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.io.common;

import java.net.MalformedURLException;

import java.net.URI;

import java.net.URISyntaxException;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.Arrays;

import java.util.HashSet;

import java.util.List;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.api.service.pager.Pager;

import eu.etaxonomy.cdm.common.CdmUtils;

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

import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;

import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;

import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;

import eu.etaxonomy.cdm.io.markup.MarkupTransformer;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.location.NamedArea;

import eu.etaxonomy.cdm.model.location.NamedAreaLevel;

import eu.etaxonomy.cdm.model.location.NamedAreaType;

import eu.etaxonomy.cdm.model.location.ReferenceSystem;

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.name.NonViralName;

import eu.etaxonomy.cdm.model.name.Rank;

import eu.etaxonomy.cdm.model.reference.Reference;

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

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

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

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

/**

 * @author a.mueller

 * @created 01.07.2008

 * @version 1.0

 */

public abstract class CdmImportBase<CONFIG extends IImportConfigurator, STATE extends ImportStateBase> extends CdmIoBase<STATE> implements ICdmImport<CONFIG, STATE>{

	private static Logger logger = Logger.getLogger(CdmImportBase.class);

	protected static final boolean CREATE = true;

	protected static final boolean IMAGE_GALLERY = true;

	public static final UUID uuidUserDefinedNamedAreaLevelVocabulary = UUID.fromString("255144da-8d95-457e-a327-9752a8f85e5a");

	public static final UUID uuidUserDefinedNamedAreaVocabulary = UUID.fromString("b2238399-a3af-4f6d-b7eb-ff5d0899bf1b");

	public static final UUID uuidUserDefinedExtensionTypeVocabulary = UUID.fromString("e28c1394-1be8-4847-8b81-ab44eb6d5bc8");

	public static final UUID uuidUserDefinedReferenceSystemVocabulary = UUID.fromString("467591a3-10b4-4bf1-9239-f06ece33e90a");

	public static final UUID uuidUserDefinedFeatureVocabulary = UUID.fromString("fe5fccb3-a2f2-4b97-b199-6e2743cf1627");

	public static final UUID uuidUserDefinedAnnotationTypeVocabulary = UUID.fromString("cd9ecdd2-9cae-4890-9032-ad83293ae883");

	public static final UUID uuidUserDefinedMarkerTypeVocabulary = UUID.fromString("5f02a261-fd7d-4fce-bbe4-21472de8cd51");

	private static final String UuidOnly = "UUIDOnly";

	private static final String UuidLabel = "UUID or label";

	private static final String UuidLabelAbbrev = "UUID, label or abbreviation";

	private static final String UuidAbbrev = "UUID or abbreviation";

	public enum TermMatchMode{

		UUID_ONLY(0, UuidOnly)

		,UUID_LABEL(1, UuidLabel)

		,UUID_LABEL_ABBREVLABEL(2, UuidLabelAbbrev)

		,UUID_ABBREVLABEL(3, UuidAbbrev)

		;

		private int id;

		private String representation;

		private TermMatchMode(int id, String representation){

			this.id = id;

			this.representation = representation;

		}

		public int getId() {

			return id;

		}

		public String getRepresentation() {

			return representation;

		}

		public TermMatchMode valueOf(int id){

			switch (id){

				case 0: return UUID_ONLY;

				case 1: return UUID_LABEL;

				case 2: return UUID_LABEL_ABBREVLABEL;

				case 3: return UUID_ABBREVLABEL;

				default: return UUID_ONLY;

			}

 		}

	}

	protected Classification makeTree(STATE state, Reference reference){

		Reference ref = CdmBase.deproxy(reference, Reference.class);

		String treeName = "Classification (Import)";

		if (ref != null && CdmUtils.isNotEmpty(ref.getTitleCache())){

			treeName = ref.getTitleCache();

		}

		Classification tree = Classification.NewInstance(treeName);

		tree.setReference(ref);

		// use defined uuid for first tree

		CONFIG config = (CONFIG)state.getConfig();

		if (state.countTrees() < 1 ){

			tree.setUuid(config.getClassificationUuid());

		}

		getClassificationService().save(tree);

		state.putTree(ref, tree);

		return tree;

