EDIT

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.app.wp6.cichorieae;

import java.io.File;

import java.net.MalformedURLException;

import java.net.URISyntaxException;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.regex.Matcher;

import java.util.regex.Pattern;

import org.apache.log4j.Logger;

import org.joda.time.DateTime;

import org.joda.time.format.DateTimeFormat;

import org.joda.time.format.DateTimeFormatter;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.api.application.CdmApplicationController;

import eu.etaxonomy.cdm.api.service.config.MatchingTaxonConfigurator;

import eu.etaxonomy.cdm.api.service.media.MediaInfoFactory;

import eu.etaxonomy.cdm.api.service.media.MediaInfoFileReader;

import eu.etaxonomy.cdm.app.common.CdmDestinations;

import eu.etaxonomy.cdm.common.URI;

import eu.etaxonomy.cdm.common.UTF8;

import eu.etaxonomy.cdm.common.media.CdmImageInfo;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.io.api.application.CdmIoApplicationController;

import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper;

import eu.etaxonomy.cdm.model.agent.AgentBase;

import eu.etaxonomy.cdm.model.agent.Institution;

import eu.etaxonomy.cdm.model.agent.Person;

import eu.etaxonomy.cdm.model.common.CdmBase;

import eu.etaxonomy.cdm.model.common.Language;

import eu.etaxonomy.cdm.model.common.TimePeriod;

import eu.etaxonomy.cdm.model.description.DescriptionElementBase;

import eu.etaxonomy.cdm.model.description.Feature;

import eu.etaxonomy.cdm.model.description.TaxonDescription;

import eu.etaxonomy.cdm.model.description.TextData;

import eu.etaxonomy.cdm.model.media.ImageFile;

import eu.etaxonomy.cdm.model.media.Media;

import eu.etaxonomy.cdm.model.media.MediaRepresentation;

import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;

import eu.etaxonomy.cdm.model.media.Rights;

import eu.etaxonomy.cdm.model.media.RightsType;

import eu.etaxonomy.cdm.model.taxon.Synonym;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonBase;

/**

 * TODO copied from cyprus

 *

 * Creates CDM Media from images stored in the given path.

 *

 * Note: Currently adapted to also change from Scaler IIF API to default Scaler API.

 * Note2: updateMetadata() still needs to be adapted to support 3 MediaRepresentations

 *

 * @author a.mueller

 * @since 05.2017

 */

public class CichorieaImageUpdateActivator {

	private static final Logger logger = Logger.getLogger(CichorieaImageUpdateActivator.class);

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_cichorieae();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_cyprus();

	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_cichorieae();

	static boolean testOnly = false;

	static boolean update_notCreate = true;

	//if true, data will always be updated, if false, only missing data will be updated

	static boolean forceUpdate = true;

	static boolean sizeOnly = true;

    private static final String path = "//media/digitalimages/EditWP6/Cichorieae/photos/";

    private static final String oldUrlPath = "https://pictures.bgbm.org/digilib/Scaler/IIIF/Cichorieae!";

    private static final String newUrlPath = "https://pictures.bgbm.org/digilib/Scaler?fn=Cichorieae/";

    private static final String oldPostfix = "/full/full/0/default.jpg";

    private static final String newPostfix = "&mo=file";

    private static final String mediumPostfix ="&mo=fit&dw=400&dh=400&uvfix=1";

    private static final String smallPostfix ="&mo=fit&dw=200&dh=200&uvfix=1";

    private ImportDeduplicationHelper deduplicationHelper;

    private void doImport(ICdmDataSource cdmDestination){

		CdmApplicationController app = CdmIoApplicationController.NewInstance(cdmDestination, DbSchemaValidation.VALIDATE);

		TransactionStatus tx = app.startTransaction();

		deduplicationHelper = ImportDeduplicationHelper.NewInstance(app, null);

        File file = new File(path);

        String[] fileList = file.list();

        Set<String> notFound = new HashSet<>();

        String regEx = "([A-Z][a-z]+_[a-z\\-]{3,}(?:_s_[a-z\\-]{3,})?)_[A-F]\\d{1,2}\\.(?:jpg|JPG)";

