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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.app.cyprus;
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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.util.ArrayList;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import org.apache.commons.imaging.ImageReadException;
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import org.apache.commons.imaging.Imaging;
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import org.apache.commons.imaging.common.GenericImageMetadata.GenericImageMetadataItem;
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import org.apache.commons.imaging.common.ImageMetadata;
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import org.apache.commons.imaging.common.ImageMetadata.ImageMetadataItem;
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import org.apache.log4j.Logger;
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import org.joda.time.DateTime;
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import org.joda.time.format.DateTimeFormat;
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import org.joda.time.format.DateTimeFormatter;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.api.application.CdmApplicationController;
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import eu.etaxonomy.cdm.api.service.config.MatchingTaxonConfigurator;
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import eu.etaxonomy.cdm.app.common.CdmDestinations;
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import eu.etaxonomy.cdm.common.UTF8;
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import eu.etaxonomy.cdm.common.media.ImageInfo;
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import eu.etaxonomy.cdm.database.DbSchemaValidation;
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import eu.etaxonomy.cdm.database.ICdmDataSource;
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import eu.etaxonomy.cdm.io.api.application.CdmIoApplicationController;
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import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper;
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import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
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import eu.etaxonomy.cdm.model.agent.AgentBase;
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import eu.etaxonomy.cdm.model.agent.Institution;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Language;
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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.media.MediaRepresentationPart;
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import eu.etaxonomy.cdm.model.media.Rights;
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import eu.etaxonomy.cdm.model.media.RightsType;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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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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* @since 05.2017
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*/
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public class CyprusImagesActivator {
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private static final Logger logger = Logger.getLogger(CyprusImagesActivator.class);
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_dev();
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static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_production();
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static boolean testOnly = false;
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static boolean update_notCreate = false;
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//if true, data will always be updated, if false, only missing data will be updated
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static boolean forceUpdate = false;
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private static final String path = "//media/digitalimages/EditWP6/Zypern/photos/";
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private static final String urlPath = "http://media.bgbm.org/erez/erez?src=EditWP6/zypern/photos/";
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private ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>> deduplicationHelper;
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private void doImport(ICdmDataSource cdmDestination){
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CdmApplicationController app = CdmIoApplicationController.NewInstance(cdmDestination, DbSchemaValidation.VALIDATE);
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TransactionStatus tx = app.startTransaction();
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deduplicationHelper = (ImportDeduplicationHelper)ImportDeduplicationHelper.NewInstance(app);
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File file = new File(path);
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String[] fileList = file.list();
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Set<String> notFound = new HashSet<>();
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String regEx = "([A-Z][a-z]+_[a-z\\-]{3,}(?:_s_[a-z\\-]{3,})?)_[A-F]\\d{1,2}\\.(?:jpg|JPG)";
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Pattern pattern = Pattern.compile(regEx);
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for (String fileName : fileList){
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Matcher matcher = pattern.matcher(fileName);
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if (matcher.matches()){
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// System.out.println(fileName);
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String taxonName = matcher.group(1);
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taxonName = taxonName.replace("_s_", " subsp. ").replace("_", " ");
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Taxon taxon = getAcceptedTaxon(app, taxonName);
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if (taxon == null){
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if (!notFound.contains(taxonName)){
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notFound.add(taxonName);
