809c-4b42-9498-6ff034066ed7");
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final static UUID uuidFeatureAlgaTerraClimate = UUID.fromString("8754674c-9ab9-4f28-95f1-91eeee2314ee");
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final static UUID uuidFeatureAlgaTerraHabitat = UUID.fromString("7def3fc2-cdc5-4739-8e13-62edbd053415");
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final static UUID uuidFeatureAlgaTerraLifeForm = UUID.fromString("9b657901-1b0d-4a2a-8d21-dd8c1413e2e6");
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private static int modCount = 5000;
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private static final String pluralString = "specimen and observation";
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private static final String dbTableName = "Fact"; //??
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public AlgaTerraSpecimenImport(){
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super();
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery()
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*/
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@Override
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protected String getIdQuery(BerlinModelImportState state) {
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String result = " SELECT factId " +
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" FROM Fact " +
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" INNER JOIN EcoFact ON Fact.ExtensionFk = EcoFact.EcoFactId " +
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"INNER JOIN PTaxon ON Fact.PTNameFk = PTaxon.PTNameFk AND Fact.PTRefFk = PTaxon.PTRefFk "
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+ " WHERE FactCategoryFk = 202 "
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+ " ORDER BY EcoFact.EcoFactId, PTaxon.RIdentifier, Fact.FactId ";
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return result;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
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*/
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@Override
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protected String getRecordQuery(BerlinModelImportConfigurator config) {
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String strQuery = //DISTINCT because otherwise emOccurrenceSource creates multiple records for a single distribution
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" SELECT PTaxon.RIdentifier as taxonId, Fact.FactId, Fact.RecordBasis, EcoFact.*, " +
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" tg.ID AS GazetteerId, tg.L2Code, tg.L3Code, tg.L4Code, tg.Country, tg.ISOCountry, " +
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" ec.UUID as climateUuid, eh.UUID as habitatUuid, elf.UUID as lifeFormUuid" +
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" FROM Fact " +
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" INNER JOIN EcoFact ON Fact.ExtensionFk = EcoFact.EcoFactId " +
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" INNER JOIN PTaxon ON dbo.Fact.PTNameFk = dbo.PTaxon.PTNameFk AND dbo.Fact.PTRefFk = dbo.PTaxon.PTRefFk " +
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" LEFT OUTER JOIN TDWGGazetteer tg ON EcoFact.TDWGGazetteerFk = tg.ID " +
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" LEFT OUTER JOIN EcoClimate ec ON EcoFact.ClimateFk = ec.ClimateId " +
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" LEFT OUTER JOIN EcoHabitat eh ON EcoFact.HabitatFk = eh.HabitatId " +
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" LEFT OUTER JOIN EcoLifeForm elf ON EcoFact.LifeFormFk = elf.LifeFormId " +
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" WHERE Fact.FactCategoryFk = 202 AND (Fact.FactId IN (" + ID_LIST_TOKEN + ") )"
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+ " ORDER BY EcoFact.EcoFactId, PTaxon.RIdentifier, Fact.FactId "
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;
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return strQuery;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
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*/
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public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
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boolean success = true;
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AlgaTerraImportState state = (AlgaTerraImportState)bmState;
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try {
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makeVocabulariesAndFeatures(state);
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} catch (SQLException e1) {
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logger.warn("Exception occurred when trying to create Ecofact vocabularies: " + e1.getMessage());
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e1.printStackTrace();
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}
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Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
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Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
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Map<String, FieldObservation> fieldObservationMap = (Map<String, FieldObservation>) partitioner.getObjectMap(FIELD_OBSERVATION_NAMESPACE);
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ResultSet rs = partitioner.getResultSet();
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try {
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int i = 0;
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//for each reference
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while (rs.next()){
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if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("Specimen facts handled: " + (i-1));}
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int newTaxonId = rs.getInt("taxonId");
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int factId = rs.getInt("FactId");
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int ecoFactId = rs.getInt("EcoFactId");
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String recordBasis = rs.getString("RecordBasis");
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try {
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//source ref
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Reference<?> sourceRef = state.getTransactionalSourceReference();
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//facade
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FieldObservation fieldObservation = getFieldObservation(ecoFactId, fieldObservationMap);
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DerivedUnitType type = makeDerivedUnitType(recordBasis);
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DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(type, fieldObservation);
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//field observation
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handleSingleSpecimen(rs, facade, state);
