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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 static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_FACT_ALSO_PUBLISHED_IN;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_FACT_BIBLIOGRAPHY;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.NAME_FACT_PROTOLOGUE;
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import java.io.File;
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import java.io.IOException;
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import java.net.MalformedURLException;
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import java.net.URI;
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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.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.commons.lang.StringUtils;
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import org.apache.http.HttpException;
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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.media.ImageInfo;
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import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelNameFactsImportValidator;
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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.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
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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.media.MediaRepresentationPart;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.Reference;
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/**
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* @author a.mueller
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* @since 20.03.2008
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*/
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@Component
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public class BerlinModelNameFactsImport extends BerlinModelImportBase {
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private static final long serialVersionUID = 4174085686074314138L;
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private static final Logger logger = Logger.getLogger(BerlinModelNameFactsImport.class);
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public static final String NAMESPACE = "NameFact";
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/**
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* write info message after modCount iterations
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*/
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private int modCount = 500;
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private static final String pluralString = "name facts";
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private static final String dbTableName = "NameFact";
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public BerlinModelNameFactsImport(){
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super(dbTableName, pluralString);
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}
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@Override
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protected String getIdQuery(BerlinModelImportState state) {
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if (isNotBlank(state.getConfig().getNameIdTable())){
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String result = super.getIdQuery(state);
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result += " WHERE ptNameFk IN (SELECT NameId FROM " + state.getConfig().getNameIdTable() + ")";
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if (state.getConfig().isEuroMed()){
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result += " AND NOT (NameFactCategoryFk = 3 AND NameFactRefFk = 8500000) "; //#7796#note-11
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}
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return result;
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}else{
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return super.getIdQuery(state);
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}
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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 NameFact.*, Name.NameID as nameId, NameFactCategory.NameFactCategory " +
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" FROM NameFact INNER JOIN " +
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" Name ON NameFact.PTNameFk = Name.NameId INNER JOIN "+
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" NameFactCategory ON NameFactCategory.NameFactCategoryID = NameFact.NameFactCategoryFK " +
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" WHERE (NameFactId IN ("+ ID_LIST_TOKEN+") )";
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return strQuery;
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}
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@Override
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public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, BerlinModelImportState state) {
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boolean success = true ;
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BerlinModelImportConfigurator config = state.getConfig();
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Set<TaxonName> nameToSave = new HashSet<>();
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Map<String, TaxonName> nameMap = partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);
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Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);
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ResultSet rs = partitioner.getResultSet();
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Reference sourceRef = state.getTransactionalSourceReference();
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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() && (config.getMaximumNumberOfNameFacts() == 0 || i < config.getMaximumNumberOfNameFacts())){
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if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("NameFacts handled: " + (i-1));}
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int nameFactId = rs.getInt("nameFactId");
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int nameId = rs.getInt("nameId");
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Object nameFactRefFkObj = rs.getObject("nameFactRefFk");
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String nameFactRefDetail = rs.getString("nameFactRefDetail");
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String category = CdmUtils.Nz(rs.getString("NameFactCategory"));
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String nameFact = CdmUtils.Nz(rs.getString("nameFact"));
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TaxonName taxonNameBase = nameMap.get(String.valueOf(nameId));
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String nameFactRefFk = String.valueOf(nameFactRefFkObj);
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Reference citation = refMap.get(nameFactRefFk);
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if (taxonNameBase != null){
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//PROTOLOGUE
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if (category.equalsIgnoreCase(NAME_FACT_PROTOLOGUE)){
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//Reference ref = (Reference)taxonNameBase.getNomenclaturalReference();
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//ref = Book.NewInstance();
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try{
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Media media = getMedia(nameFact, config.getMediaUrl(), config.getMediaPath());
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if (media.getRepresentations().size() > 0){
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TaxonNameDescription description = TaxonNameDescription.NewInstance();
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TextData protolog = TextData.NewInstance(Feature.PROTOLOGUE());
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protolog.addMedia(media);
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protolog.addSource(OriginalSourceType.Import, String.valueOf(nameFactId), NAMESPACE, null, null, null, null);