        Pattern pattern = Pattern.compile(regEx);

        String start = "O";  //O

        String end = "Q";      //Q

        String startLetter = "";

        for (String fileName : fileList){

            if(fileName.compareToIgnoreCase(start) < 0 || fileName.compareToIgnoreCase(end) >= 0){

                continue;

            }

            Matcher matcher = pattern.matcher(fileName);

            if (matcher.matches() ){

//                System.out.println(fileName);

                if (!fileName.substring(0,3).equals(startLetter)){

                    startLetter = fileName.substring(0,3);

                    System.out.println(startLetter);

                }

                String taxonName = matcher.group(1);

                taxonName = taxonName.replace("_s_", " subsp. ").replace("_", " ");

                Taxon taxon = getAcceptedTaxon(app, taxonName);

                if (taxon == null){

                    if (!notFound.contains(taxonName)){

                        notFound.add(taxonName);

                        logger.warn("Taxon not found: " + taxonName);

                    }

                }else{

                    try {

                        handleTaxon(app, taxon, fileName);

                    } catch (Exception e) {

                        logger.error("Unhandled exception ("+e.getMessage()+") when reading file " + fileName +". File not imported: ");

                        e.printStackTrace();

                    }

                }

            }else{

                if (!fileName.matches("(?:\\.erez|Thumbs\\.db.*|zypern_.*|__Keywords_template\\.txt)")){

                    logger.warn("Incorrect filename:" + fileName);

                }else{

                    System.out.println("Not clear yet: " + fileName);

                }

            }

        }

//		app.getTaxonService().saveOrUpdate(taxaToSave);

		if (testOnly){

		    tx.setRollbackOnly();

		}

		app.commitTransaction(tx);

	}

    private void handleTaxon(CdmApplicationController app, Taxon taxon, String fileName) {

        Map<String, Media> existingUrls = getAllExistingUrls(taxon);

        String pathToOldImage = oldUrlPath + fileName + oldPostfix;

        String pathToFullImage = newUrlPath + fileName + newPostfix;

        String pathToMediumImage = newUrlPath + fileName + mediumPostfix;

        String pathToSmallImage = newUrlPath + fileName + smallPostfix;

        if (containsAll(existingUrls, pathToFullImage, pathToMediumImage, pathToSmallImage)){

            return;

        }else{

            Media media;

            if (containsAny(existingUrls, pathToOldImage, pathToMediumImage, pathToSmallImage)){

                media = getExistingMedia(existingUrls, pathToOldImage, pathToMediumImage, pathToSmallImage);

                if (media == null){

                    return;

                }else if (media.getAllTitles().isEmpty()){

                    media.setTitleCache(null, false);

                    media.putTitle(Language.LATIN(), fileName);

                }

            }else{

                media = Media.NewInstance();

                makeMetaData(media, fileName, null, false, sizeOnly);

                makeTitle(media, fileName, false);

                if (!testOnly){

                    makeTextData(fileName, media, taxon);

                }

            }

            fillMediaWithAllRepresentations(media, pathToFullImage, pathToMediumImage, pathToSmallImage, pathToOldImage);

        }

    }

    private Media getExistingMedia(Map<String, Media> existingUrls, String pathToFullImage, String pathToMediumImage,

            String pathToSmallImage) {

        Set<Media> result = new HashSet<>();

        for(String existingUrl : existingUrls.keySet()){

            if (existingUrl.equals(pathToFullImage) || existingUrl.equals(pathToMediumImage) ||

                    existingUrl.equals(pathToSmallImage)){

                result.add(existingUrls.get(existingUrl));

            }

        }

        if (result.isEmpty()){

            logger.warn("Media for existing URL not found. This should not happen.");

            return null;

        }else if (result.size() > 1){

            logger.warn("Existing URLs have more than 1 Media. This should not happen.");

            return null;

        }else{

            return result.iterator().next();