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//description element
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TaxonDescription taxonDescription = getTaxonDescription(state, newTaxonId, taxonMap, factId, sourceRef);
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IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();
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Feature feature = makeFeature(type);
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indAssociation.setAssociatedSpecimenOrObservation(facade.innerDerivedUnit());
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indAssociation.setFeature(feature);
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taxonDescription.addElement(indAssociation);
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taxaToSave.add(taxonDescription.getTaxon());
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} catch (Exception e) {
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logger.warn("Exception in ecoFact: FactId " + factId + ". " + e.getMessage());
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// e.printStackTrace();
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}
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}
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// logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );
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logger.warn("Taxa to save: " + taxaToSave.size());
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getTaxonService().save(taxaToSave);
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return success;
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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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return false;
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}
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}
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/**
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* Creates the vocabularies and the features for Climate, Habitat and Lifeform
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* @param state
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* @throws SQLException
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*/
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private void makeVocabulariesAndFeatures(AlgaTerraImportState state) throws SQLException {
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String abbrevLabel = null;
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URI uri = null;
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if (! state.isSpecimenVocabulariesCreated()){
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TransactionStatus txStatus = this.startTransaction();
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boolean isOrdered = true;
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OrderedTermVocabulary<State> climateVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraClimate, "Climate", "Climate", abbrevLabel, uri, isOrdered, null);
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OrderedTermVocabulary<State> habitatVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraHabitat, "Habitat", "Habitat", abbrevLabel, uri, isOrdered, null);
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OrderedTermVocabulary<State> lifeformVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraLifeForm, "Lifeform", "Lifeform", abbrevLabel, uri, isOrdered, null);
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Feature feature = getFeature(state, uuidFeatureAlgaTerraClimate, "Climate","Climate", null, null);
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feature.setSupportsCategoricalData(true);
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feature = getFeature(state, uuidFeatureAlgaTerraLifeForm, "LifeForm","LifeForm", null, null);
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feature.setSupportsCategoricalData(true);
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feature = Feature.HABITAT();
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feature.setSupportsCategoricalData(true);
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getTermService().saveOrUpdate(feature);
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Source source = state.getAlgaTerraConfigurator().getSource();
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String climateSql = "SELECT * FROM EcoClimate";
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ResultSet rs = source.getResultSet(climateSql);
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while (rs.next()){
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String climate = rs.getString("Climate");
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String description = rs.getString("Description");
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Integer id = rs.getInt("ClimateId");
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UUID uuid = UUID.fromString(rs.getString("UUID"));
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State stateTerm = getStateTerm(state, uuid, climate, description, null, climateVoc);
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addOriginalSource(stateTerm, id.toString(), "EcoClimate", state.getTransactionalSourceReference());
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getTermService().saveOrUpdate(stateTerm);
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}
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String habitatSql = "SELECT * FROM EcoHabitat";
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rs = source.getResultSet(habitatSql);
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while (rs.next()){
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String habitat = rs.getString("Habitat");
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String description = rs.getString("Description");
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Integer id = rs.getInt("HabitatId");
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UUID uuid = UUID.fromString(rs.getString("UUID"));
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State stateTerm = getStateTerm(state, uuid, habitat, description, null, habitatVoc);
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addOriginalSource(stateTerm, id.toString(), "EcoHabitat", state.getTransactionalSourceReference());
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getTermService().saveOrUpdate(stateTerm);
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}
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String lifeformSql = "SELECT * FROM EcoLifeForm";
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rs = source.getResultSet(lifeformSql);
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while (rs.next()){
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String lifeform = rs.getString("LifeForm");
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String description = rs.getString("Description");
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Integer id = rs.getInt("LifeFormId");