	}

	/**

	 * Alternative memory saving method variant of

	 * {@link #makeTree(STATE state, Reference ref)} which stores only the

	 * UUID instead of the full tree in the <code>ImportStateBase</code> by 

	 * using <code>state.putTreeUuid(ref, tree);</code>

	 * 

	 * @param state

	 * @param ref

	 * @return

	 */

	protected Classification makeTreeMemSave(STATE state, Reference ref){

		String treeName = "Classification (Import)";

		if (ref != null && CdmUtils.isNotEmpty(ref.getTitleCache())){

			treeName = ref.getTitleCache();

		}

		Classification tree = Classification.NewInstance(treeName);

		tree.setReference(ref);

		// use defined uuid for first tree

		CONFIG config = (CONFIG)state.getConfig();

		if (state.countTrees() < 1 ){

			tree.setUuid(config.getClassificationUuid());

		}

		getClassificationService().save(tree);

		state.putTreeUuid(ref, tree);

		return tree;

	}

	protected ExtensionType getExtensionType(STATE state, UUID uuid, String label, String text, String labelAbbrev){

		return getExtensionType(state, uuid, label, text, labelAbbrev, null);

	}

	protected ExtensionType getExtensionType(STATE state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<ExtensionType> voc){

		if (uuid == null){

			uuid = UUID.randomUUID();

		}

		ExtensionType extensionType = state.getExtensionType(uuid);

		if (extensionType == null){

			extensionType = (ExtensionType)getTermService().find(uuid);

			if (extensionType == null){

				extensionType = ExtensionType.NewInstance(text, label, labelAbbrev);

				extensionType.setUuid(uuid);

				if (voc == null){

					boolean isOrdered = false;

					voc = getVocabulary(uuidUserDefinedExtensionTypeVocabulary, "User defined vocabulary for extension types", "User Defined Extension Types", null, null, isOrdered, extensionType);

				}

				voc.addTerm(extensionType);

				getTermService().saveOrUpdate(extensionType);

			}

			state.putExtensionType(extensionType);

		}

		return extensionType;

	}

	protected MarkerType getMarkerType(STATE state, String keyString) {

		IInputTransformer transformer = state.getTransformer();

		MarkerType markerType = null;

		try {

			markerType = transformer.getMarkerTypeByKey(keyString);

		} catch (UndefinedTransformerMethodException e) {

			logger.info("getMarkerTypeByKey not yet implemented for this import");

		}

		if (markerType == null ){

			UUID uuid;

			try {

				uuid = transformer.getMarkerTypeUuid(keyString);

				return getMarkerType(state, uuid, keyString, keyString, keyString);

			} catch (UndefinedTransformerMethodException e) {

				logger.warn("getMarkerTypeUuid not yet implemented for this import");

			}

		}

		return null;

	}

	protected MarkerType getMarkerType(STATE state, UUID uuid, String label, String text, String labelAbbrev){

		return getMarkerType(state, uuid, label, text, labelAbbrev, null);

	}

	protected MarkerType getMarkerType(STATE state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<MarkerType> voc){

		if (uuid == null){

			uuid = UUID.randomUUID();

		}

		MarkerType markerType = state.getMarkerType(uuid);

		if (markerType == null){

			markerType = (MarkerType)getTermService().find(uuid);

			if (markerType == null){

				markerType = MarkerType.NewInstance(label, text, labelAbbrev);

				markerType.setUuid(uuid);

				if (voc == null){

					boolean isOrdered = false;

					voc = getVocabulary(uuidUserDefinedMarkerTypeVocabulary, "User defined vocabulary for marker types", "User Defined Marker Types", null, null, isOrdered, markerType);

				}

				voc.addTerm(markerType);

				getTermService().save(markerType);

			}

			state.putMarkerType(markerType);

		}

		return markerType;

	}

	protected AnnotationType getAnnotationType(STATE state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<AnnotationType> voc){

		if (uuid == null){

			uuid = UUID.randomUUID();