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description.addElement(protolog);
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taxonNameBase.addDescription(description);
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if (citation != null){
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description.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, citation, null);
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protolog.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, citation, nameFactRefDetail, null, null);
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}
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}//end NAME_FACT_PROTOLOGUE
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}catch(NullPointerException e){
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logger.warn("MediaUrl and/or MediaPath not set. Could not get protologue.");
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success = false;
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}
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}else if (category.equalsIgnoreCase(NAME_FACT_ALSO_PUBLISHED_IN)){
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if (StringUtils.isNotBlank(nameFact)){
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TaxonNameDescription description = TaxonNameDescription.NewInstance();
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TextData additionalPublication = TextData.NewInstance(Feature.ADDITIONAL_PUBLICATION());
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//TODO language
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Language language = Language.DEFAULT();
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additionalPublication.putText(language, nameFact);
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additionalPublication.addSource(OriginalSourceType.Import, String.valueOf(nameFactId), NAMESPACE, null,null, null, null);
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if (citation != null || isNotBlank(nameFactRefDetail)){
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additionalPublication.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, citation, nameFactRefDetail, null, null);
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}
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description.addElement(additionalPublication);
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taxonNameBase.addDescription(description);
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}
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}else if (category.equalsIgnoreCase(NAME_FACT_BIBLIOGRAPHY)){
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if (isNotBlank(nameFact)){
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TaxonNameDescription description = TaxonNameDescription.NewInstance();
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TextData bibliography = TextData.NewInstance(Feature.CITATION());
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//TODO language
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Language language = Language.DEFAULT();
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bibliography.putText(language, nameFact);
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bibliography.addSource(OriginalSourceType.Import, String.valueOf(nameFactId), NAMESPACE, null,null, null, null);
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if (citation != null || isNotBlank(nameFactRefDetail)){
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bibliography.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, citation, nameFactRefDetail, null, null);
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}
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description.addElement(bibliography);
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taxonNameBase.addDescription(description);
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}
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}else {
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//TODO
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logger.warn("NameFactCategory '" + category + "' not yet implemented");
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success = false;
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}
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//TODO
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// DoubtfulFlag bit Checked
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// PublishFlag bit Checked
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// Created_When datetime Checked
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// Updated_When datetime Checked
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// Created_Who nvarchar(255) Checked
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// Updated_Who nvarchar(255) Checked
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// Notes nvarchar(1000) Checked
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nameToSave.add(taxonNameBase);
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}else{
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//TODO
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logger.warn("TaxonName for NameFact " + nameFactId + " does not exist in store");
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success = false;
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}
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//put
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}
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if (config.getMaximumNumberOfNameFacts() != 0 && i >= config.getMaximumNumberOfNameFacts() - 1){
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logger.warn("ONLY " + config.getMaximumNumberOfNameFacts() + " NAMEFACTS imported !!!" )
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;};
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logger.info("Names to save: " + nameToSave.size());
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getNameService().save(nameToSave);
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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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@Override
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
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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> nameIdSet = new HashSet<String>();
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Set<String> referenceIdSet = new HashSet<String>();
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while (rs.next()){
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handleForeignKey(rs, nameIdSet, "PTnameFk");
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handleForeignKey(rs, referenceIdSet, "nameFactRefFk");
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}
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//name map
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nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
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cdmClass = TaxonName.class;
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idSet = nameIdSet;
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Map<String, Person> objectMap = (Map<String, Person>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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result.put(nameSpace, objectMap);
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//reference map
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nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
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cdmClass = Reference.class;
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idSet = referenceIdSet;
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Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
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result.put(nameSpace, referenceMap);
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} catch (SQLException e) {
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throw new RuntimeException(e);
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}
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return result;
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}
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//FIXME gibt es da keine allgemeine Methode in common?