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UUID uuid = UUID.fromString(rs.getString("UUID"));
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State stateTerm = getStateTerm(state, uuid, lifeform, description, null, lifeformVoc);
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addOriginalSource(stateTerm, id.toString(), "EcoLifeForm", state.getTransactionalSourceReference());
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getTermService().saveOrUpdate(stateTerm);
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}
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this.commitTransaction(txStatus);
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state.setSpecimenVocabulariesCreated(true);
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}
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}
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private void handleSingleSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state) throws SQLException {
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//CollectionFk, Collector, AltitudeMethod,
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//ISOCountrySub, CreatedWhen/Who/Updated/who
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//P1-10Value/Unit/Parameter/Method
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try {
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Object alkalinityFlag = rs.getBoolean("AlkalinityFlag");
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String locality = rs.getString("Locality");
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Double latitude = nullSafeDouble(rs, "Latitude");
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Double longitude = nullSafeDouble(rs, "Longitude");
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Integer errorRadius = nullSafeInt(rs,"Prec");
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String geoCodeMethod = rs.getString("GeoCodeMethod");
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Integer altitude = nullSafeInt(rs, "Altitude");
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Integer lowerAltitude = nullSafeInt(rs,"AltitudeLowerValue");
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String altitudeUnit = rs.getString("AltitudeUnit");
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Double depth = nullSafeDouble(rs, "Depth");
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Double depthLow = nullSafeDouble(rs, "DepthLow");
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String collectorsNumber = rs.getString("CollectorsNumber");
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Date collectionDateStart = rs.getDate("CollectionDate");
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Date collectionDateEnd = rs.getDate("CollectionDateEnd");
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String climateUuid = rs.getString("climateUuid");
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String habitatUuid = rs.getString("habitatUuid");
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String lifeFormUuid = rs.getString("lifeFormUuid");
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String habitat = rs.getString("HabitatExplanation");
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String community = rs.getString("Comunity");
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String additionalData = rs.getString("AdditionalData");
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FieldObservation fieldObservation = facade.innerFieldObservation();
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//alkalinity marker
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if (alkalinityFlag != null){
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MarkerType alkalinityMarkerType = getMarkerType(state, uuidMarkerAlkalinity, "Alkalinity", "Alkalinity", null);
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boolean alkFlag = Boolean.valueOf(alkalinityFlag.toString());
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Marker alkalinityMarker = Marker.NewInstance(alkalinityMarkerType, alkFlag);
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fieldObservation.addMarker(alkalinityMarker);
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}
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//location
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facade.setLocality(locality);
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//exact location
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ReferenceSystem referenceSystem = makeRefrenceSystem(geoCodeMethod, state);
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Point exactLocation = Point.NewInstance(longitude, latitude, referenceSystem, errorRadius);
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facade.setExactLocation(exactLocation);
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//altitude, depth
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if (StringUtils.isNotBlank(altitudeUnit) && ! altitudeUnit.trim().equalsIgnoreCase("m")){
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logger.warn("Altitude unit is not [m] but: " + altitudeUnit);
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}
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if ( altitude != null){
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if (lowerAltitude == null){
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facade.setAbsoluteElevation(altitude);
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}else{
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if (! facade.isEvenDistance(lowerAltitude, altitude)){
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//FIXME there is a ticket for this
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altitude = altitude + 1;
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logger.warn("Current implementation of altitude does not allow uneven distances");
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}
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facade.setAbsoluteElevationRange(lowerAltitude,altitude);
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}
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}
|
366
|
if ( depth != null){
|
367
|
//FIXME needs model change to accept double #3072
|
368
|
Integer intDepth = depth.intValue();
|
369
|
if (depthLow == null){
|
370
|
facade.setDistanceToWaterSurface(intDepth);
|
371
|
}else{
|
372
|
//FIXME range not yet in model #3074
|
373
|
facade.setDistanceToWaterSurface(intDepth);
|
374
|
}
|
375
|
}
|
376
|
|
377
|
//habitat, ecology, community, etc.
|
378
|
DescriptionBase<?> fieldDescription = getFieldObservationDescription(facade);
|
379
|
addCategoricalValue(state, fieldDescription, climateUuid, uuidFeatureAlgaTerraClimate);
|
380
|
addCategoricalValue(state, fieldDescription, habitatUuid, Feature.HABITAT().getUuid());
|
381
|
addCategoricalValue(state, fieldDescription, lifeFormUuid, uuidFeatureAlgaTerraLifeForm);
|
382
|
|
383
|
if (isNotBlank(habitat)){
|
384
|
//FIXME
|
385
|
facade.setEcology(habitat); //or use an own feature ??