        }

    }

    /**

     * <code>true</code> if all 3 paths exist in the URL set

     */

    private boolean containsAll(Map<String, Media> existingUrlMap, String pathToFullImage, String pathToMediumImage,

            String pathToSmallImage) {

        Set<String> existingUrls = existingUrlMap.keySet();

        return existingUrls.contains(pathToFullImage) && existingUrls.contains(pathToMediumImage)

                && existingUrls.contains(pathToSmallImage);

    }

    /**

     * <code>true</code> if any of the 3 paths exists in the URL set

     */

    private boolean containsAny(Map<String, Media> existingUrlMap, String pathToFullImage, String pathToMediumImage,

            String pathToSmallImage) {

        Set<String> existingUrls = existingUrlMap.keySet();

        return existingUrls.contains(pathToFullImage) || existingUrls.contains(pathToMediumImage)

                || existingUrls.contains(pathToSmallImage);

    }

    private void makeTitle(Media media, String fileName, boolean updateOnly) {

        String title = fileName.replace("_s_"," subsp. ")

                .replace("_"," ").replace(".jpg","").replace(".JPG","");

        if ( (!updateOnly) || media.getAllTitles().isEmpty()){

            media.putTitle(Language.LATIN(), title);

        }

    }

    private void makeMetaData(Media media, String fileName, ImageFile part, boolean updateOnly, boolean sizeOnly) {

        URI uri = part.getUri();

        Map<String, String> keywords = new HashMap<>();

        String copyright = null;

        String artistStr = null;

        String created = null;

        try{

            MediaInfoFactory mediaFactory = new MediaInfoFactory();

            CdmImageInfo imageInfo;

            try {

                imageInfo = mediaFactory.cdmImageInfo(uri, !sizeOnly);

            } catch (Exception e) {

                URI lowerCaseUri = URI.create(uri.toString().replace(".JPG", ".jpg"));

                try {

                    imageInfo = mediaFactory.cdmImageInfo(lowerCaseUri, !sizeOnly);

                    part.setUri(lowerCaseUri);  //if no error arises we expect this to be the better URI

                } catch (Exception e1) {

                    logger.error("Metadata not readable: " + uri.toString());

                    return;

                }

            }

            //size

            makeSize(part, imageInfo);

            if (sizeOnly){

                return;

            }

            //additional metadata

            for (String metaDataKey : imageInfo.getMetaData().keySet()){

                String value = imageInfo.getMetaData().get(metaDataKey);

//                System.out.println(metaDataKey +  ":    " + value);

                value = removeQuots(value); //not sure if still necessary

                if ("Copyright Notice".equalsIgnoreCase(metaDataKey)){

                    copyright = value;

                }else if ("artist".equals(metaDataKey)){

                    artistStr = value;

                }else if ("DateTimeOriginal".equalsIgnoreCase(metaDataKey)){  //TODO seems not to exist anymore

                    created = value;

                }else{

                    keywords.put(metaDataKey.trim().toLowerCase(), value);

                }

            }

        } catch (Exception e1) {

            logger.warn("       Problem (" + e1.getMessage() + ") when reading metadata from uri: " + part);

            e1.printStackTrace();

            return;

        }

        AgentBase<?> artistAgent = null;

        Rights right = null;

        DateTime createdDate = null;

        String locality = null;

        //artist

        if (keywords.get("photographer") != null){

            String artist = keywords.get("photographer");

            artistAgent = getOrCreatePerson(artist, fileName);

        }

        if (artistStr != null){

            if (keywords.get("photographer") == null){

                artistAgent = getOrCreatePerson(artistStr, fileName);

            }else if (!keywords.get("photographer").toLowerCase().replace(" ", "")

                    .contains(artistStr.toLowerCase().replace(" ", ""))){

                logger.warn("Artist '" + artistStr + "' could not be handled for " + fileName);

            }

        }

        //locality

        if (keywords.get("locality") != null){

            locality = keywords.get("locality");

        }

        //copyright

        if (copyright != null){

            AgentBase<?> agent;

            if (copyright.equals("Botanic Garden and Botanical Museum Berlin-Dahlem (BGBM)")){

                agent = Institution.NewNamedInstance(copyright);