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logger.warn("Taxon not found: " + taxonName);
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}
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}else{
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handleTaxon(app, taxon, fileName);
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}
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}else{
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if (!fileName.matches("(?:\\.erez|Thumbs\\.db.*|zypern_.*|__Keywords_template\\.txt)")){
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logger.warn("Incorrect filename:" + fileName);
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}
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}
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}
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// app.getTaxonService().saveOrUpdate(taxaToSave);
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if (testOnly){
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tx.setRollbackOnly();
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}
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app.commitTransaction(tx);
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}
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/**
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* @param app
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* @param taxon
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* @param fileName
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*/
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private void handleTaxon(CdmApplicationController app, Taxon taxon, String fileName) {
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Set<String> urlStr = getAllExistingUrls(taxon);
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String fullName = urlPath + fileName;
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if (urlStr.contains(fullName)){
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return;
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}else{
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addMedia(app, taxon, fileName);
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}
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}
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/**
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* @param app
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* @param taxon
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* @param fileName
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*/
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private void addMedia(CdmApplicationController app, Taxon taxon, String fileName) {
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try {
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String fullName = urlPath + fileName;
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Media media = getImageMedia(fullName, null, true);
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makeMetaData(media, fileName, false);
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makeTitle(media, fileName, false);
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if (!testOnly){
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makeTextData(fileName, media, taxon);
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}
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} catch (Exception e) {
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e.printStackTrace();
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return;
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}
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}
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/**
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* @param media
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* @param fileName
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* @param b
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*/
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private void makeTitle(Media media, String fileName, boolean updateOnly) {
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String title = fileName.replace("_s_"," subsp. ")
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.replace("_"," ").replace(".jpg","").replace(".JPG","");
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if ( (!updateOnly) || media.getAllTitles().isEmpty()){
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media.putTitle(Language.LATIN(), title);
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}
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}
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/**
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* @param media
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*/
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private void makeMetaData(Media media, String fileName, boolean updateOnly) {
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File file = new File(path + fileName);
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if (!file.exists()){
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logger.warn("File for filename " + fileName + " does not exist.");
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return;
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}
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Map<String, String> keywords = new HashMap<>();
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String copyright = null;
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String artistStr = null;
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String created = null;
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try{
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// IImageMetadata metadata = Sanselan.getMetadata(file);
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ImageMetadata metadata = Imaging.getMetadata(file);
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List<? extends ImageMetadataItem> items = metadata.getItems();
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for (Object object : items){