|
386
|
}
|
387
|
if (isNotBlank(community)){
|
388
|
Feature communityFeature = getFeature(state, uuidFeatureSpecimenCommunity, "Community", "The community of a specimen (e.g. other algae in the same sample)", null, null);
|
389
|
TextData textData = TextData.NewInstance(communityFeature);
|
390
|
textData.putText(Language.DEFAULT(), community);
|
391
|
getFieldObservationDescription(facade).addElement(textData);
|
392
|
}
|
393
|
if (isNotBlank(additionalData)){ //or handle it as Annotation ??
|
394
|
Feature additionalDataFeature = getFeature(state, uuidFeatureAdditionalData, "Additional Data", "Additional Data", null, null);
|
395
|
TextData textData = TextData.NewInstance(additionalDataFeature);
|
396
|
textData.putText(Language.DEFAULT(), additionalData);
|
397
|
getFieldObservationDescription(facade).addElement(textData);
|
398
|
}
|
399
|
|
400
|
//field
|
401
|
facade.setFieldNumber(collectorsNumber);
|
402
|
TimePeriod gatheringPeriod = TimePeriod.NewInstance(collectionDateStart, collectionDateEnd);
|
403
|
facade.setGatheringPeriod(gatheringPeriod);
|
404
|
handleCollectorTeam(state, facade, rs);
|
405
|
|
406
|
//areas
|
407
|
makeAreas(state, rs, facade);
|
408
|
|
409
|
//parameters
|
410
|
//TODO
|
411
|
|
412
|
//collection
|
413
|
String voucher = rs.getString("Voucher");
|
414
|
if (StringUtils.isNotBlank(voucher)){
|
415
|
facade.setAccessionNumber(voucher);
|
416
|
}
|
417
|
|
418
|
|
419
|
//notes
|
420
|
//TODO is this an annotation on field observation or on the derived unit?
|
421
|
|
422
|
//TODO id, created for fact + ecoFact
|
423
|
// this.doIdCreatedUpdatedNotes(state, descriptionElement, rs, id, namespace);
|
424
|
|
425
|
} catch (IllegalArgumentException e) {
|
426
|
throw e;
|
427
|
}
|
428
|
|
429
|
}
|
430
|
|
431
|
|
432
|
private void addCategoricalValue(AlgaTerraImportState importState, DescriptionBase description, String uuidTerm, UUID featureUuid) {
|
433
|
if (uuidTerm != null){
|
434
|
State state = this.getStateTerm(importState, UUID.fromString(uuidTerm));
|
435
|
Feature feature = getFeature(importState, featureUuid);
|
436
|
CategoricalData categoricalData = CategoricalData.NewInstance(state, feature);
|
437
|
description.addElement(categoricalData);
|
438
|
}
|
439
|
}
|
440
|
|
441
|
|
442
|
private void handleCollectorTeam(AlgaTerraImportState state, DerivedUnitFacade facade, ResultSet rs) throws SQLException {
|
443
|
// FIXME parsen
|
444
|
String collector = rs.getString("Collector");
|
445
|
Team team = Team.NewTitledInstance(collector, collector);
|
446
|
facade.setCollector(team);
|
447
|
|
448
|
|
449
|
|
450
|
}
|
451
|
|
452
|
private void makeAreas(AlgaTerraImportState state, ResultSet rs, DerivedUnitFacade facade) throws SQLException {
|
453
|
Object gazetteerId = rs.getObject("GazetteerId");
|
454
|
if (gazetteerId != null){
|
455
|
//TDWG
|
456
|
NamedArea tdwgArea;
|
457
|
String tdwg4 = rs.getString("L4Code");
|
458
|
if (isNotBlank(tdwg4)){
|
459
|
tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(tdwg4);
|
460
|
}else{
|
461
|
String tdwg3 = rs.getString("L3Code");
|
462
|
if (isNotBlank(tdwg3)){
|
463
|
tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(tdwg3);
|
464
|
}else{
|
465
|