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public Media getMedia(String nameFact, URL mediaUrl, File mediaPath){
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if (mediaUrl == null){
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logger.warn("Media Url should not be null");
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return null;
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}
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String mimeTypeTif = "image/tiff";
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String mimeTypeJpg = "image/jpeg";
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String mimeTypePng = "image/png";
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String mimeTypePdf = "application/pdf";
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String suffixTif = "tif";
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String suffixJpg = "jpg";
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String suffixPng = "png";
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String suffixPdf = "pdf";
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String sep = File.separator;
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Integer size = null;
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logger.debug("Getting media for NameFact: " + nameFact);
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Media media = Media.NewInstance();
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String mediaUrlString = mediaUrl.toString();
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//tiff
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String urlStringTif = mediaUrlString + "tif/" + nameFact + "." + suffixTif;
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File file = new File(mediaPath, "tif" + sep + nameFact + "." + suffixTif);
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MediaRepresentation representationTif = MediaRepresentation.NewInstance(mimeTypeTif, suffixTif);
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if (file.exists()){
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representationTif.addRepresentationPart(makeImage(urlStringTif, size, file));
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}
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if(representationTif.getParts().size() > 0){
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media.addRepresentation(representationTif);
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}
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// end tif
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// jpg
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boolean fileExists = true;
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int jpgCount = 0;
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MediaRepresentation representationJpg = MediaRepresentation.NewInstance(mimeTypeJpg, suffixJpg);
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while(fileExists){
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String urlStringJpeg = mediaUrlString + "cmd_jpg/" + nameFact + "_page_000" + jpgCount + "." + suffixJpg;
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file = new File(mediaPath, "cmd_jpg" + sep + nameFact + "_page_000" + jpgCount + "." + suffixJpg);
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jpgCount++;
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if (file.exists()){
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representationJpg.addRepresentationPart(makeImage(urlStringJpeg, size, file));
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}else{
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fileExists = false;
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}
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}
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if(representationJpg.getParts().size() > 0){
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media.addRepresentation(representationJpg);
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}
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// end jpg
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//png
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String urlStringPng = mediaUrlString + "png/" + nameFact + "." + suffixPng;
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file = new File(mediaPath, "png" + sep + nameFact + "." + suffixPng);
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MediaRepresentation representationPng = MediaRepresentation.NewInstance(mimeTypePng, suffixPng);
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if (file.exists()){
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representationPng.addRepresentationPart(makeImage(urlStringPng, size, file));
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}else{
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fileExists = true;
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int pngCount = 0;
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while (fileExists){
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pngCount++;
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urlStringPng = mediaUrlString + "png/" + nameFact + "00" + pngCount + "." + suffixPng;