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ImageMetadataItem metadataItem = (ImageMetadataItem) object;
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// System.out.println(item.getKeyword() + ": " + item.getText());
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if (metadataItem instanceof GenericImageMetadataItem){
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GenericImageMetadataItem item = (GenericImageMetadataItem) metadataItem;
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String keyword = item.getKeyword().toLowerCase();
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String value =removeQuots(item.getText());
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if("keywords".equals(keyword)){
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String[] splits = value.split(":");
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if (splits.length == 2){
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keywords.put(splits[0].trim().toLowerCase(), splits[1].trim());
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}else{
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logger.warn("Keyword has not correct format and can not be parsed: " + value + " for file " + fileName);
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}
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}else if ("Copyright Notice".equalsIgnoreCase(keyword)){
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copyright = value;
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}else if ("artist".equals(keyword)){
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artistStr = value;
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}else if ("date time original".equalsIgnoreCase(item.getKeyword())){
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created = value;
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}
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}
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}
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} catch (ImageReadException | IOException e1) {
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logger.warn(" Problem (" + e1.getMessage() + ") when reading metadata from file: " + fileName);
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e1.printStackTrace();
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}
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AgentBase<?> artistAgent = null;
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Rights right = null;
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DateTime createdDate = null;
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String locality = null;
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//artist
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if (keywords.get("photographer") != null){
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String artist = keywords.get("photographer");
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artistAgent = makePerson(artist, fileName);
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}
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if (artistStr != null){
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if (keywords.get("photographer") == null){
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artistAgent = makePerson(artistStr, fileName);
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}else if (!keywords.get("photographer").toLowerCase().replace(" ", "")
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.contains(artistStr.toLowerCase().replace(" ", ""))){
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logger.warn("Artist '" + artistStr + "' could not be handled for " + fileName);
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}
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}
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//locality
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if (keywords.get("locality") != null){
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locality = keywords.get("locality");
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}
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//copyright
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if (copyright != null){
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AgentBase<?> agent;
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if (copyright.equals("Botanic Garden and Botanical Museum Berlin-Dahlem (BGBM)")){
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agent = Institution.NewNamedInstance(copyright);
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}else{
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agent = makePerson(copyright, fileName);
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}
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right = Rights.NewInstance(null, null, RightsType.COPYRIGHT());
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right.setAgent(agent);
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right = deduplicationHelper.getExistingCopyright(null, right);
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}
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//created
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if (created != null){
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DateTimeFormatter f = DateTimeFormat.forPattern("yyyy:MM:dd HH:mm:ss");
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try {
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createdDate = f/*.withZone(DateTimeZone.forID("Europe/Athens"))*/.parseDateTime(created);
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} catch (Exception e) {
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logger.warn("Exception (" + e.getMessage() + ") when parsing create date " + created + " for file " + fileName);
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}
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}
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280
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boolean force = !updateOnly || forceUpdate;
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//add to media
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282