Integer tdwg2 = rs.getInt("L2Code");
|
466
|
tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(String.valueOf(tdwg2));
|
467
|
}
|
468
|
}
|
469
|
if (tdwgArea == null){
|
470
|
logger.warn("TDWG area could not be defined for gazetterId: " + gazetteerId);
|
471
|
}else{
|
472
|
facade.addCollectingArea(tdwgArea);
|
473
|
}
|
474
|
|
475
|
//Countries
|
476
|
WaterbodyOrCountry country = null;
|
477
|
String isoCountry = rs.getString("ISOCountry");
|
478
|
String countryStr = rs.getString("Country");
|
479
|
if (isNotBlank(isoCountry)){
|
480
|
country = WaterbodyOrCountry.getWaterbodyOrCountryByIso3166A2(isoCountry);
|
481
|
}else if (isNotBlank(countryStr)){
|
482
|
logger.warn("Country exists but no ISO code");
|
483
|
}
|
484
|
if (country == null){
|
485
|
logger.warn("Country does not exist for GazetteerID " + gazetteerId);
|
486
|
}else{
|
487
|
facade.setCountry(country);
|
488
|
}
|
489
|
|
490
|
}
|
491
|
|
492
|
//Waterbody
|
493
|
WaterbodyOrCountry waterbody = null;
|
494
|
String waterbodyStr = rs.getString("WaterBody");
|
495
|
if (isNotBlank(waterbodyStr)){
|
496
|
if (waterbodyStr.equals("Atlantic Ocean")){
|
497
|
waterbody = WaterbodyOrCountry.ATLANTICOCEAN();
|
498
|
}else{
|
499
|
logger.warn("Waterbody not recognized: " + waterbody);
|
500
|
}
|
501
|
if (waterbody != null){
|
502
|
facade.addCollectingArea(waterbody);
|
503
|
}
|
504
|
}
|
505
|
|
506
|
|
507
|
//countries sub
|
508
|
//TODO
|
509
|
}
|
510
|
|
511
|
private DescriptionBase getFieldObservationDescription(DerivedUnitFacade facade) {
|
512
|
Set<DescriptionBase> descriptions = facade.innerFieldObservation().getDescriptions();
|
513
|
for (DescriptionBase desc : descriptions){
|
514
|
if (desc.isImageGallery() == false){
|
515
|
return desc;
|
516
|
}
|
517
|
}
|
518
|
SpecimenDescription specDesc = SpecimenDescription.NewInstance(facade.innerFieldObservation());
|
519
|
descriptions.add(specDesc);
|
520
|
return specDesc;
|
521
|
}
|
522
|
|
523
|
private ReferenceSystem makeRefrenceSystem(String geoCodeMethod, AlgaTerraImportState state) {
|
524
|
if (StringUtils.isBlank(geoCodeMethod)){
|
525
|
return null;
|
526
|
}else if(geoCodeMethod.startsWith("GPS")){
|
527
|
getReferenceSystem(state, uuidRefSystemGps, "GPS", "GPS", "GPS", ReferenceSystem.GOOGLE_EARTH().getVocabulary());
|
528
|
return ReferenceSystem.WGS84();
|
529
|
}else if(geoCodeMethod.startsWith("Google")){
|
530
|
return ReferenceSystem.GOOGLE_EARTH();
|
531
|
}else if(geoCodeMethod.startsWith("Map")){
|
532
|
logger.warn("Reference system " + geoCodeMethod + " not yet supported.");
|
533
|
return null;
|
534
|
}else if(geoCodeMethod.startsWith("WikiProjekt Georeferenzierung") || geoCodeMethod.startsWith("http://toolserver.org/~geohack/geohack.php") ){
|
535
|
return ReferenceSystem.WGS84();
|
536
|
}else {
|
537
|
logger.warn("Reference system " + geoCodeMethod + " not yet supported.");
|
538
|
return null;
|
539
|
}
|
540
|
}
|
541
|
|
542
|
private FieldObservation getFieldObservation(int ecoFactId, Map<String, FieldObservation> fieldObservationMap) {
|
543
|
String key = String.valueOf(ecoFactId);
|
544
|
FieldObservation fieldObservation = fieldObservationMap.get(key);
|
545
|
if (fieldObservation == null){
|
546
|