            }else{

                agent = getOrCreatePerson(copyright, fileName);

            }

            right = Rights.NewInstance(null, null, RightsType.COPYRIGHT());

            right.setAgent(agent);

            right = deduplicationHelper.getExistingCopyright(right);

        }

        //created

        if (created != null){

            DateTimeFormatter f = DateTimeFormat.forPattern("yyyy:MM:dd HH:mm:ss");

            try {

                createdDate = f/*.withZone(DateTimeZone.forID("Europe/Athens"))*/.parseDateTime(created);

            } catch (Exception e) {

                logger.warn("Exception (" + e.getMessage() + ") when parsing create date " + created + " for file " + fileName);

            }

        }

        boolean force = !updateOnly || forceUpdate;

        //add to media

        if (artistAgent != null && (force || media.getArtist() == null)){

            media.setArtist(artistAgent);

        }

        if (right != null && (force || media.getRights().isEmpty())){

            media.removeRights(right);

            media.addRights(right);

        }

        if (createdDate != null && (force || media.getMediaCreated() == null)){

            media.setMediaCreated(TimePeriod.NewInstance(createdDate));

        }

        if (locality != null && (force || media.getDescription(Language.ENGLISH()) == null)){

            media.putDescription(Language.ENGLISH(), locality);

        }

    }

    private void makeSize(ImageFile part, CdmImageInfo imageInfo) {

        //h

        Integer height = part.getHeight();

        if (height == null || height != imageInfo.getHeight()){

            part.setHeight(imageInfo.getHeight());

        }

        //w

        Integer width = part.getWidth();

        if (width == null || width != imageInfo.getWidth()){

            part.setWidth(imageInfo.getWidth());

        }

        //s

        Integer size = part.getSize();

        if(size == null || size != imageInfo.getLength()){

            part.setSize((int)imageInfo.getLength());

        }

    }

    private Person getOrCreatePerson(String artist, String fileName) {

        artist = artist.trim();

        String regEx = "((?:[A-Z](?:\\.|[a-z\\-\u00E4\u00F6\u00FC]+) ?)+)([A-Z][a-z\\-\u00E4\u00F6\u00FC]+)";

        Matcher matcher = Pattern.compile(regEx).matcher(artist);

        Person person = Person.NewInstance();

        if (matcher.matches()){

            person.setGivenName(matcher.group(1).trim());

            person.setFamilyName(matcher.group(2).trim());

        }else{

            person.setTitleCache(artist, true);

            logger.warn("Person could not be parsed: " + artist + " for file " + fileName);

        }

        person = deduplicationHelper.getExistingAuthor(person);

        return person;

    }

    private String removeQuots(String text) {

        if (text.startsWith("'") && text.endsWith("'")){

            return text.substring(1, text.length() -1);

        }else{

            return text;

        }

    }

    private void makeTextData(String fileStr, Media media, Taxon taxon) {

        TaxonDescription imageGallery = taxon.getImageGallery(true);

        TextData textData = null;

        if (!imageGallery.getElements().isEmpty()){

            DescriptionElementBase el = imageGallery.getElements().iterator().next();

            if (el.isInstanceOf(TextData.class)){

                textData = CdmBase.deproxy(el, TextData.class);

            }else{

                logger.warn("Image gallery had non-textdata description element: " +  fileStr);

            }

        }

        if (textData == null){

            textData = TextData.NewInstance();

            textData.setFeature(Feature.IMAGE());

        }

        imageGallery.addElement(textData);

        textData.addMedia(media);

    }

    private void fillMediaWithAllRepresentations(Media media, String fullPath, String mediumPath, String smallPath, String oldFullPath){

        Set<MediaRepresentation> existingRepresentations = new HashSet<>(media.getRepresentations());

        makeMediaRepresentation(oldFullPath, media, existingRepresentations, fullPath);

        makeMediaRepresentation(mediumPath, media, existingRepresentations, null);

        makeMediaRepresentation(smallPath, media, existingRepresentations, null);

        if(!existingRepresentations.isEmpty()){

            logger.warn("Media contains existing representations which are not contained in the 3 paths: " + media.getTitleCache());

