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.diptera;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import org.apache.log4j.Logger;

import org.springframework.transaction.TransactionStatus;

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

import eu.etaxonomy.cdm.api.service.INameService;

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

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

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.io.common.ImportResult;

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

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

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

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

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

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.name.TaxonName;

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

/**

 * @author a.mueller

 * @since 01.10.2009

 * @version 1.0

 */

public class DipteraPostImportUpdater {

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

	static final ICdmDataSource cdmDestination = CdmDestinations.localH2Palmae();

	/**

	 * This method updateds the citation text by deleting <code>OriginalName</code> tags and

	 * adding the original name to the source either as a link to an existing taxon name

	 * or as a string. The later becomes true if there is not exactly one matching name

	 * @param dataSource

	 * @return

	 */

	public ImportResult updateCitations(ICdmDataSource dataSource) {

			logger.warn("start updating citations");

			ImportResult result = new ImportResult();

			try{

			CdmApplicationController cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);

			Set<DescriptionElementBase> citationsToSave = new HashSet<DescriptionElementBase>();

			TransactionStatus tx = cdmApp.startTransaction();

			logger.warn("start updating citations ... application context started");

			int modCount = 100;

			int page = 0;

			int count = cdmApp.getTaxonService().count(Taxon.class);

			List<Taxon> taxonList = cdmApp.getTaxonService().list(Taxon.class, 100000, page, null, null);

			List<TaxonName> nameList = cdmApp.getNameService().list(null, 100000, page, null, null);

			Map<String, TaxonName> nameMap = new HashMap<>();

			Map<String, TaxonName> nameDuplicateMap = new HashMap<>();

			fillNameMaps(nameList, nameMap, nameDuplicateMap);

			int i = 0;

			for (Taxon taxon : taxonList){

				if ((i++ % modCount) == 0){ logger.warn("taxa handled: " + (i-1));}

				Set<TextData> citations = getCitations(taxon);

				for (TextData citation : citations){

					Language language = Language.DEFAULT();

					String text = citation.getText(language);

					String originalNameString = parseOriginalNameString(text);

					String newText = parseNewText(text);

					citation.removeText(language);

					citation.putText(language, newText);

					TaxonName scientificName = getScientificName(originalNameString, nameMap, nameDuplicateMap);

					Set<DescriptionElementSource> sources = citation.getSources();

					if (sources.size() > 1){

						logger.warn("There are more then 1 sources for a description");

					}else if (sources.size() == 0){

						DescriptionElementSource source = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource);

						citation.addSource(source);

						sources = citation.getSources();

					}

					for (DescriptionElementSource source : sources){

						if (scientificName != null){

							source.setNameUsedInSource(scientificName);

						}else{

							source.setOriginalNameString(originalNameString);

						}

					}

					citationsToSave.add(citation);

				}

			}

			cdmApp.getDescriptionService().saveDescriptionElement(citationsToSave);

			//commit

			cdmApp.commitTransaction(tx);

			logger.warn("Citations updated!");

			return result;

		} catch (Exception e) {

			e.printStackTrace();

			result.addError("ERROR in citation update");

			result.addException(e);

			return result;

		}

	}

	public ImportResult updateCollections(ICdmDataSource dataSource){

		DipteraCollectionImport collectionImport = new DipteraCollectionImport();

		return collectionImport.invoke(dataSource);

	}

	private void fillNameMaps(List<TaxonName> nameList, Map<String, TaxonName> nameMap, Map<String, TaxonName> duplicateMap) {

		for (TaxonName name : nameList){

			String nameCache = name.getNameCache();

			if (nameMap.containsKey(nameCache)){

				duplicateMap.put(nameCache, name);

			}else{

				nameMap.put(nameCache, name);

			}

		}

	}

	private TaxonName getScientificName(String originalNameString, Map<String, TaxonName> nameMap, Map<String, TaxonName> nameDuplicateMap) {

		originalNameString = originalNameString.trim();

		TaxonName result = nameMap.get(originalNameString);

		if (nameDuplicateMap.containsKey(originalNameString)){

			result = null;

		}

		return result;

	}

	private TaxonName getScientificName(String originalNameString, INameService nameService) {

		Pager<TaxonName> names = nameService.findByName(null, originalNameString, null, null, null, null, null, null);

		if (names.getCount() != 1){

			return null;

		}else{

			return names.getRecords().get(0);

		}

	}

	private String parseOriginalNameString(String text) {

		String originalName = "<OriginalName>";

		int start = text.indexOf(originalName);

		int end = text.indexOf("</OriginalName>");

		if (start >-1 ){

			text = text.substring(start + originalName.length(), end);

		}

		text = text.trim();

		return text;

	}

	private String parseNewText(String text) {

		int start = text.indexOf("</OriginalName>");

		text = text.substring(start + "</OriginalName>".length());

		text = text.trim();

		if (text.startsWith(":")){

			text = text.substring(1);

		}

		text = text.trim();

		return text;

	}

	private Set<TextData> getCitations(Taxon taxon) {

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

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

		for (DescriptionBase description : descriptions){

			Set<DescriptionElementBase> elements = description.getElements();

			for (DescriptionElementBase element : elements){

				Feature feature = element.getFeature();

				if (feature.equals(Feature.CITATION())){

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

						logger.warn("Citation is not of class TextData but " + element.getClass().getSimpleName());

					}else{

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

						result.add(textData);

					}

				}

			}

		}

		return result;

	}

	/**

	 * @param args

	 */

	public static void main(String[] args) {

		DipteraPostImportUpdater updater = new DipteraPostImportUpdater();

		try {

			updater.updateCitations(cdmDestination);

		} catch (Exception e) {

			e.printStackTrace();

			logger.error("ERROR in feature tree update");

		}

	}

}