fieldObservation = FieldObservation.NewInstance();
|
547
|
|
548
|
fieldObservationMap.put(key, fieldObservation);
|
549
|
}
|
550
|
|
551
|
return fieldObservation;
|
552
|
}
|
553
|
|
554
|
private Feature makeFeature(DerivedUnitType type) {
|
555
|
if (type.equals(DerivedUnitType.DerivedUnit)){
|
556
|
return Feature.INDIVIDUALS_ASSOCIATION();
|
557
|
}else if (type.equals(DerivedUnitType.FieldObservation) || type.equals(DerivedUnitType.Observation) ){
|
558
|
return Feature.OBSERVATION();
|
559
|
}else if (type.equals(DerivedUnitType.Fossil) || type.equals(DerivedUnitType.LivingBeing) || type.equals(DerivedUnitType.Specimen )){
|
560
|
return Feature.SPECIMEN();
|
561
|
}
|
562
|
logger.warn("No feature defined for derived unit type: " + type);
|
563
|
return null;
|
564
|
}
|
565
|
|
566
|
|
567
|
private DerivedUnitType makeDerivedUnitType(String recordBasis) {
|
568
|
DerivedUnitType result = null;
|
569
|
if (StringUtils.isBlank(recordBasis)){
|
570
|
result = DerivedUnitType.DerivedUnit;
|
571
|
} else if (recordBasis.equalsIgnoreCase("FossileSpecimen")){
|
572
|
result = DerivedUnitType.Fossil;
|
573
|
}else if (recordBasis.equalsIgnoreCase("HumanObservation")){
|
574
|
result = DerivedUnitType.Observation;
|
575
|
}else if (recordBasis.equalsIgnoreCase("Literature")){
|
576
|
logger.warn("Literature record basis not yet supported");
|
577
|
result = DerivedUnitType.DerivedUnit;
|
578
|
}else if (recordBasis.equalsIgnoreCase("LivingSpecimen")){
|
579
|
result = DerivedUnitType.LivingBeing;
|
580
|
}else if (recordBasis.equalsIgnoreCase("MachineObservation")){
|
581
|
logger.warn("MachineObservation record basis not yet supported");
|
582
|
result = DerivedUnitType.Observation;
|
583
|
}else if (recordBasis.equalsIgnoreCase("PreservedSpecimen")){
|
584
|
result = DerivedUnitType.Specimen;
|
585
|
}
|
586
|
return result;
|
587
|
}
|
588
|
|
589
|
/* (non-Javadoc)
|
590
|
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
|
591
|
*/
|
592
|
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
|
593
|
String nameSpace;
|
594
|
Class cdmClass;
|
595
|
Set<String> idSet;
|
596
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
597
|
|
598
|
try{
|
599
|
Set<String> taxonIdSet = new HashSet<String>();
|
600
|
Set<String> fieldObservationIdSet = new HashSet<String>();
|
601
|
Set<String> termsIdSet = new HashSet<String>();
|
602
|
|
603
|
while (rs.next()){
|
604
|
handleForeignKey(rs, taxonIdSet, "taxonId");
|
605
|
handleForeignKey(rs, fieldObservationIdSet, "ecoFactId");
|
606
|
handleForeignKey(rs, termsIdSet, "ClimateFk");
|
607
|
handleForeignKey(rs, termsIdSet, "HabitatFk");
|
608
|
handleForeignKey(rs, termsIdSet, "LifeFormFk");
|
609
|
}
|
610
|
|
611
|
//taxon map
|
612
|
nameSpace = BerlinModelTaxonImport.NAMESPACE;
|
613
|
cdmClass = TaxonBase.class;
|
614
|
idSet = taxonIdSet;
|
615
|
Map<String, TaxonBase> objectMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
616
|
result.put(nameSpace, objectMap);
|
617
|
|
618
|
//field observation map map
|
619
|
nameSpace = AlgaTerraSpecimenImport.FIELD_OBSERVATION_NAMESPACE;
|
620
|
cdmClass = FieldObservation.class;
|
621
|
idSet = taxonIdSet;
|
622
|