        }

    }

    private void makeMediaRepresentation(String uriString, Media media,

            Set<MediaRepresentation> existingRepresentations, String replaceUri) {

        MediaRepresentation existingMediaRep = getExistingMediaRepresentation(uriString, existingRepresentations);

        boolean readMediaData = true;

        MediaRepresentation newMediaRep = makeMediaRepresentation(replaceUri != null? replaceUri : uriString, readMediaData);

        if (existingMediaRep == null){

            media.addRepresentation(newMediaRep);

        }else{

            existingRepresentations.remove(existingMediaRep);

            mergeToExistingRepresentation(existingMediaRep, newMediaRep);

        }

    }

    private void mergeToExistingRepresentation(MediaRepresentation existingMediaRep, MediaRepresentation newMediaRep) {

        existingMediaRep.setMimeType(newMediaRep.getMimeType());

        existingMediaRep.setSuffix(newMediaRep.getSuffix());

        if(!existingMediaRep.getParts().isEmpty() && !newMediaRep.getParts().isEmpty()){

            MediaRepresentationPart existingPart = existingMediaRep.getParts().iterator().next();

            ImageFile newPart = (ImageFile)newMediaRep.getParts().iterator().next();

            if(existingPart.isInstanceOf(ImageFile.class)){

                ImageFile existingImage = CdmBase.deproxy(existingPart, ImageFile.class);

                existingImage.setHeight(newPart.getHeight());

                existingImage.setWidth(newPart.getWidth());

            }else{

                logger.warn("MediaRepresentationPart was not of type ImageFile. Height and width not merged: " + existingPart.getUri());

            }

            existingPart.setSize(newPart.getSize());

            existingPart.setUri(newPart.getUri());

        }

    }

    private MediaRepresentation getExistingMediaRepresentation(String uriString,

            Set<MediaRepresentation> existingRepresentations) {

        for (MediaRepresentation rep : existingRepresentations){

            for (MediaRepresentationPart part : rep.getParts()){

                if (part.getUri() != null && part.getUri().toString().equals(uriString)){

                    return rep;

                }

            }

        }

        return null;

    }

    /**

     * Creates

     * @see #READ_MEDIA_DATA

     * @return

     * @throws MalformedURLException

     */

    protected Media getImageMedia(String uriString, String uriStrThumb, boolean readMediaData) throws MalformedURLException {

        if( uriString == null){

            return null;

        } else {

            uriString = uriString.replace(" ", "%20");  //replace whitespace

            try {

                MediaRepresentation representation = makeMediaRepresentation(uriString, readMediaData);

                Media media = Media.NewInstance();

                media.addRepresentation(representation);

                if (uriStrThumb != null){

                    CdmImageInfo imageInfoThumb = null;

                    uriStrThumb = uriStrThumb.replace(" ", "%20");  //replace whitespace

                    URI uriThumb = new URI(uriStrThumb);

                    try {

                        if (readMediaData){

                            logger.info("Read media data from: " + uriThumb);

//                          //imageInfoThumb = CdmImageInfo.NewInstance(uriThumb, 0);

                            imageInfoThumb = MediaInfoFileReader.legacyFactoryMethod(uriThumb)

                                    .readBaseInfo()

                                    .getCdmImageInfo();

                        }

                    } catch (Exception e) {

                        String message = "An error occurred when trying to read image meta data for " + uriThumb.toString() + ": " +  e.getMessage();

                        logger.warn(message);

                    }

                    ImageFile imageFileFhumb = ImageFile.NewInstance(uriThumb, null, imageInfoThumb);

                    MediaRepresentation reprThumb = MediaRepresentation.NewInstance();

                    if(imageInfoThumb != null){

                        reprThumb.setMimeType(imageInfoThumb.getMimeType());

                        reprThumb.setSuffix(imageInfoThumb.getSuffix());