		}

		AnnotationType annotationType = state.getAnnotationType(uuid);

		if (annotationType == null){

			annotationType = (AnnotationType)getTermService().find(uuid);

			if (annotationType == null){

				annotationType = AnnotationType.NewInstance(label, text, labelAbbrev);

				annotationType.setUuid(uuid);

				if (voc == null){

					boolean isOrdered = false;

					voc = getVocabulary(uuidUserDefinedAnnotationTypeVocabulary, "User defined vocabulary for annotation types", "User Defined Annotation Types", null, null, isOrdered, annotationType);

				}

				voc.addTerm(annotationType);

				getTermService().save(annotationType);

			}

			state.putAnnotationType(annotationType);

		}

		return annotationType;

	}

	protected ReferenceSystem getReferenceSystem(STATE state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary voc){

		if (uuid == null){

			uuid = UUID.randomUUID();

		}

		ReferenceSystem refSystem = state.getReferenceSystem(uuid);

		if (refSystem == null){

			refSystem = (ReferenceSystem)getTermService().find(uuid);

			if (refSystem == null){

				refSystem = ReferenceSystem.NewInstance(text, label, labelAbbrev);

				if (voc == null){

					boolean isOrdered = false;

					voc = getVocabulary(uuidUserDefinedReferenceSystemVocabulary, "User defined vocabulary for named areas", "User Defined Reference System", null, null, isOrdered, refSystem);

				}

				voc.addTerm(refSystem);

				refSystem.setUuid(uuid);

				getTermService().save(refSystem);

			}

			state.putReferenceSystem(refSystem);

		}

		return refSystem;

	}

	/**

	 * Returns a named area for a given uuid by first . If the named area does not

	 * @param state

	 * @param uuid

	 * @param label

	 * @param text

	 * @param labelAbbrev

	 * @param areaType

	 * @param level

	 * @return

	 */

	protected NamedArea getNamedArea(STATE state, UUID uuid, String label, String text, String labelAbbrev, NamedAreaType areaType, NamedAreaLevel level){

		return getNamedArea(state, uuid, label, text, labelAbbrev, areaType, level, null, null);

	}

	protected NamedArea getNamedArea(STATE state, UUID uuid, String label, String text, String labelAbbrev, NamedAreaType areaType, NamedAreaLevel level, TermVocabulary voc, TermMatchMode matchMode){

		if (uuid == null){

			uuid = UUID.randomUUID();

		}

		if (matchMode == null){

			matchMode = TermMatchMode.UUID_ONLY;

		}

		NamedArea namedArea = state.getNamedArea(uuid);

		if (namedArea == null){

			//TODO matching still experimental

			namedArea = (NamedArea)getTermService().find(uuid);

			if (namedArea == null && matchMode.equals(TermMatchMode.UUID_LABEL)){

				logger.warn("UUID_LABEL not yet implemented");

			}

			if (namedArea == null && matchMode.equals(TermMatchMode.UUID_ABBREVLABEL)){

				Pager<NamedArea> areaPager = getTermService().findByRepresentationAbbreviation(labelAbbrev, NamedArea.class, null, null);

				namedArea = findBestMatchingArea(areaPager, uuid, label, text, labelAbbrev, areaType, level, voc);

			}

			if (namedArea == null && matchMode.equals(TermMatchMode.UUID_LABEL_ABBREVLABEL)){

				logger.warn("UUID_LABEL not yet implemented");

			}

			if (namedArea == null){

				namedArea = NamedArea.NewInstance(text, label, labelAbbrev);

				if (voc == null){

					boolean isOrdered = true;

					voc = getVocabulary(uuidUserDefinedNamedAreaVocabulary, "User defined vocabulary for named areas", "User Defined Named Areas", null, null, isOrdered, namedArea);

				}

				voc.addTerm(namedArea);

				namedArea.setType(areaType);

				namedArea.setLevel(level);

				namedArea.setUuid(uuid);

				getTermService().save(namedArea);

			}

			state.putNamedArea(namedArea);

		}

		return namedArea;

	}

	private NamedArea findBestMatchingArea(Pager<NamedArea> areaPager, UUID uuid, String label, String text, String abbrev,

			NamedAreaType areaType, NamedAreaLevel level, TermVocabulary voc) {

		// TODO preliminary implementation

		List<NamedArea> list = areaPager.getRecords();

		if (list.size() == 0){

			return null;

