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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.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.URI;
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import eu.etaxonomy.cdm.common.UTF8;
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import eu.etaxonomy.cdm.common.media.CdmImageInfo;
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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.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.common.TimePeriod;
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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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* Creates CDM Media from images stored in the given path.
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*
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* Note: Currently adapted to also change from Scaler IIF API to default Scaler API.
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* Note2: updateMetadata() still needs to be adapted to support 3 MediaRepresentations
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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.local_cyprus();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_cyprus();
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// static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_cyprus();
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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 oldUrlPath = "https://pictures.bgbm.org/digilib/Scaler/IIIF/Cyprus!";
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private static final String newUrlPath = "https://pictures.bgbm.org/digilib/Scaler?fn=Cyprus/";
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private static final String oldPostfix = "/full/full/0/default.jpg";
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private static final String newPostfix = "&mo=file";
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private static final String mediumPostfix ="&mo=fit&dw=400&dh=400&uvfix=1";
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private static final String smallPostfix ="&mo=fit&dw=200&dh=200&uvfix=1";
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private ImportDeduplicationHelper 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.NewInstance(app, null);
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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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String start = "O"; //O
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String end = "Q"; //Q
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String startLetter = "";
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for (String fileName : fileList){
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if(fileName.compareToIgnoreCase(start) < 0 || fileName.compareToIgnoreCase(end) >= 0){
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continue;
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}
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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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if (!fileName.substring(0,3).equals(startLetter)){
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startLetter = fileName.substring(0,3);
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System.out.println(startLetter);
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}
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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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try {
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handleTaxon(app, taxon, fileName);
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} catch (Exception e) {
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logger.error("Unhandled exception ("+e.getMessage()+") when reading file " + fileName +". File not imported: ");
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e.printStackTrace();
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}
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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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}else{
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System.out.println("Not clear yet: " + 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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private void handleTaxon(CdmApplicationController app, Taxon taxon, String fileName) {
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Map<String, Media> existingUrls = getAllExistingUrls(taxon);
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String pathToOldImage = oldUrlPath + fileName + oldPostfix;
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String pathToFullImage = newUrlPath + fileName + newPostfix;
