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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.berlinModel.in;
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import java.io.IOException;
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import java.net.MalformedURLException;
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import java.net.URISyntaxException;
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import java.net.URL;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.Collection;
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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 org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.common.mediaMetaData.ImageMetaData;
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import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
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import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelFactsImportValidator;
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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.common.Annotation;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DescriptionElementSource;
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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.TermVocabulary;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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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.media.ImageFile;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.media.MediaRepresentation;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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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 BerlinModelFactsImport extends BerlinModelImportBase {
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private static final Logger logger = Logger.getLogger(BerlinModelFactsImport.class);
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public static final String NAMESPACE = "Fact";
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public static final String SEQUENCE_PREFIX = "ORDER: ";
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private int modCount = 10000;
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private static final String pluralString = "facts";
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private static final String dbTableName = "Fact";
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//FIXME don't use as class variable
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private Map<Integer, Feature> featureMap;
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public BerlinModelFactsImport(){
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super();
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}
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private TermVocabulary<Feature> getFeatureVocabulary(){
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try {
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//TODO work around until service method works
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TermVocabulary<Feature> featureVocabulary = BerlinModelTransformer.factCategory2Feature(1).getVocabulary();
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//TermVocabulary<Feature> vocabulary = getTermService().getVocabulary(vocabularyUuid);
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return featureVocabulary;
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} catch (UnknownCdmTypeException e) {
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logger.error("Feature vocabulary not available. New vocabulary created");
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return new TermVocabulary<Feature>() ;
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}
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}
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private Map<Integer, Feature> invokeFactCategories(BerlinModelImportConfigurator bmiConfig){
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Map<Integer, Feature> result = bmiConfig.getFeatureMap();
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Source source = bmiConfig.getSource();
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try {
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//get data from database
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String strQuery =
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" SELECT FactCategory.* " +
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" FROM FactCategory "+
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" WHERE (1=1)";
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ResultSet rs = source.getResultSet(strQuery) ;
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TermVocabulary<Feature> featureVocabulary = getFeatureVocabulary();
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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("FactCategories handled: " + (i-1));}
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int factCategoryId = rs.getInt("factCategoryId");
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String factCategory = rs.getString("factCategory");
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Feature feature;
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try {
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feature = BerlinModelTransformer.factCategory2Feature(factCategoryId);
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} catch (UnknownCdmTypeException e) {
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logger.warn("New Feature (FactCategoryId: " + factCategoryId + ")");
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feature = Feature.NewInstance(factCategory, factCategory, null);
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feature.setVocabulary(featureVocabulary);
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feature.setSupportsTextData(true);
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//TODO
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// MaxFactNumber int Checked
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// ExtensionTableName varchar(100) Checked
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// Description nvarchar(1000) Checked
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// locExtensionFormName nvarchar(80) Checked
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// RankRestrictionFk int Checked
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}
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result.put(factCategoryId, feature);
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}
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Collection<Feature> col = result.values();
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getTermService().save((Collection)col);
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return result;
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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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return null;
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}
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#doInvoke(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
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*/
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@Override
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protected boolean doInvoke(BerlinModelImportState state) {
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featureMap = invokeFactCategories(state.getConfig());
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return super.doInvoke(state);
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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 =