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

			return list.get(0);

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

			String message = "There is more than 1 matching area for %s, %s, %s. As a preliminary implementation I take the first";

			message = String.format(message, label, abbrev, text);

			logger.warn(message);

			return list.get(0);

		}

		return null;

	}

	protected NamedAreaLevel getNamedAreaLevel(STATE state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<NamedAreaLevel> voc){

		if (uuid == null){

			uuid = UUID.randomUUID();

		}

		NamedAreaLevel namedAreaLevel = state.getNamedAreaLevel(uuid);

		if (namedAreaLevel == null){

			namedAreaLevel = CdmBase.deproxy(getTermService().find(uuid), NamedAreaLevel.class);

			if (namedAreaLevel == null){

				namedAreaLevel = NamedAreaLevel.NewInstance(text, label, labelAbbrev);

				if (voc == null){

					boolean isOrdered = true;

					voc = getVocabulary(uuidUserDefinedNamedAreaLevelVocabulary, "User defined vocabulary for named area levels", "User Defined Named Area Levels", null, null, isOrdered, namedAreaLevel);

				}

				voc.addTerm(namedAreaLevel);

				namedAreaLevel.setUuid(uuid);

				getTermService().save(namedAreaLevel);

			}

			state.putNamedAreaLevel(namedAreaLevel);

		}

		return namedAreaLevel;

	}

	/**

	 * Returns a feature if it exists, null otherwise.

	 * @see #getFeature(ImportStateBase, UUID, String, String, String, TermVocabulary)

	 * @param state

	 * @param uuid

	 * @return

	 */

	protected Feature getFeature(STATE state, UUID uuid){

		return getFeature(state, uuid, null, null, null, null);

	}

	/**

	 * Returns a feature for a given uuid by first checking if the uuid has already been used in this import, if not

	 * checking if the feature exists in the database, if not creating it anew (with vocabulary etc.).

	 * If label, text and labelAbbrev are all <code>null</code> no feature is created.

	 * @param state

	 * @param uuid

	 * @param label

	 * @param text

	 * @param labelAbbrev

	 * @return

	 */

	protected Feature getFeature(STATE state, UUID uuid, String label, String text, String labelAbbrev, TermVocabulary<Feature> voc){

		if (uuid == null){

			return null;

		}

		Feature feature = state.getFeature(uuid);

		if (feature == null){

			feature = (Feature)getTermService().find(uuid);

			if (feature == null && ! hasNoLabel(label, text, labelAbbrev)){

				feature = Feature.NewInstance(text, label, labelAbbrev);

				feature.setUuid(uuid);

				feature.setSupportsTextData(true);

//				UUID uuidFeatureVoc = UUID.fromString("b187d555-f06f-4d65-9e53-da7c93f8eaa8"); 

				if (voc == null){

					boolean isOrdered = false;

					voc = getVocabulary(uuidUserDefinedFeatureVocabulary, "User defined vocabulary for features", "User Defined Features", null, null, isOrdered, feature);

				}

				voc.addTerm(feature);

				getTermService().save(feature);

			}

			state.putFeature(feature);

		}

		return feature;

	}

	private boolean hasNoLabel(String label, String text, String labelAbbrev) {

		return label == null && text == null && labelAbbrev == null;

	}

	/**

	 * Returns a presence term for a given uuid by first ...

	 * @param state

	 * @param uuid

	 * @param label

	 * @param text

	 * @param labelAbbrev

	 * @return

	 */

	protected PresenceTerm getPresenceTerm(STATE state, UUID uuid, String label, String text, String labelAbbrev){

		if (uuid == null){

			return null;

		}

		PresenceTerm presenceTerm = state.getPresenceTerm(uuid);

		if (presenceTerm == null){

			presenceTerm = (PresenceTerm)getTermService().find(uuid);

			if (presenceTerm == null){

				presenceTerm = PresenceTerm.NewInstance(text, label, labelAbbrev);

				presenceTerm.setUuid(uuid);

				//set vocabulary ; FIXME use another user-defined vocabulary

				UUID uuidPresenceVoc = UUID.fromString("adbbbe15-c4d3-47b7-80a8-c7d104e53a05"); 

				TermVocabulary<PresenceTerm> voc = getVocabularyService().find(uuidPresenceVoc);

				voc.addTerm(presenceTerm);

				getTermService().save(presenceTerm);

			}

			state.putPresenceTerm(presenceTerm);

		}

		return presenceTerm;

	}

	/**

	 * Returns a language for a given uuid by first ...