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String pathToMediumImage = newUrlPath + fileName + mediumPostfix;
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String pathToSmallImage = newUrlPath + fileName + smallPostfix;
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if (containsAll(existingUrls, pathToFullImage, pathToMediumImage, pathToSmallImage)){
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return;
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}else{
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Media media;
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if (containsAny(existingUrls, pathToOldImage, pathToMediumImage, pathToSmallImage)){
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media = getExistingMedia(existingUrls, pathToOldImage, pathToMediumImage, pathToSmallImage);
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if (media == null){
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return;
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}else if (media.getAllTitles().isEmpty()){
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media.setTitleCache(null, false);
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media.putTitle(Language.LATIN(), fileName);
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}
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}else{
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media = Media.NewInstance();
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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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}
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fillMediaWithAllRepresentations(media, pathToFullImage, pathToMediumImage, pathToSmallImage, pathToOldImage);
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}
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}
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private Media getExistingMedia(Map<String, Media> existingUrls, String pathToFullImage, String pathToMediumImage,
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String pathToSmallImage) {
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Set<Media> result = new HashSet<>();
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for(String existingUrl : existingUrls.keySet()){
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if (existingUrl.equals(pathToFullImage) || existingUrl.equals(pathToMediumImage) ||
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existingUrl.equals(pathToSmallImage)){
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result.add(existingUrls.get(existingUrl));
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}
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}
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if (result.isEmpty()){
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logger.warn("Media for existing URL not found. This should not happen.");
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return null;
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}else if (result.size() > 1){
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logger.warn("Existing URLs have more than 1 Media. This should not happen.");
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return null;
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}else{
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return result.iterator().next();
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}
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}
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/**
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* <code>true</code> if all 3 paths exist in the URL set
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*/
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private boolean containsAll(Map<String, Media> existingUrlMap, String pathToFullImage, String pathToMediumImage,
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String pathToSmallImage) {
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Set<String> existingUrls = existingUrlMap.keySet();
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return existingUrls.contains(pathToFullImage) && existingUrls.contains(pathToMediumImage)
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&& existingUrls.contains(pathToSmallImage);
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}
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/**
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* <code>true</code> if any of the 3 paths exists in the URL set
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*/
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private boolean containsAny(Map<String, Media> existingUrlMap, String pathToFullImage, String pathToMediumImage,