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if (artistAgent != null && (force || media.getArtist() == null)){
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media.setArtist(artistAgent);
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}
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285
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if (right != null && (force || media.getRights().isEmpty())){
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media.removeRights(right);
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287
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media.addRights(right);
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}
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289
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if (createdDate != null && (force || media.getMediaCreated() == null)){
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media.setMediaCreated(createdDate);
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}
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292
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if (locality != null && (force || media.getDescription(Language.ENGLISH()) == null)){
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293
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media.putDescription(Language.ENGLISH(), locality);
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294
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}
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295
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}
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296
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297
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/**
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298
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* @param artist
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299
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* @return
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300
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*/
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301
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private Person makePerson(String artist, String fileName) {
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302
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artist = artist.trim();
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303
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String regEx = "((?:[A-Z]\\. ?)+)([A-Z][a-z\\-\u00E4\u00F6\u00FC]+)";
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304
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Matcher matcher = Pattern.compile(regEx).matcher(artist);
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305
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Person person = Person.NewInstance();
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306
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if (matcher.matches()){
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307
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person.setGivenName(matcher.group(1).trim());
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308
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person.setFamilyName(matcher.group(2).trim());
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309
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}else{
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310
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person.setTitleCache(artist, true);
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311
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logger.warn("Person could not be parsed: " + artist + " for file " + fileName);
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312
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}
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313
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314
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person = (Person)deduplicationHelper.getExistingAuthor(null, person);
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315
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return person;
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316
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}
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317
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318
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private String removeQuots(String text) {
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319
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if (text.startsWith("'") && text.endsWith("'")){
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320
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return text.substring(1, text.length() -1);
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321
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}else{
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322
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return text;
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323
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}
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324
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}
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325
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326
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private void makeTextData(String fileStr, Media media, Taxon taxon) {
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327
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TaxonDescription imageGallery = taxon.getImageGallery(true);
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328
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TextData textData = null;
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329
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if (!imageGallery.getElements().isEmpty()){
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330
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DescriptionElementBase el = imageGallery.getElements().iterator().next();
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331