	 * @param state

	 * @param uuid

	 * @param label

	 * @param text

	 * @param labelAbbrev

	 * @return

	 */

	protected Language getLanguage(STATE state, UUID uuid, String label, String text, String labelAbbrev){

		if (uuid == null){

			return null;

		}

		Language language = state.getLanguage(uuid);

		if (language == null){

			language = (Language)getTermService().find(uuid);

			if (language == null){

				language = Language.NewInstance(text, label, labelAbbrev);

				language.setUuid(uuid);

				//set vocabulary ; FIXME use another user-defined vocabulary

				UUID uuidLanguageVoc = UUID.fromString("45ac7043-7f5e-4f37-92f2-3874aaaef2de"); 

				TermVocabulary<Language> voc = getVocabularyService().find(uuidLanguageVoc);

				voc.addTerm(language);

				getTermService().save(language);

			}

			state.putLanguage(language);

		}

		return language;

	}

	/**

	 * @param uuid 

	 * @return

	 * 

	 */

	protected <T extends DefinedTermBase> TermVocabulary<T> getVocabulary(UUID uuid, String text, String label, String abbrev, URI termSourceUri, boolean isOrdered, T type) {

		List<String> propPath = Arrays.asList(new String[]{"terms"});

		TermVocabulary<T> voc = getVocabularyService().load(uuid, propPath);

		if (voc == null){

			if (isOrdered){

				voc = OrderedTermVocabulary.NewInstance(text, label, abbrev, termSourceUri);

			}else{

				voc = TermVocabulary.NewInstance(text, label, abbrev, termSourceUri);

			}

			voc.setUuid(uuid);

			getVocabularyService().save(voc);

		}

		return voc;

	}

	/**

	 * Adds an orginal source to a sourceable objects (implemented for Identifiable entity and description element.

	 * If cdmBase is not sourceable nothing happens.

	 * TODO Move to DbImportBase once this exists.

	 * TODO also implemented in DbImportObjectCreationMapper (reduce redundance)

	 * @param rs

	 * @param cdmBase

	 * @param dbIdAttribute

	 * @param namespace

	 * @param citation

	 * @throws SQLException

	 */

	public void addOriginalSource(CdmBase cdmBase, Object idAttributeValue, String namespace, Reference citation)  {

		if (cdmBase instanceof ISourceable ){

			IOriginalSource source;

			ISourceable sourceable = (ISourceable)cdmBase;

			Object id = idAttributeValue;

			String strId = String.valueOf(id);

			String microCitation = null;

			if (cdmBase instanceof IdentifiableEntity){

				source = IdentifiableSource.NewInstance(strId, namespace, citation, microCitation);

			}else if (cdmBase instanceof DescriptionElementBase){

				source = DescriptionElementSource.NewInstance(strId, namespace, citation, microCitation);

			}else{

				logger.warn("ISourceable not beeing identifiable entities or description element base are not yet supported. CdmBase is of type " + cdmBase.getClass().getName() + ". Original source not added.");

				return;

			}

			sourceable.addSource(source);

		}else if (cdmBase != null){

			logger.warn("Sourced object does not implement ISourceable: " + cdmBase.getClass() + "," + cdmBase.getUuid());

		}else{

			logger.warn("Sourced object is null");

		}

	}

	/**

	 * @see #addOriginalSource(CdmBase, Object, String, Reference)

	 * @param rs

	 * @param cdmBase

	 * @param dbIdAttribute

	 * @param namespace

	 * @param citation

	 * @throws SQLException

	 */

	public void addOriginalSource(ResultSet rs, CdmBase cdmBase, String dbIdAttribute, String namespace, Reference citation) throws SQLException {

		Object id = rs.getObject(dbIdAttribute);

		addOriginalSource(cdmBase, id, namespace, citation);

	}

	/**

	 * If the child taxon is missing genus or species epithet information and the rank is below <i>genus</i>

	 * or <i>species</i> respectively the according epithets are taken from the parent taxon.