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String pathToSmallImage) {
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Set<String> existingUrls = existingUrlMap.keySet();
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return existingUrls.contains(pathToFullImage) || existingUrls.contains(pathToMediumImage)
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|| existingUrls.contains(pathToSmallImage);
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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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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 (ImageMetadataItem metadataItem : items){
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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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265
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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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283
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284
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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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288
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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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294
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if (artistStr != null){
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295
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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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301
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}
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302
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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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307
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308
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//copyright
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309
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if (copyright != null){
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310
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AgentBase<?> agent;
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311
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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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318
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right = deduplicationHelper.getExistingCopyright(right);
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319
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}
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320
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321
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//created
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322
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if (created != null){
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323
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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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328
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}
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329
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}
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330
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331
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boolean force = !updateOnly || forceUpdate;
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332
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//add to media
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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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336
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if (right != null && (force || media.getRights().isEmpty())){
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337
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media.removeRights(right);
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338
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media.addRights(right);
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339
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}
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340
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if (createdDate != null && (force || media.getMediaCreated() == null)){
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341
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media.setMediaCreated(TimePeriod.NewInstance(createdDate));
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342
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}
|
|
343
|
if (locality != null && (force || media.getDescription(Language.ENGLISH()) == null)){
|
|
344
|
media.putDescription(Language.ENGLISH(), locality);
|
|
345
|
}
|
|
346
|
}
|
|
347
|
|
|
348
|
private Person makePerson(String artist, String fileName) {
|
|
349
|
artist = artist.trim();
|
|
350
|
String regEx = "((?:[A-Z]\\. ?)+)([A-Z][a-z\\-\u00E4\u00F6\u00FC]+)";
|
|
351
|
Matcher matcher = Pattern.compile(regEx).matcher(artist);
|
|
352
|
Person person = Person.NewInstance();
|
|
353
|
if (matcher.matches()){
|
|
354
|
person.setGivenName(matcher.group(1).trim());
|
|
355
|
person.setFamilyName(matcher.group(2).trim());
|
|
356
|
}else{
|
|
357
|
person.setTitleCache(artist, true);
|
|
358
|
logger.warn("Person could not be parsed: " + artist + " for file " + fileName);
|
|
359
|
}
|
|
360
|
|
|
361
|
person = deduplicationHelper.getExistingAuthor(person);
|
|
362
|
return person;
|
|
363
|
}
|
|
364
|
|
|
365
|
private String removeQuots(String text) {
|
|
366
|
if (text.startsWith("'") && text.endsWith("'")){
|
|
367
|
return text.substring(1, text.length() -1);
|
|
368
|
}else{
|
|
369
|
return text;
|
|
370
|
}
|
|
371
|
}
|
|
372
|
|
|
373
|
private void makeTextData(String fileStr, Media media, Taxon taxon) {
|
|
374
|
TaxonDescription imageGallery = taxon.getImageGallery(true);
|
|
375
|
TextData textData = null;
|
|
376
|
if (!imageGallery.getElements().isEmpty()){
|
|
377
|
DescriptionElementBase el = imageGallery.getElements().iterator().next();
|
|
378
|
if (el.isInstanceOf(TextData.class)){
|
|
379
|
textData = CdmBase.deproxy(el, TextData.class);
|
|
380
|
}else{
|
|
381
|
logger.warn("Image gallery had non-textdata description element: " + fileStr);
|
|
382
|
}
|
|
383
|
}
|
|
384
|
if (textData == null){
|
|
385
|
textData = TextData.NewInstance();
|
|
386
|
textData.setFeature(Feature.IMAGE());
|
|
387
|
}
|
|
388
|
imageGallery.addElement(textData);
|
|
389
|
textData.addMedia(media);
|
|
390
|
}
|
|
391
|
|
|
392
|
private void fillMediaWithAllRepresentations(Media media, String fullPath, String mediumPath, String smallPath, String oldFullPath){
|
|
393
|
Set<MediaRepresentation> existingRepresentations = new HashSet<>(media.getRepresentations());
|
|
394
|
makeMediaRepresentation(oldFullPath, media, existingRepresentations, fullPath);
|
|
395
|
makeMediaRepresentation(mediumPath, media, existingRepresentations, null);
|
|
396
|
makeMediaRepresentation(smallPath, media, existingRepresentations, null);
|
|
397
|
if(!existingRepresentations.isEmpty()){
|
|
398
|
logger.warn("Media contains existing representations which are not contained in the 3 paths: " + media.getTitleCache());
|
|
399
|
}
|
|
400
|
}
|
|
401
|
|
|
402
|
private void makeMediaRepresentation(String uriString, Media media,
|
|
403
|
Set<MediaRepresentation> existingRepresentations, String replaceUri) {
|
|
404
|
MediaRepresentation existingMediaRep = getExistingMediaRepresentation(uriString, existingRepresentations);
|
|
405
|
boolean readMediaData = true;
|
|
406
|
MediaRepresentation newMediaRep = makeMediaRepresentation(replaceUri != null? replaceUri : uriString, readMediaData);
|
|
407
|
if (existingMediaRep == null){
|
|
408
|
media.addRepresentation(newMediaRep);
|
|
409
|
}else{
|
|
410
|
existingRepresentations.remove(existingMediaRep);
|
|
411
|
mergeToExistingRepresentation(existingMediaRep, newMediaRep);
|
|
412
|
}
|
|
413
|
}
|
|
414
|
|
|
415
|
private void mergeToExistingRepresentation(MediaRepresentation existingMediaRep, MediaRepresentation newMediaRep) {
|
|
416
|
existingMediaRep.setMimeType(newMediaRep.getMimeType());
|
|
417
|
existingMediaRep.setSuffix(newMediaRep.getSuffix());
|
|
418
|
if(!existingMediaRep.getParts().isEmpty() && !newMediaRep.getParts().isEmpty()){
|
|
419
|
MediaRepresentationPart existingPart = existingMediaRep.getParts().iterator().next();
|
|
420
|
ImageFile newPart = (ImageFile)newMediaRep.getParts().iterator().next();
|
|
421
|
if(existingPart.isInstanceOf(ImageFile.class)){
|
|
422
|
ImageFile existingImage = CdmBase.deproxy(existingPart, ImageFile.class);
|
|
423
|
existingImage.setHeight(newPart.getHeight());
|
|
424
|
existingImage.setWidth(newPart.getWidth());
|
|
425
|
}else{
|
|
426
|
logger.warn("MediaRepresentationPart was not of type ImageFile. Height and width not merged: " + existingPart.getUri());
|
|
427
|
}
|
|
428
|
existingPart.setSize(newPart.getSize());
|
|
429
|
existingPart.setUri(newPart.getUri());
|
|
430
|
}
|
|
431
|
}
|
|
432
|
|
|
433
|
private MediaRepresentation getExistingMediaRepresentation(String uriString,
|
|
434
|
Set<MediaRepresentation> existingRepresentations) {
|
|
435
|
for (MediaRepresentation rep : existingRepresentations){
|
|
436
|
for (MediaRepresentationPart part : rep.getParts()){
|
|
437
|
if (part.getUri() != null && part.getUri().toString().equals(uriString)){