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if (el.isInstanceOf(TextData.class)){
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332
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textData = CdmBase.deproxy(el, TextData.class);
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333
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}else{
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334
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logger.warn("Image gallery had non-textdata description element: " + fileStr);
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335
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}
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336
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}
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337
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if (textData == null){
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338
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textData = TextData.NewInstance();
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339
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textData.setFeature(Feature.IMAGE());
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340
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}
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341
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imageGallery.addElement(textData);
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342
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textData.addMedia(media);
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343
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}
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344
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345
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/**
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|
346
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* Creates
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347
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* @param uriString
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348
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* @param readDataFromUrl
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349
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* @see #READ_MEDIA_DATA
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350
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* @return
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351
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* @throws MalformedURLException
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352
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*/
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353
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protected Media getImageMedia(String uriString, String uriStrThumb, boolean readMediaData) throws MalformedURLException {
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354
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if( uriString == null){
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355
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return null;
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356
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} else {
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357
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uriString = uriString.replace(" ", "%20"); //replace whitespace
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358
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try {
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359
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ImageInfo imageInfo = null;
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360
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URI uri = new URI(uriString);
|
|
361
|
|
|
362
|
try {
|
|
363
|
if (readMediaData){
|
|
364
|
logger.info("Read media data from: " + uri);
|
|
365
|
imageInfo = ImageInfo.NewInstance(uri, 0);
|
|
366
|
}
|
|
367
|
} catch (Exception e) {
|
|
368
|
String message = "An error occurred when trying to read image meta data for " + uri.toString() + ": " + e.getMessage();
|
|
369
|
logger.warn(message);
|
|
370
|
}
|
|
371
|
ImageFile imageFile = ImageFile.NewInstance(uri, null, imageInfo);
|
|
372
|
|
|
373
|
MediaRepresentation representation = MediaRepresentation.NewInstance();
|
|
374
|
|
|
375
|
if(imageInfo != null){
|
|
376
|
representation.setMimeType(imageInfo.getMimeType());
|
|
377
|
representation.setSuffix(imageInfo.getSuffix());
|
|
378
|
}
|
|
379
|
representation.addRepresentationPart(imageFile);
|
|
380
|
Media media = Media.NewInstance();
|
|
381
|
media.addRepresentation(representation);
|
|
382
|
|
|
383
|
if (uriStrThumb != null){
|
|
384
|
ImageInfo imageInfoThumb = null;
|
|
385
|
uriStrThumb = uriStrThumb.replace(" ", "%20"); //replace whitespace
|
|
386
|
URI uriThumb = new URI(uriStrThumb);
|
|
387
|
try {
|
|
388
|
if (readMediaData){
|
|
389
|
logger.info("Read media data from: " + uriThumb);
|
|
390
|
imageInfoThumb = ImageInfo.NewInstance(uriThumb, 0);
|
|
391
|
}
|
|
392
|
} catch (Exception e) {
|
|
393
|
String message = "An error occurred when trying to read image meta data for " + uriThumb.toString() + ": " + e.getMessage();
|
|
394
|
logger.warn(message);
|
|
395
|
}
|
|
396
|
|
|
397
|
ImageFile imageFileFhumb = ImageFile.NewInstance(uriThumb, null, imageInfoThumb);
|
|
398
|
MediaRepresentation reprThumb = MediaRepresentation.NewInstance();
|
|
399
|
if(imageInfoThumb != null){
|
|
400
|
reprThumb.setMimeType(imageInfoThumb.getMimeType());
|
|
401
|
reprThumb.setSuffix(imageInfoThumb.getSuffix());
|
|
402
|
}
|
|
403
|
reprThumb.addRepresentationPart(imageFileFhumb);
|
|
404
|
media.addRepresentation(reprThumb);
|
|
405
|
}
|
|
406
|
|
|
407
|
return media;
|
|
408
|
} catch (URISyntaxException e1) {
|
|
409
|
String message = "An URISyntaxException occurred when trying to create uri from multimedia objcet string: " + uriString;
|
|
410
|
logger.warn(message);
|
|
411
|
return null;
|
|
412
|
}
|
|
413
|
}
|
|
414
|
}
|
|
415
|
|
|
416
|
/**
|
|
417
|
* @param taxon
|
|
418
|
* @return