	 * If the name is an autonym and has no combination author/basionym author the authors are taken from

	 * the parent.

	 * @param parentTaxon

	 * @param childTaxon

	 */

	protected void fillMissingEpithetsForTaxa(Taxon parentTaxon, Taxon childTaxon) {

		NonViralName parentName = HibernateProxyHelper.deproxy(parentTaxon.getName(), NonViralName.class);

		NonViralName childName = HibernateProxyHelper.deproxy(childTaxon.getName(), NonViralName.class);

		fillMissingEpithets(parentName, childName);

	}

	/**

	 * If the child name is missing genus or species epithet information and the rank is below <i>genus</i>

	 * or <i>species</i> respectively the according epithets are taken from the parent name.

	 * If the name is an autonym and has no combination author/basionym author the authors are taken from

	 * the parent.

	 * @param parentTaxon

	 * @param childTaxon

	 */

	protected void fillMissingEpithets(NonViralName parentName, NonViralName childName) {

		if (CdmUtils.isEmpty(childName.getGenusOrUninomial()) && childName.getRank().isLower(Rank.GENUS()) ){

			childName.setGenusOrUninomial(parentName.getGenusOrUninomial());

		}

		if (CdmUtils.isEmpty(childName.getSpecificEpithet()) && childName.getRank().isLower(Rank.SPECIES()) ){

			childName.setSpecificEpithet(parentName.getSpecificEpithet());

		}

		if (childName.isAutonym() && childName.getCombinationAuthorTeam() == null && childName.getBasionymAuthorTeam() == null ){

			childName.setCombinationAuthorTeam(parentName.getCombinationAuthorTeam());

			childName.setBasionymAuthorTeam(parentName.getBasionymAuthorTeam());

		}	

	}

	/**

	 * Returns the taxon description for a taxon. If there are multiple taxon descriptions

	 * an arbitrary one is chosen.

	 * If no taxon description exists, a new one is created if <code>createNewIfNotExists</code>

	 * is <code>true</code>.

	 * @param createNewIfNotExists

	 * @param isImageGallery if true only taxon description being image galleries are considered.

	 * If false only taxon description being no image galleries are considered.

	 * @return

	 */

	public TaxonDescription getTaxonDescription(Taxon taxon, boolean isImageGallery, boolean createNewIfNotExists) {

		Reference ref = null;

		return getTaxonDescription(taxon, ref, isImageGallery, createNewIfNotExists);

	}

	/**

	 * Like {@link #getTaxonDescription(Taxon, boolean, boolean)}

	 * Only matches a description if the given reference is a source of the description.<BR>

	 * If a new description is created the given reference will be added as a source.

	 * 

	 * @see #getTaxonDescription(Taxon, boolean, boolean)

	 */

	public TaxonDescription getTaxonDescription(Taxon taxon, Reference ref, boolean isImageGallery, boolean createNewIfNotExists) {

		TaxonDescription result = null;

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

		for (TaxonDescription description : descriptions){

			if (description.isImageGallery() == isImageGallery){

				if (hasCorrespondingSource(ref, description)){

					result = description;

					break;

				}

			}

		}

		if (result == null && createNewIfNotExists){

			result = TaxonDescription.NewInstance(taxon);

			result.setImageGallery(isImageGallery);

			if (ref != null){

				result.addSource(null, null, ref, null);

			}

		}

		return result;

	}

	/**

	 * Returns the textdata that holds general information about a feature for a taxon description.

	 * This is mainly necessary for descriptions that have more than one description element for

	 * a given feature such as 'distribution', 'description' or 'common name'. It may also hold

	 * for hierarchical features where no description element exists for a higher hierarchie level.

	 * Example: the description feature has subfeatures. But some information like authorship, figures,

	 * sources need to be added to the description itself.

	 * Currently a feature placeholder is marked by a marker of type 'feature placeholder'. Maybe in future

	 * there will be a boolean marker in the TextData class itself.