|
|
438
|
return rep;
|
|
439
|
}
|
|
440
|
}
|
|
441
|
}
|
|
442
|
return null;
|
|
443
|
}
|
|
444
|
|
|
445
|
/**
|
|
446
|
* Creates
|
|
447
|
* @see #READ_MEDIA_DATA
|
|
448
|
* @return
|
|
449
|
* @throws MalformedURLException
|
|
450
|
*/
|
|
451
|
protected Media getImageMedia(String uriString, String uriStrThumb, boolean readMediaData) throws MalformedURLException {
|
|
452
|
if( uriString == null){
|
|
453
|
return null;
|
|
454
|
} else {
|
|
455
|
uriString = uriString.replace(" ", "%20"); //replace whitespace
|
|
456
|
try {
|
|
457
|
MediaRepresentation representation = makeMediaRepresentation(uriString, readMediaData);
|
|
458
|
Media media = Media.NewInstance();
|
|
459
|
media.addRepresentation(representation);
|
|
460
|
|
|
461
|
if (uriStrThumb != null){
|
|
462
|
CdmImageInfo imageInfoThumb = null;
|
|
463
|
uriStrThumb = uriStrThumb.replace(" ", "%20"); //replace whitespace
|
|
464
|
URI uriThumb = new URI(uriStrThumb);
|
|
465
|
try {
|
|
466
|
if (readMediaData){
|
|
467
|
logger.info("Read media data from: " + uriThumb);
|
|
468
|
imageInfoThumb = CdmImageInfo.NewInstance(uriThumb, 0);
|
|
469
|
}
|
|
470
|
} catch (Exception e) {
|
|
471
|
String message = "An error occurred when trying to read image meta data for " + uriThumb.toString() + ": " + e.getMessage();
|
|
472
|
logger.warn(message);
|
|
473
|
}
|
|
474
|
|
|
475
|
ImageFile imageFileFhumb = ImageFile.NewInstance(uriThumb, null, imageInfoThumb);
|
|
476
|
MediaRepresentation reprThumb = MediaRepresentation.NewInstance();
|
|
477
|
if(imageInfoThumb != null){
|
|
478
|
reprThumb.setMimeType(imageInfoThumb.getMimeType());
|
|
479
|
reprThumb.setSuffix(imageInfoThumb.getSuffix());
|
|
480
|
}
|
|
481
|
reprThumb.addRepresentationPart(imageFileFhumb);
|
|
482
|
media.addRepresentation(reprThumb);
|
|
483
|
}
|
|
484
|
|
|
485
|
return media;
|
|
486
|
} catch (URISyntaxException e1) {
|
|
487
|
String message = "An URISyntaxException occurred when trying to create uri from multimedia objcet string: " + uriString;
|
|
488
|
logger.warn(message);
|
|
489
|
return null;
|
|
490
|
}
|
|
491
|
}
|
|
492
|
}
|
|
493
|
|
|
494
|
private MediaRepresentation makeMediaRepresentation(String uriString, boolean readMediaData) {
|
|
495
|
|
|
496
|
uriString = uriString.replace(" ", "%20"); //replace whitespace
|
|
497
|
CdmImageInfo imageInfo = null;
|
|
498
|
URI uri;
|
|
499
|
try {
|
|
500
|
uri = new URI(uriString);
|
|
501
|
} catch (URISyntaxException e1) {
|
|
502
|
logger.error("Malformed URI. Could not create media representation: " + uriString);
|
|
503
|
return null;
|
|
504
|
}
|
|
505
|
try {
|
|
506
|
if (readMediaData){
|
|
507
|
logger.info("Read media data from: " + uri);
|
|
508
|
imageInfo = CdmImageInfo.NewInstance(uri, 0);
|
|
509
|
}
|
|
510
|
} catch (Exception e) {
|
|
511
|
try {
|
|
512
|
//try again
|
|
513
|
imageInfo = CdmImageInfo.NewInstance(uri, 0);
|
|
514
|
} catch (Exception e1) {
|
|
515
|
String message = "An error occurred when trying to read image meta data for " + uri.toString() + ": " + e1.getMessage();
|
|
516
|
e1.printStackTrace();
|
|
517
|
logger.warn(message);
|
|
518
|
}
|
|
519
|
}
|
|
520
|
ImageFile imageFile = ImageFile.NewInstance(uri, null, imageInfo);
|
|
521
|
|
|
522
|
MediaRepresentation representation = MediaRepresentation.NewInstance();
|
|
523
|
|
|
524
|
if(imageInfo != null){
|
|
525
|
representation.setMimeType(imageInfo.getMimeType());
|
|
526
|
representation.setSuffix(imageInfo.getSuffix());
|
|
527
|
}
|
|
528
|
representation.addRepresentationPart(imageFile);
|
|
529
|
return representation;
|
|
530
|
}
|
|
531
|
|
|
532
|
private Map<String, Media> getAllExistingUrls(Taxon taxon) {
|
|
533
|
Map<String, Media> result = new HashMap<>();
|
|
534
|
Set<TaxonDescription> descriptions = taxon.getDescriptions();
|
|
535
|
for (TaxonDescription td : descriptions){
|
|
536
|
if (td.isImageGallery()){
|
|
537
|
for (DescriptionElementBase deb : td.getElements()){
|
|
538
|
if (deb.isInstanceOf(TextData.class)){
|
|
539
|
TextData textData = CdmBase.deproxy(deb, TextData.class);
|
|
540
|
for (Media media :textData.getMedia()){
|
|
541
|
for (MediaRepresentation rep : media.getRepresentations()){
|
|
542
|
for (MediaRepresentationPart part : rep.getParts()){
|
|
543
|
URI uri = part.getUri();
|
|
544
|
if (uri != null){
|
|
545
|
String uriStr = uri.toString();
|
|
546
|
result.put(uriStr, media);
|
|
547
|
}
|
|
548
|
}
|
|
549
|
}
|
|
550
|
}
|
|
551
|
}
|
|
552
|
}
|
|
553
|
}
|
|
554
|
}
|
|
555
|
return result;
|
|
556
|
}
|
|
557
|
|
|
558
|
private Taxon getAcceptedTaxon(CdmApplicationController app, String taxonNameStr) {
|
|
559
|
|
|
560
|
MatchingTaxonConfigurator config = new MatchingTaxonConfigurator();
|
|
561
|
taxonNameStr = adaptName(taxonNameStr);
|
|
562
|
config.setTaxonNameTitle(taxonNameStr);
|
|
563
|
config.setIncludeSynonyms(false);
|
|
564
|