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" SELECT Fact.*, PTaxon.RIdentifier as taxonId, RefDetail.Details " +
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" FROM Fact " +
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" INNER JOIN PTaxon ON Fact.PTNameFk = PTaxon.PTNameFk AND Fact.PTRefFk = PTaxon.PTRefFk " +
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" LEFT OUTER JOIN RefDetail ON Fact.FactRefDetailFk = RefDetail.RefDetailId AND Fact.FactRefFk = RefDetail.RefFk " +
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" WHERE (FactId IN (" + ID_LIST_TOKEN + "))" +
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" ORDER By Sequence";
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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 state) {
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boolean success = true ;
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BerlinModelImportConfigurator config = state.getConfig();
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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, ReferenceBase> biblioRefMap = (Map<String, ReferenceBase>) partitioner.getObjectMap(BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE);
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Map<String, ReferenceBase> nomRefMap = (Map<String, ReferenceBase>) partitioner.getObjectMap(BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE);
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ResultSet rs = partitioner.getResultSet();
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ReferenceBase<?> sourceRef = state.getConfig().getSourceReference();
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try{
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int i = 0;
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//for each fact
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while (rs.next()){
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try{
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if ((i++ % modCount) == 0){ logger.info("Facts handled: " + (i-1));}
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int factId = rs.getInt("factId");
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Object taxonIdObj = rs.getObject("taxonId");
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int taxonId = rs.getInt("taxonId");
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Object factRefFkObj = rs.getObject("factRefFk");
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Object categoryFkObj = rs.getObject("factCategoryFk");
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Integer categoryFk = rs.getInt("factCategoryFk");
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String details = rs.getString("Details");
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String fact = CdmUtils.Nz(rs.getString("Fact"));
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String notes = CdmUtils.Nz(rs.getString("notes"));
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Boolean doubtfulFlag = rs.getBoolean("DoubtfulFlag");
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Boolean publishFlag = rs.getBoolean("publishFlag");
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TaxonBase taxonBase = getTaxon(taxonMap, taxonIdObj, taxonId);
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Feature feature = getFeature(featureMap, categoryFkObj, categoryFk) ;
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if (taxonBase == null){
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logger.warn("Taxon for Fact " + factId + " does not exist in store");
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success = false;
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}else{
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Taxon taxon;
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if ( taxonBase instanceof Taxon ) {
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taxon = (Taxon) taxonBase;
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}else{
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logger.warn("TaxonBase " + (taxonIdObj==null?"(null)":taxonIdObj) + " for Fact " + factId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());
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success = false;
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continue;
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}
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TaxonDescription taxonDescription = null;
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Set<TaxonDescription> descriptionSet= taxon.getDescriptions();
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boolean isImage = false;
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Media media = null;
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//for diptera images
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if (categoryFk == 51){ //TODO check also FactCategory string
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isImage = true;
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media = Media.NewInstance();
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taxonDescription = makeImage(state, fact, media, descriptionSet, taxon);
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if (taxonDescription == null){
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continue;
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}
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}
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//all others (no image)
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else{
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for (TaxonDescription desc: descriptionSet){
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if (! desc.isImageGallery()){
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taxonDescription = desc;
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}
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}
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if (taxonDescription == null){
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taxonDescription = TaxonDescription.NewInstance();
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taxonDescription.setTitleCache(sourceRef == null ? null : sourceRef.getTitleCache(), true);
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taxon.addDescription(taxonDescription);
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}
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}
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//textData
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TextData textData = null;
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boolean newTextData = true;
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// For Cichorieae DB: If fact category is 31 (Systematics) and there is already a Systematics TextData
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// description element append the fact text to the existing TextData
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if(categoryFk == 31) {
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Set<DescriptionElementBase> descriptionElements = taxonDescription.getElements();
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for (DescriptionElementBase descriptionElement : descriptionElements) {
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String featureString = descriptionElement.getFeature().getRepresentation(Language.DEFAULT()).getLabel();
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if (descriptionElement instanceof TextData && featureString.equals("Systematics")) { // TODO: test
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textData = (TextData)descriptionElement;