	 * @param state 

	 * @param feature 

	 * @param taxon

	 * @param ref

	 * @param createIfNotExists

	 * @return

	 */

	protected TextData getFeaturePlaceholder(STATE state, DescriptionBase<?> description, Feature feature, boolean createIfNotExists) {

		UUID featurePlaceholderUuid = MarkupTransformer.uuidFeaturePlaceholder;

		for (DescriptionElementBase element : description.getElements()){

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

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

				if (textData.getFeature() == null || ! textData.getFeature().equals(feature)){

					continue;

				}

				for (Marker marker : textData.getMarkers()){

					MarkerType markerType = marker.getMarkerType();

					if (markerType != null && 

							markerType.getUuid().equals(featurePlaceholderUuid) && 

							marker.getValue() == true){

						return textData;

					}

				}

			}

		}

		if (createIfNotExists){

			TextData newPlaceholder = TextData.NewInstance(feature);

			MarkerType placeholderMarkerType = getMarkerType(state, featurePlaceholderUuid, "Feature Placeholder", "Feature Placeholder", null);

			Marker marker = Marker.NewInstance(placeholderMarkerType, true);

			newPlaceholder.addMarker(marker);

			description.addElement(newPlaceholder);

			return newPlaceholder;

		}else{

			return null;

		}

	}

	/**

	 * Returns true, if this description has a source with a citation equal to the given reference.

	 * Returns true if the given reference is null.

	 * @param ref

	 * @param description

	 */

	private boolean hasCorrespondingSource(Reference ref, TaxonDescription description) {

		if (ref != null){

			for (IdentifiableSource source : description.getSources()){

				if (ref.equals(source.getCitation())){

					return true;

				}

			}

			return false;

		}

		return true;

	}

	/**

	 * Returns the accepted taxon of a {@link TaxonBase taxon base}. <BR>

	 * If taxonBase is of type taxon the same object is returned. If taxonBase is of type

	 * synonym the accepted taxon is returned if one exists. If no accepted taxon exists

	 * <code>null</code> is returned. If multiple accepted taxa exist the one taxon with the 

	 * same secundum reference is returned. If no such single taxon exists an 

	 * {@link IllegalStateException illegal state exception} is thrown.  

	 * @param taxonBase

	 * @return

	 */

	protected Taxon getAcceptedTaxon(TaxonBase<?> taxonBase) {

		if (taxonBase == null){

			return null;

		}else if(taxonBase.isInstanceOf(Taxon.class)){

			return CdmBase.deproxy(taxonBase, Taxon.class);

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

			Synonym synonym = CdmBase.deproxy(taxonBase, Synonym.class);

			Set<Taxon> acceptedTaxa = synonym.getAcceptedTaxa();

			if (acceptedTaxa.size() == 0){

				return null;

			}else if (acceptedTaxa.size() == 1){

				return acceptedTaxa.iterator().next();

			}else{

				Reference sec = synonym.getSec();

				if (sec != null){

					Set<Taxon> taxaWithSameSec = new HashSet<Taxon>();

					for (Taxon taxon: acceptedTaxa){

						if (sec.equals(taxon.getSec())){

							taxaWithSameSec.add(taxon);

						}

					}

					if (taxaWithSameSec.size() == 1){

						return taxaWithSameSec.iterator().next();

					}

				}

				throw new IllegalStateException("Can't define the one accepted taxon for a synonym out of multiple accept taxa");

			}

		}else{

			throw new IllegalStateException("Unknown TaxonBase subclass: " + taxonBase.getClass().getName());

		}

	}

	/**

	 * @param derivedUnitFacade

	 * @param multimediaObject

	 * @throws MalformedURLException

	 */

	protected Media getImageMedia(String multimediaObject, boolean readDataFromUrl) throws MalformedURLException {

		if( multimediaObject == null){

			return null;

		} else {

			ImageInfo imageInfo = null;

			URI uri;

			try {

				uri = new URI(multimediaObject);

				try {

					if (readDataFromUrl){

						imageInfo = ImageInfo.NewInstance(uri, 0);

					}

				} catch (Exception e) {

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

					logger.warn(message);

				}

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