                    }

                    reprThumb.addRepresentationPart(imageFileFhumb);

                    media.addRepresentation(reprThumb);

                }

                return media;

            } catch (URISyntaxException e1) {

                String message = "An URISyntaxException occurred when trying to create uri from multimedia objcet string: " +  uriString;

                logger.warn(message);

                return null;

            }

        }

    }

    private MediaRepresentation makeMediaRepresentation(String uriString, boolean readMediaData) {

        uriString = uriString.replace(" ", "%20");  //replace whitespace

        CdmImageInfo imageInfo = null;

        URI uri;

        try {

            uri = new URI(uriString);

        } catch (URISyntaxException e1) {

            logger.error("Malformed URI. Could not create media representation: " + uriString);

            return null;

        }

        try {

            if (readMediaData){

                logger.info("Read media data from: " + uri);

                //imageInfo = CdmImageInfo.NewInstance(uri, 0);

                imageInfo = MediaInfoFileReader.legacyFactoryMethod(uri)

                        .readBaseInfo()

                        .getCdmImageInfo();

            }

        } catch (Exception e) {

            try {

                //try again

                //imageInfo = CdmImageInfo.NewInstance(uri, 0);

                imageInfo = MediaInfoFileReader.legacyFactoryMethod(uri)

                        .readBaseInfo()

                        .getCdmImageInfo();

            } catch (Exception e1) {

                String message = "An error occurred when trying to read image meta data for " + uri.toString() + ": " +  e1.getMessage();

                e1.printStackTrace();

                logger.warn(message);

            }

        }

        ImageFile imageFile = ImageFile.NewInstance(uri, null, imageInfo);

        MediaRepresentation representation = MediaRepresentation.NewInstance();

        if(imageInfo != null){

            representation.setMimeType(imageInfo.getMimeType());

            representation.setSuffix(imageInfo.getSuffix());

        }

        representation.addRepresentationPart(imageFile);

        return representation;

    }

    private Map<String, Media> getAllExistingUrls(Taxon taxon) {

        Map<String, Media> result = new HashMap<>();

        Set<TaxonDescription> descriptions = taxon.getDescriptions();

        for (TaxonDescription td : descriptions){

            if (td.isImageGallery()){

                for (DescriptionElementBase deb : td.getElements()){

                    if (deb.isInstanceOf(TextData.class)){

                        TextData textData = CdmBase.deproxy(deb, TextData.class);

                        for (Media media :textData.getMedia()){

                            for (MediaRepresentation rep : media.getRepresentations()){

                                for (MediaRepresentationPart part : rep.getParts()){

                                    URI uri = part.getUri();

                                    if (uri != null){

                                        String uriStr = uri.toString();

                                        result.put(uriStr, media);

                                    }

                                }

                            }

                        }

                    }

                }

            }

        }

        return result;

    }

    private Taxon getAcceptedTaxon(CdmApplicationController app, String taxonNameStr) {

        MatchingTaxonConfigurator config = new MatchingTaxonConfigurator();

        taxonNameStr = adaptName(taxonNameStr);

        config.setTaxonNameTitle(taxonNameStr);

        config.setIncludeSynonyms(false);

        List<TaxonBase> list = app.getTaxonService().findTaxaByName(config);

        if (list.isEmpty()){

//            logger.warn("Taxon not found for media: " + taxonNameStr);

            taxonNameStr = taxonNameStr.replaceFirst(" ", " " + UTF8.HYBRID.toString());

            config.setTaxonNameTitle(taxonNameStr);

            list = app.getTaxonService().findTaxaByName(config);

            if (list.isEmpty()){

                return null;

            }else if (list.size() > 1){

                logger.warn("After searching for hybrids more than 1 taxon was foung: " + taxonNameStr);

            }

        }

        if (list.size()>1){

            Iterator<TaxonBase> it = list.iterator();

            while (it.hasNext()){

                Taxon next = (Taxon)it.next();

                if (next.getTaxonNodes().isEmpty() && !next.getTaxaForMisappliedName(true).isEmpty()){

                    it.remove();