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String factTextStr = textData.getText(Language.DEFAULT());
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// FIXME: Removing newlines doesn't work
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if (factTextStr.contains("\\r\\n")) {
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factTextStr = factTextStr.replaceAll("\\r\\n","");
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}
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StringBuilder factText = new StringBuilder(factTextStr);
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factText.append(fact);
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fact = factText.toString();
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newTextData = false;
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break;
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}
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}
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}
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if(newTextData == true) {
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textData = TextData.NewInstance();
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}
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//for diptera database
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if (categoryFk == 99 && notes.contains("<OriginalName>")){
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// notes = notes.replaceAll("<OriginalName>", "");
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// notes = notes.replaceAll("</OriginalName>", "");
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fact = notes + ": " + fact ;
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}
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//TODO textData.putText(fact, bmiConfig.getFactLanguage()); //doesn't work because bmiConfig.getFactLanguage() is not not a persistent Language Object
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//throws in thread "main" org.springframework.dao.InvalidDataAccessApiUsageException: object references an unsaved transient instance - save the transient instance before flushing: eu.etaxonomy.cdm.model.common.Language; nested exception is org.hibernate.TransientObjectException: object references an unsaved transient instance - save the transient instance before flushing: eu.etaxonomy.cdm.model.common.Language
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if (isImage){
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textData.addMedia(media);
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textData.setType(Feature.IMAGE());
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}else{
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textData.putText(fact, Language.DEFAULT());
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textData.setType(feature);
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}
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//reference
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ReferenceBase citation = null;
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String factRefFk = String.valueOf(factRefFkObj);
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if (factRefFkObj != null){
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citation = getReferenceOnlyFromMaps(
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biblioRefMap, nomRefMap, factRefFk);
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}
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if (citation == null && (factRefFkObj != null)){
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logger.warn("Citation not found in referenceMap: " + factRefFk);
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success = false;
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}
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if (citation != null || CdmUtils.isNotEmpty(details)){
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DescriptionElementSource originalSource = DescriptionElementSource.NewInstance();
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originalSource.setCitation(citation);
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originalSource.setCitationMicroReference(details);
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textData.addSource(originalSource);
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}
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taxonDescription.addElement(textData);
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//doubtfulFlag
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if (doubtfulFlag){
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textData.addMarker(Marker.NewInstance(MarkerType.IS_DOUBTFUL(), true));
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}
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//publisheFlag
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textData.addMarker(Marker.NewInstance(MarkerType.PUBLISH(), publishFlag));
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//Sequence
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Integer sequence = rs.getInt("Sequence");
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if (sequence != null && sequence != 999){
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String strSequence = String.valueOf(sequence);
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strSequence = SEQUENCE_PREFIX + strSequence;
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//TODO make it an Extension when possible
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//Extension datesExtension = Extension.NewInstance(textData, strSequence, ExtensionType.ORDER());
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Annotation annotation = Annotation.NewInstance(strSequence, Language.DEFAULT());
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textData.addAnnotation(annotation);
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}
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// if (categoryFkObj == FACT_DESCRIPTION){
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// //;
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// }else if (categoryFkObj == FACT_OBSERVATION){
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// //;
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// }else if (categoryFkObj == FACT_DISTRIBUTION_EM){
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// //
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// }else {
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// //TODO
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// //logger.warn("FactCategory " + categoryFk + " not yet implemented");
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// }
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//notes
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doCreatedUpdatedNotes(state, textData, rs);
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//TODO
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//Designation References -> unclear how to map to CDM
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//factId -> OriginalSource for descriptionElements not yet implemented
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//sequence -> textData is not an identifiable entity therefore extensions are not possible
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//fact category better
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taxaToSave.add(taxon);
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}
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} catch (Exception re){