List<TaxonBase> list = app.getTaxonService().findTaxaByName(config);
|
|
565
|
if (list.isEmpty()){
|
|
566
|
// logger.warn("Taxon not found for media: " + taxonNameStr);
|
|
567
|
taxonNameStr = taxonNameStr.replaceFirst(" ", " " + UTF8.HYBRID.toString());
|
|
568
|
config.setTaxonNameTitle(taxonNameStr);
|
|
569
|
list = app.getTaxonService().findTaxaByName(config);
|
|
570
|
if (list.isEmpty()){
|
|
571
|
return null;
|
|
572
|
}else if (list.size() > 1){
|
|
573
|
logger.warn("After searching for hybrids more than 1 taxon was foung: " + taxonNameStr);
|
|
574
|
}
|
|
575
|
}
|
|
576
|
if (list.size()>1){
|
|
577
|
Iterator<TaxonBase> it = list.iterator();
|
|
578
|
while (it.hasNext()){
|
|
579
|
Taxon next = (Taxon)it.next();
|
|
580
|
if (next.getTaxonNodes().isEmpty() && !next.getTaxaForMisappliedName(true).isEmpty()){
|
|
581
|
it.remove();
|
|
582
|
}
|
|
583
|
}
|
|
584
|
if (list.size()>1){
|
|
585
|
logger.warn("More than 1 taxon found for media: " + taxonNameStr + " . Will now try to use only taxon with taxon node.");
|
|
586
|
it = list.iterator();
|
|
587
|
while (it.hasNext()){
|
|
588
|
Taxon next = (Taxon)it.next();
|
|
589
|
if (next.getTaxonNodes().isEmpty()){
|
|
590
|
it.remove();
|
|
591
|
}
|
|
592
|
}
|
|
593
|
if (list.size()>1){
|
|
594
|
logger.warn("Still more than 1 taxon found for media: " + taxonNameStr);
|
|
595
|
}else if (list.size() < 1){
|
|
596
|
logger.warn("After removing nodeless taxa no taxon was left: " + taxonNameStr);
|
|
597
|
return null;
|
|
598
|
}
|
|
599
|
}else if (list.size() < 1){
|
|
600
|
logger.warn("After removing misapplications no taxon was left: " + taxonNameStr);
|
|
601
|
return null;
|
|
602
|
}
|
|
603
|
}
|
|
604
|
TaxonBase<?> taxonBase = list.get(0);
|
|
605
|
Taxon result;
|
|
606
|
if (taxonBase.isInstanceOf(Synonym.class)){
|
|
607
|
result = CdmBase.deproxy(taxonBase, Synonym.class).getAcceptedTaxon();
|
|
608
|
}else{
|
|
609
|
result = CdmBase.deproxy(taxonBase, Taxon.class);
|
|
610
|
}
|
|
611
|
return result;
|
|
612
|
}
|
|
613
|
|
|
614
|
private String adaptName(String taxonNameStr) {
|
|
615
|
// if (taxonNameStr.equals("Hypericum cerastoides")){
|
|
616
|
// taxonNameStr = "Hypericum cerastioides";
|
|
617
|
// }
|
|
618
|
return taxonNameStr;
|
|
619
|
}
|
|
620
|
|
|
621
|
private void test(){
|
|
622
|
File f = new File(path);
|
|
623
|
String[] list = f.list();
|
|
624
|
List<String> fullFileNames = new ArrayList<>();
|
|
625
|
for (String fileName : list){
|
|
626
|
fullFileNames.add(path + fileName);
|
|
627
|
if (! fileName.matches("([A-Z][a-z]+_[a-z\\-]{3,}(?:_s_[a-z\\-]{3,})?)_[A-F]\\d{1,2}\\.(jpg|JPG)")){
|
|
628
|
System.out.println(fileName);
|
|
629
|
}
|
|
630
|
}
|
|
631
|
}
|
|
632
|
|
|
633
|
private void updateMetadata(ICdmDataSource cdmDestination){
|
|
634
|
CdmApplicationController app = CdmIoApplicationController.NewInstance(cdmDestination, DbSchemaValidation.VALIDATE);
|
|
635
|
TransactionStatus tx = app.startTransaction();
|
|
636
|
|
|
637
|
deduplicationHelper = ImportDeduplicationHelper.NewInstance(app, null);
|
|
638
|
|
|
639
|
List<Media> list = app.getMediaService().list(Media.class, null, null, null, null);
|
|
640
|
for (Media media : list){
|
|
641
|
String fileName = getUrlStringForMedia(media);
|
|
642
|
if (fileName.startsWith(newUrlPath)){
|
|
643
|
//TODO not yet adapted to new image server URLs
|
|
644
|
fileName = fileName.replace(newUrlPath, "");
|
|
645
|
if (fileName.equals("Acinos_exiguus_C1.jpg")){ //for debugging only
|
|
646
|
// System.out.println(fileName);
|
|
647
|
makeMetaData(media, fileName, true);
|
|
648
|
makeTitle(media, fileName, true);
|
|
649
|
}
|
|
650
|
}else{
|
|
651
|
logger.warn("Filename does not start with standard url path: " + fileName);
|
|
652
|
}
|
|
653
|
}
|
|
654
|
|
|
655
|
if (testOnly){
|
|
656
|
tx.setRollbackOnly();
|
|
657
|
}
|
|
658
|
app.commitTransaction(tx);
|
|
659
|
}
|
|
660
|
|
|
661
|
private String getUrlStringForMedia(Media media) {
|
|
662
|
String result = null;
|
|
663
|
for (MediaRepresentation rep : media.getRepresentations()){
|
|
664
|
for (MediaRepresentationPart part : rep.getParts()){
|
|
665
|
URI uri = part.getUri();
|
|
666
|
if (uri != null){
|
|
667
|
if (result != null){
|
|
668
|
//TODO this still needs to be adapted to the 3 representations of media
|
|
669
|
logger.warn("More than 1 uri exists for media "+ media.getId());
|
|
670
|
}else{
|
|
671
|
result = uri.toString();
|
|
672
|
}
|
|
673
|
}
|
|
674
|
}
|
|
675
|
}
|
|
676
|
return result;
|
|
677
|
}
|
|
678
|
|
|
679
|
public static void main(String[] args) {
|
|
680
|
CyprusImagesActivator me = new CyprusImagesActivator();
|
|
681
|
if (update_notCreate){
|
|
682
|
me.updateMetadata(cdmDestination);
|
|
683
|
}else{
|
|
684
|
me.doImport(cdmDestination);
|
|
685
|
}
|
|
686
|
// me.test();
|
|
687
|
System.exit(0);
|
|
688
|
}
|
|
689
|
}
|