Map<String, FieldObservation> fieldObservationMap = (Map<String, FieldObservation>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
623
|
result.put(nameSpace, fieldObservationMap);
|
624
|
|
625
|
//terms
|
626
|
nameSpace = AlgaTerraSpecimenImport.TERMS_NAMESPACE;
|
627
|
cdmClass = FieldObservation.class;
|
628
|
idSet = taxonIdSet;
|
629
|
Map<String, DefinedTermBase> termMap = (Map<String, DefinedTermBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
630
|
result.put(nameSpace, termMap);
|
631
|
|
632
|
|
633
|
|
634
|
|
635
|
} catch (SQLException e) {
|
636
|
throw new RuntimeException(e);
|
637
|
}
|
638
|
return result;
|
639
|
}
|
640
|
|
641
|
|
642
|
/**
|
643
|
* Use same TaxonDescription if two records belong to the same taxon
|
644
|
* @param state
|
645
|
* @param newTaxonId
|
646
|
* @param oldTaxonId
|
647
|
* @param oldDescription
|
648
|
* @param taxonMap
|
649
|
* @return
|
650
|
*/
|
651
|
private TaxonDescription getTaxonDescription(AlgaTerraImportState state, int newTaxonId, Map<String, TaxonBase> taxonMap, int factId, Reference<?> sourceSec){
|
652
|
TaxonDescription result = null;
|
653
|
TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(newTaxonId));
|
654
|
|
655
|
//TODO for testing
|
656
|
if (taxonBase == null && ! state.getConfig().isDoTaxa()){
|
657
|
taxonBase = Taxon.NewInstance(BotanicalName.NewInstance(Rank.SPECIES()), null);
|
658
|
}
|
659
|
|
660
|
Taxon taxon;
|
661
|
if ( taxonBase instanceof Taxon ) {
|
662
|
taxon = (Taxon) taxonBase;
|
663
|
} else if (taxonBase != null) {
|
664
|
logger.warn("TaxonBase for Fact(Specimen) with factId" + factId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());
|
665
|
return null;
|
666
|
} else {
|
667
|
logger.warn("TaxonBase for Fact(Specimen) " + factId + " is null.");
|
668
|
return null;
|
669
|
}
|
670
|
Set<TaxonDescription> descriptionSet= taxon.getDescriptions();
|
671
|
if (descriptionSet.size() > 0) {
|
672
|
result = descriptionSet.iterator().next();
|
673
|
}else{
|
674
|
result = TaxonDescription.NewInstance();
|
675
|
result.setTitleCache(sourceSec.getTitleCache(), true);
|
676
|
taxon.addDescription(result);
|
677
|
}
|
678
|
return result;
|
679
|
}
|
680
|
|
681
|
|
682
|
/* (non-Javadoc)
|
683
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
|
684
|
*/
|
685
|
@Override
|
686
|
protected boolean doCheck(BerlinModelImportState state){
|
687
|
IOValidator<BerlinModelImportState> validator = new AlgaTerraSpecimenImportValidator();
|
688
|
return validator.validate(state);
|
689
|
}
|
690
|
|
691
|
/* (non-Javadoc)
|
692
|
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getTableName()
|
693
|
*/
|
694
|
@Override
|
695
|
protected String getTableName() {
|
696
|
return dbTableName;
|
697
|
}
|
698
|
|
699
|
/* (non-Javadoc)
|
700
|
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getPluralString()
|
701
|
*/
|
702
|
@Override
|
703
|
public String getPluralString() {
|
704
|
return pluralString;
|
705
|
}
|
706
|
|
707
|
/* (non-Javadoc)
|
708
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
709
|
*/
|
710
|
protected boolean isIgnore(BerlinModelImportState state){
|
711
|
return ! ((AlgaTerraImportState)state).getAlgaTerraConfigurator().isDoSpecimen();
|
712
|
}
|
713
|
|
714
|
}
|