                }

            }

            if (list.size()>1){

                logger.warn("More than 1 taxon found for media: " + taxonNameStr + " . Will now try to use only taxon with taxon node.");

                it = list.iterator();

                while (it.hasNext()){

                    Taxon next = (Taxon)it.next();

                    if (next.getTaxonNodes().isEmpty()){

                        it.remove();

                    }

                }

                if (list.size()>1){

                    logger.warn("Still more than 1 taxon found for media: " + taxonNameStr);

                }else if (list.size() < 1){

                    logger.warn("After removing nodeless taxa no taxon was left: " +  taxonNameStr);

                    return null;

                }

            }else if (list.size() < 1){

                logger.warn("After removing misapplications no taxon was left: " +  taxonNameStr);

                return null;

            }

        }

        TaxonBase<?> taxonBase = list.get(0);

        Taxon result;

        if (taxonBase.isInstanceOf(Synonym.class)){

            result = CdmBase.deproxy(taxonBase, Synonym.class).getAcceptedTaxon();

        }else{

            result = CdmBase.deproxy(taxonBase, Taxon.class);

        }

        return result;

    }

    private String adaptName(String taxonNameStr) {

//        if (taxonNameStr.equals("Hypericum cerastoides")){

//            taxonNameStr = "Hypericum cerastioides";

//        }

        return taxonNameStr;

    }

	private void test(){

	    File f = new File(path);

	    String[] list = f.list();

	    List<String> fullFileNames = new ArrayList<>();

	    for (String fileName : list){

	        fullFileNames.add(path + fileName);

	        if (! fileName.matches("([A-Z][a-z]+_[a-z\\-]{3,}(?:_s_[a-z\\-]{3,})?)_[A-F]\\d{1,2}\\.(jpg|JPG)")){

	            System.out.println(fileName);

	        }

	    }

	}

	private void updateMetadata(ICdmDataSource cdmDestination){

        CdmApplicationController app = CdmIoApplicationController.NewInstance(cdmDestination, DbSchemaValidation.VALIDATE);

        TransactionStatus tx = app.startTransaction();

        deduplicationHelper = ImportDeduplicationHelper.NewInstance(app, null);

        List<Media> list = app.getMediaService().list(Media.class, null, null, null, null);

        for (Media media : list){

            handleSingleMediaUpdate(media);

        }

        if (testOnly){

            tx.setRollbackOnly();

        }

        app.commitTransaction(tx);

	}

    private void handleSingleMediaUpdate(Media media){

        ImageFile part = getUrlStringForMedia(media);

        if (part == null || part.getUri() == null){

            logger.warn("No uri found for media (id = " + media.getId() + ")");

            return;

        }

        String url = part.getUri().toString();

        if (url.startsWith(newUrlPath)){

            String fileName = url.replace(newUrlPath, "").replace("&mo=file", "");

            makeMetaData(media, fileName, part, true, sizeOnly);

            makeTitle(media, fileName, true);

            System.out.println(fileName);

        }else{

            logger.warn("URL does not start with standard url path: " + url);

        }

    }

    private ImageFile getUrlStringForMedia(Media media) {

        ImageFile result = null;

        for (MediaRepresentation rep : media.getRepresentations()){

            for (MediaRepresentationPart part : rep.getParts()){

                URI uri = part.getUri();

                if (uri != null){

                    if (result != null){

                        //TODO this still needs to be adapted to the 3 representations of media

                        logger.warn("More than 1 uri exists for media "+ media.getId());

                    }else if (!part.isInstanceOf(ImageFile.class)){

                        logger.warn("MediaRepresentationPart is not an ImageFile: " + uri);

                    }else{

                        result = CdmBase.deproxy(part, ImageFile.class);

                    }

                }

            }

        }

        return result;

    }

	public static void main(String[] args) {

		CichorieaImageUpdateActivator me = new CichorieaImageUpdateActivator();

		if (update_notCreate){

		    me.updateMetadata(cdmDestination);

		}else{

		    me.doImport(cdmDestination);

		}

//		me.test();

		System.exit(0);

	}

}