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file = new File(mediaPath, "png" + sep + nameFact + "00" + pngCount + "." + suffixPng);
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if (file.exists()){
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representationPng.addRepresentationPart(makeImage(urlStringPng, size, file));
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}else{
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fileExists = false;
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}
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}
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}
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if(representationPng.getParts().size() > 0){
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media.addRepresentation(representationPng);
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}
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//end png
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//pdf
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String urlStringPdf = mediaUrlString + "pdf/" + nameFact + "." + suffixPdf;
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URI uriPdf;
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try {
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uriPdf = new URI(urlStringPdf);
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file = new File(mediaPath, "pdf" + sep + nameFact + "." + suffixPdf);
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343
|
MediaRepresentation representationPdf = MediaRepresentation.NewInstance(mimeTypePdf, suffixPdf);
|
|
344
|
if (file.exists()){
|
|
345
|
representationPdf.addRepresentationPart(MediaRepresentationPart.NewInstance(uriPdf, size));
|
|
346
|
}else{
|
|
347
|
fileExists = true;
|
|
348
|
int pdfCount = 0;
|
|
349
|
while (fileExists){
|
|
350
|
pdfCount++;
|
|
351
|
urlStringPdf = mediaUrlString + "pdf/" + nameFact + "00" + pdfCount + "." + suffixPdf;
|
|
352
|
file = new File(mediaPath, "pdf/" + sep + nameFact + "00" + pdfCount + "." + suffixPdf);
|
|
353
|
|
|
354
|
if (file.exists()){
|
|
355
|
representationPdf.addRepresentationPart(MediaRepresentationPart.NewInstance(uriPdf, size));
|
|
356
|
}else{
|
|
357
|
fileExists = false;
|
|
358
|
}
|
|
359
|
}
|
|
360
|
}
|
|
361
|
if(representationPdf.getParts().size() > 0){
|
|
362
|
media.addRepresentation(representationPdf);
|
|
363
|
}
|
|
364
|
} catch (URISyntaxException e) {
|
|
365
|
e.printStackTrace();
|
|
366
|
logger.error("URISyntaxException" + urlStringPdf);
|
|
367
|
}
|
|
368
|
//end pdf
|
|
369
|
|
|
370
|
if(logger.isDebugEnabled()){
|
|
371
|
for (MediaRepresentation rep : media.getRepresentations()){
|
|
372
|
for (MediaRepresentationPart part : rep.getParts()){
|
|
373
|
logger.debug("in representation: " + part.getUri());
|
|
374
|
}
|
|
375
|
}
|
|
376
|
}
|
|
377
|
|
|
378
|
return media;
|
|
379
|
}
|
|
380
|
|
|
381
|
|
|
382
|
private ImageFile makeImage(String imageUri, Integer size, File file){
|
|
383
|
ImageInfo imageMetaData = null;
|
|
384
|
URI uri;
|
|
385
|
try {
|
|
386
|
uri = new URI(imageUri);
|
|
387
|
try {
|
|
388
|
imageMetaData = ImageInfo.NewInstance(uri, 0);
|
|
389
|
} catch (IOException e) {
|
|
390
|
logger.error("IOError reading image metadata." , e);
|
|
391
|
} catch (HttpException e) {
|
|
392
|
logger.error("HttpException reading image metadata." , e);
|
|
393
|
}
|
|
394
|
ImageFile image = ImageFile.NewInstance(uri, size, imageMetaData);
|
|
395
|
return image;
|
|
396
|
} catch (URISyntaxException e1) {
|
|
397
|
logger.warn("URISyntaxException: " + imageUri);
|
|
398
|
return null;
|
|
399
|
}
|
|
400
|
|
|
401
|
}
|
|
402
|
|
|
403
|
|
|
404
|
/* (non-Javadoc)
|
|
405
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
|
|
406
|
*/
|
|
407
|
@Override
|
|
408
|
protected boolean doCheck(BerlinModelImportState state){
|
|
409
|
IOValidator<BerlinModelImportState> validator = new BerlinModelNameFactsImportValidator();
|
|
410
|
return validator.validate(state);
|
|
411
|
}
|
|
412
|
|
|
413
|
|
|
414
|
/* (non-Javadoc)
|
|
415
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
|
416
|
*/
|
|
417
|
@Override
|
|
418
|
protected boolean isIgnore(BerlinModelImportState state){
|
|
419
|
return ! state.getConfig().isDoNameFacts();
|
|
420
|
}
|
|
421
|
|
|
422
|
|
|
423
|
|
|
424
|
//for testing only
|
|
425
|
public static void main(String[] args) {
|
|
426
|
|
|
427
|
BerlinModelNameFactsImport nf = new BerlinModelNameFactsImport();
|
|
428
|
|
|
429
|
URL url;
|
|
430
|
try {
|
|
431
|
url = new URL("http://wp5.e-taxonomy.eu/dataportal/cichorieae/media/protolog/");
|
|
432
|
File path = new File("/Volumes/protolog/protolog/");
|
|
433
|
if(path.exists()){
|
|
434
|
String fact = "Acanthocephalus_amplexifolius";
|
|
435
|
// make getMedia public for this to work
|
|
436
|
Media media = nf.getMedia(fact, url, path);
|
|
437
|
logger.info(media);
|
|
438
|
for (MediaRepresentation rep : media.getRepresentations()){
|
|
439
|
logger.info(rep.getMimeType());
|
|
440
|
for (MediaRepresentationPart part : rep.getParts()){
|
|
441
|
logger.info(part.getUri());
|
|
442
|
}
|
|
443
|
}
|
|
444
|
}
|
|
445
|
} catch (MalformedURLException e) {
|
|
446
|
e.printStackTrace();
|
|
447
|
}
|
|
448
|
}
|
|
449
|
}
|