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logger.error("An exception occurred during the facts import");
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re.printStackTrace();
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success = false;
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}
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//put
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}
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logger.info("Facts handled: " + (i-1));
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logger.info("Taxa to save: " + taxaToSave.size());
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getTaxonService().save(taxaToSave);
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}catch(SQLException e){
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throw new RuntimeException(e);
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}
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return success;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
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*/
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
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String nameSpace;
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Class cdmClass;
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Set<String> idSet;
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
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try{
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Set<String> taxonIdSet = new HashSet<String>();
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Set<String> referenceIdSet = new HashSet<String>();
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Set<String> refDetailIdSet = new HashSet<String>();
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while (rs.next()){
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handleForeignKey(rs, taxonIdSet, "taxonId");
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handleForeignKey(rs, referenceIdSet, "FactRefFk");
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handleForeignKey(rs, referenceIdSet, "PTDesignationRefFk");
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handleForeignKey(rs, refDetailIdSet, "FactRefDetailFk");
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handleForeignKey(rs, refDetailIdSet, "PTDesignationRefDetailFk");
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}
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//taxon map
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nameSpace = BerlinModelTaxonImport.NAMESPACE;
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cdmClass = TaxonBase.class;
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idSet = taxonIdSet;
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Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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result.put(nameSpace, taxonMap);
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//nom reference map
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nameSpace = BerlinModelReferenceImport.NOM_REFERENCE_NAMESPACE;
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398
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cdmClass = ReferenceBase.class;
|
399
|
idSet = referenceIdSet;
|
400
|
Map<String, ReferenceBase> nomReferenceMap = (Map<String, ReferenceBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
401
|
result.put(nameSpace, nomReferenceMap);
|
402
|
|
403
|
//biblio reference map
|
404
|
nameSpace = BerlinModelReferenceImport.BIBLIO_REFERENCE_NAMESPACE;
|
405
|
cdmClass = ReferenceBase.class;
|
406
|
idSet = referenceIdSet;
|
407
|
Map<String, ReferenceBase> biblioReferenceMap = (Map<String, ReferenceBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
408
|
result.put(nameSpace, biblioReferenceMap);
|
409
|
|
410
|
//nom refDetail map
|
411
|
nameSpace = BerlinModelRefDetailImport.NOM_REFDETAIL_NAMESPACE;
|
412
|
cdmClass = ReferenceBase.class;
|
413
|
idSet = refDetailIdSet;
|
414
|
Map<String, ReferenceBase> nomRefDetailMap= (Map<String, ReferenceBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
415
|
result.put(nameSpace, nomRefDetailMap);
|
416
|
|
417
|
//biblio refDetail map
|
418
|
nameSpace = BerlinModelRefDetailImport.BIBLIO_REFDETAIL_NAMESPACE;
|
419
|
cdmClass = ReferenceBase.class;
|
420
|
idSet = refDetailIdSet;
|
421
|
Map<String, ReferenceBase> biblioRefDetailMap= (Map<String, ReferenceBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
422
|
result.put(nameSpace, biblioRefDetailMap);
|
423
|
|
424
|
} catch (SQLException e) {
|
425
|
throw new RuntimeException(e);
|
426
|
}
|
427
|
return result;
|
428
|
}
|
429
|
|
430
|
|
431
|
/**
|
432
|
* @param state
|
433
|
* @param media
|
434
|
* @param media
|
435
|
* @param descriptionSet
|
436
|
*
|
437
|
*/
|
438
|
private TaxonDescription makeImage(BerlinModelImportState state, String fact, Media media, Set<TaxonDescription> descriptionSet, Taxon taxon) {
|
439
|
TaxonDescription taxonDescription = null;
|
440
|
ReferenceBase sourceRef = state.getConfig().getSourceReference();
|
441
|
String uri = fact;
|
442
|
Integer size = null;
|
443
|
ImageMetaData imageMetaData = ImageMetaData.newInstance();
|
444
|
URL url;
|
445
|
try {
|
446
|
url = new URL(fact.trim());
|
447
|
} catch (MalformedURLException e) {
|
448
|
logger.warn("Malformed URL. Image could not be imported: " + CdmUtils.Nz(uri));
|
449
|
return null;
|
450
|
}
|
451
|
try {
|
452
|
imageMetaData.readMetaData(url.toURI(), 0);
|
453
|
}
|
454
|
catch(URISyntaxException e){
|
455
|
logger.error("URISyntaxException reading image metadata." , e);
|
456
|
} catch (IOException e) {
|
457
|
logger.error("IOError reading image metadata." , e);
|
458
|
}
|
459
|
MediaRepresentation mediaRepresentation = MediaRepresentation.NewInstance(imageMetaData.getMimeType(), null);
|
460
|
media.addRepresentation(mediaRepresentation);
|
461
|
ImageFile image = ImageFile.NewInstance(uri, size, imageMetaData);
|
462
|
mediaRepresentation.addRepresentationPart(image);
|
463
|
|
464
|
taxonDescription = taxon.getOrCreateImageGallery(sourceRef == null ? null :sourceRef.getTitleCache());
|
465
|
|
466
|
return taxonDescription;
|
467
|
}
|
468
|
|
469
|
private TaxonBase getTaxon(Map<String, TaxonBase> taxonMap, Object taxonIdObj, Integer taxonId){
|
470
|
if (taxonIdObj != null){
|
471
|
return taxonMap.get(String.valueOf(taxonId));
|
472
|
}else{
|
473
|
return null;
|
474
|
}
|
475
|
|
476
|
}
|
477
|
|
478
|
private Feature getFeature(Map<Integer, Feature> featureMap, Object categoryFkObj, Integer categoryFk){
|
479
|
if (categoryFkObj != null){
|
480
|
return featureMap.get(categoryFk);
|
481
|
}else{
|
482
|
return null;
|
483
|
}
|
484
|
|
485
|
}
|
486
|
|
487
|
|
488
|
/* (non-Javadoc)
|
489
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
|
490
|
*/
|
491
|
@Override
|
492
|
protected boolean doCheck(BerlinModelImportState state){
|
493
|
IOValidator<BerlinModelImportState> validator = new BerlinModelFactsImportValidator();
|
494
|
return validator.validate(state);
|
495
|
}
|
496
|
|
497
|
/* (non-Javadoc)
|
498
|
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getTableName()
|
499
|
*/
|
500
|
@Override
|
501
|
protected String getTableName() {
|
502
|
return dbTableName;
|
503
|
}
|
504
|
|
505
|
/* (non-Javadoc)
|
506
|
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getPluralString()
|
507
|
*/
|
508
|
@Override
|
509
|
public String getPluralString() {
|
510
|
return pluralString;
|
511
|
}
|
512
|
|
513
|
/* (non-Javadoc)
|
514
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
515
|
*/
|
516
|
protected boolean isIgnore(BerlinModelImportState state){
|
517
|
return ! state.getConfig().isDoFacts();
|
518
|
}
|
519
|
|
520
|
|
521
|
}
|