|
|
419
|
*/
|
|
420
|
private Set<String> getAllExistingUrls(Taxon taxon) {
|
|
421
|
Set<String> result = new HashSet<>();
|
|
422
|
Set<TaxonDescription> descriptions = taxon.getDescriptions();
|
|
423
|
for (TaxonDescription td : descriptions){
|
|
424
|
if (td.isImageGallery()){
|
|
425
|
for (DescriptionElementBase deb : td.getElements()){
|
|
426
|
if (deb.isInstanceOf(TextData.class)){
|
|
427
|
TextData textData = CdmBase.deproxy(deb, TextData.class);
|
|
428
|
for (Media media :textData.getMedia()){
|
|
429
|
for (MediaRepresentation rep : media.getRepresentations()){
|
|
430
|
for (MediaRepresentationPart part : rep.getParts()){
|
|
431
|
URI uri = part.getUri();
|
|
432
|
if (uri != null){
|
|
433
|
String uriStr = uri.toString();
|
|
434
|
result.add(uriStr);
|
|
435
|
}
|
|
436
|
}
|
|
437
|
}
|
|
438
|
}
|
|
439
|
|
|
440
|
}
|
|
441
|
}
|
|
442
|
}
|
|
443
|
}
|
|
444
|
return result;
|
|
445
|
}
|
|
446
|
|
|
447
|
private Taxon getAcceptedTaxon(CdmApplicationController app, String taxonNameStr) {
|
|
448
|
|
|
449
|
MatchingTaxonConfigurator config = new MatchingTaxonConfigurator();
|
|
450
|
taxonNameStr = adaptName(taxonNameStr);
|
|
451
|
config.setTaxonNameTitle(taxonNameStr);
|
|
452
|
config.setIncludeSynonyms(false);
|
|
453
|
List<TaxonBase> list = app.getTaxonService().findTaxaByName(config);
|
|
454
|
if (list.isEmpty()){
|
|
455
|
// logger.warn("Taxon not found for media: " + taxonNameStr);
|
|
456
|
taxonNameStr = taxonNameStr.replaceFirst(" ", " " + UTF8.HYBRID.toString());
|
|
457
|
config.setTaxonNameTitle(taxonNameStr);
|
|
458
|
list = app.getTaxonService().findTaxaByName(config);
|
|
459
|
if (list.isEmpty()){
|
|
460
|
return null;
|
|
461
|
}else if (list.size() > 1){
|
|
462
|
logger.warn("After searching for hybrids more than 1 taxon was foung: " + taxonNameStr);
|
|
463
|
}
|
|
464
|
}
|
|
465
|
if (list.size()>1){
|
|
466
|
Iterator<TaxonBase> it = list.iterator();
|
|
467
|
while (it.hasNext()){
|
|
468
|
Taxon next = (Taxon)it.next();
|
|
469
|
if (next.getTaxonNodes().isEmpty() && !next.getTaxaForMisappliedName(true).isEmpty()){
|
|
470
|
it.remove();
|
|
471
|
}
|
|
472
|
}
|
|
473
|
if (list.size()>1){
|
|
474
|
logger.warn("More than 1 taxon found for media: " + taxonNameStr + " . Will now try to use only taxon with taxon node.");
|
|
475
|
it = list.iterator();
|
|
476
|
while (it.hasNext()){
|
|
477
|
Taxon next = (Taxon)it.next();
|
|
478
|
if (next.getTaxonNodes().isEmpty()){
|
|
479
|
it.remove();
|
|
480
|
}
|
|
481
|
}
|
|
482
|
if (list.size()>1){
|
|
483
|
logger.warn("Still more than 1 taxon found for media: " + taxonNameStr);
|
|
484
|
}else if (list.size() < 1){
|
|
485
|
logger.warn("After removing nodeless taxa no taxon was left: " + taxonNameStr);
|
|
486
|
return null;
|
|
487
|
}
|
|
488
|
}else if (list.size() < 1){
|
|
489
|
logger.warn("After removing misapplications no taxon was left: " + taxonNameStr);
|
|
490
|
return null;
|
|
491
|
}
|
|
492
|
}
|
|
493
|
TaxonBase<?> taxonBase = list.get(0);
|
|
494
|
Taxon result;
|
|
495
|
if (taxonBase.isInstanceOf(Synonym.class)){
|
|
496
|
result = CdmBase.deproxy(taxonBase, Synonym.class).getAcceptedTaxon();
|
|
497
|
}else{
|
|
498
|
result = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
499
|
}
|
|
500
|
return result;
|
|
501
|
}
|
|
502
|
|
|
503
|
/**
|
|
504
|
* @param taxonNameStr
|
|
505
|
* @return
|
|
506
|
*/
|
|
507
|
private String adaptName(String taxonNameStr) {
|
|
508
|
// if (taxonNameStr.equals("Hypericum cerastoides")){
|
|
509
|
// taxonNameStr = "Hypericum cerastioides";
|
|
510
|
// }
|
|
511
|
return taxonNameStr;
|
|
512
|
}
|
|
513
|
|
|
514
|
private void test(){
|
|
515
|
File f = new File(path);
|
|
516
|
String[] list = f.list();
|
|
517
|
List<String> fullFileNames = new ArrayList<>();
|
|
518
|
for (String fileName : list){
|
|
519
|
fullFileNames.add(path + fileName);
|
|
520
|
if (! fileName.matches("([A-Z][a-z]+_[a-z\\-]{3,}(?:_s_[a-z\\-]{3,})?)_[A-F]\\d{1,2}\\.(jpg|JPG)")){
|
|
521
|
System.out.println(fileName);
|
|
522
|
}
|
|
523
|
}
|
|
524
|
}
|
|
525
|
|
|
526
|
private void updateMetadata(ICdmDataSource cdmDestination){
|
|
527
|
CdmApplicationController app = CdmIoApplicationController.NewInstance(cdmDestination, DbSchemaValidation.VALIDATE);
|
|
528
|
TransactionStatus tx = app.startTransaction();
|
|
529
|
|
|
530
|
deduplicationHelper = (ImportDeduplicationHelper<SimpleExcelTaxonImportState<?>>)ImportDeduplicationHelper.NewInstance(app);
|
|
531
|
|
|
532
|
List<Media> list = app.getMediaService().list(Media.class, null, null, null, null);
|
|
533
|
for (Media media : list){
|
|
534
|
String fileName = getUrlStringForMedia(media);
|
|
535
|
if (fileName.startsWith(urlPath)){
|
|
536
|
fileName = fileName.replace(urlPath, "");
|
|
537
|
if (fileName.equals("Acinos_exiguus_C1.jpg")){ //for debugging only
|
|
538
|
// System.out.println(fileName);
|
|
539
|
makeMetaData(media, fileName, true);
|
|
540
|
makeTitle(media, fileName, true);
|
|
541
|
}
|
|
542
|
}else{
|
|
543
|
logger.warn("Filename does not start with standard url path: " + fileName);
|
|
544
|
}
|
|
545
|
}
|
|
546
|
|
|
547
|
if (testOnly){
|
|
548
|
tx.setRollbackOnly();
|
|
549
|
}
|
|
550
|
app.commitTransaction(tx);
|
|
551
|
|
|
552
|
}
|
|
553
|
|
|
554
|
/**
|
|
555
|
* @param media
|
|
556
|
* @return
|
|
557
|
*/
|
|
558
|
private String getUrlStringForMedia(Media media) {
|
|
559
|
String result = null;
|
|
560
|
for (MediaRepresentation rep : media.getRepresentations()){
|
|
561
|
for (MediaRepresentationPart part : rep.getParts()){
|
|
562
|
URI uri = part.getUri();
|
|
563
|
if (uri != null){
|
|
564
|
if (result != null){
|
|
565
|
logger.warn("More than 1 uri exists for media "+ media.getId());
|
|
566
|
}else{
|
|
567
|
result = uri.toString();
|
|
568
|
}
|
|
569
|
}
|
|
570
|
}
|
|
571
|
}
|
|
572
|
return result;
|
|
573
|
}
|
|
574
|
|
|
575
|
/**
|
|
576
|
* @param args
|
|
577
|
*/
|
|
578
|
public static void main(String[] args) {
|
|
579
|
CyprusImagesActivator me = new CyprusImagesActivator();
|
|
580
|
if (update_notCreate){
|
|
581
|
me.updateMetadata(cdmDestination);
|
|
582
|
}else{
|
|
583
|
me.doImport(cdmDestination);
|
|
584
|
}
|
|
585
|
// me.test();
|
|
586
|
System.exit(0);
|
|
587
|
}
|
|
588
|
|
|
589
|
}
|