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.taxonx;

import java.util.HashMap;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import org.apache.log4j.Logger;

import org.jdom.Attribute;

import org.jdom.Content;

import org.jdom.Element;

import org.jdom.Namespace;

import org.jdom.Text;

import org.springframework.stereotype.Component;

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

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

import eu.etaxonomy.cdm.common.CdmUtils;

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

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

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

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

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

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

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.reference.Reference;

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

import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;

/**

 * @author a.mueller

 * @created 29.07.2008

 * @version 1.0

 */

@Component

public class TaxonXDescriptionImport extends CdmIoBase<TaxonXImportState> implements ICdmIO<TaxonXImportState> {

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

	public TaxonXDescriptionImport(){

		super();

	}

	public boolean doCheck(TaxonXImportState state){

		boolean result = true;

		logger.warn("Checking for Facts not yet implemented");

		//result &= checkArticlesWithoutJournal(bmiConfig);

		return result;

	}

	public Map<Integer, Feature> fillFactCategories(IImportConfigurator config, CdmApplicationDefaultController cdmApp){

		logger.warn("not yet implemented");

		Map<Integer, Feature> featureMap = new HashMap<Integer, Feature>();

//		IDescriptionService descriptionService = cdmApp.getDescriptionService();

//		ITermService termService = cdmApp.getTermService();

//

//		Object source = config.getSource();

		return featureMap;

	}

	private String getDescriptionTitle(TaxonXImportState state){

		String result = "Untitled";

		Reference<?> ref = state.getModsReference();

		if (ref != null){

			result = ref.getTitle();

			if ( CdmUtils.isEmpty(result)){

				result = ref.getTitleCache();

			}

		}

		return result;

	}

	public void doInvoke(TaxonXImportState state){

		logger.debug("not yet fully implemented");

		TaxonXImportConfigurator txConfig = state.getConfig();

		Element root = txConfig.getSourceRoot();

		Namespace nsTaxonx = root.getNamespace();

		//Object source = config.getSource();

		logger.info("start make Descriptions ...");

		//for testing only

		Taxon taxon = getTaxon(txConfig);

		if (taxon == null){

			logger.warn("Taxon could not be found");

			state.setUnsuccessfull();

		}

		Reference modsReference = state.getModsReference();

		if (modsReference == null){

			modsReference = state.getConfig().getSourceReference();

		}

		//unlazyDescription(txConfig, taxon);

		TaxonDescription description = TaxonDescription.NewInstance();

		description.setTitleCache(getDescriptionTitle(state), true);

		if (modsReference != null){

			description.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, modsReference, null);

		}

		Element elTaxonBody = root.getChild("taxonxBody", nsTaxonx);

		Element elTreatment = elTaxonBody.getChild("treatment", nsTaxonx);

		List<Element> elDivs = elTreatment.getChildren("div", nsTaxonx);

		for (Element div : elDivs){

			Attribute attrType = div.getAttribute("type", nsTaxonx);

			String strType = attrType.getValue();

			Feature feature = null;

			try {

				feature = TaxonXTransformer.descriptionType2feature(strType);

			} catch (UnknownCdmTypeException e) {

				feature = handleFeatureException(strType, e, txConfig);

			}

			String text = getText(div);

			if (!"".equals(CdmUtils.Nz(text).trim())){

				// hibernate throws an exception when a string is longer than approx. 65500 chars.

				// for now we truncate any description text to 65500 characters.

				if(text.length() > 65500){

					text = text.substring(0, 65500) + "... [text truncated]";

					logger.warn("Truncation of text: description for taxon " + taxon.getTitleCache() + " was longer than 65500 characters.");

				}

				DescriptionElementBase descriptionElement = TextData.NewInstance(text, Language.ENGLISH(), null);

				descriptionElement.setFeature(feature);

				description.addElement(descriptionElement);

				//add reference

				if (modsReference != null){

					descriptionElement.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, modsReference, null, null, null);

				}

			}

		}

		if (description.size() >0){

			taxon.addDescription(description);

			getTaxonService().save(taxon);

		}

		return;

	}

	private Feature handleFeatureException(String strType, UnknownCdmTypeException e, TaxonXImportConfigurator txConfig){

		Feature feature = null;

		TermVocabulary<Feature> featureVoc = Feature.BIOLOGY_ECOLOGY().getVocabulary();

		for (Feature oneFeature : featureVoc.getTerms()){

			if (strType.equals(oneFeature.getLabel()) || strType.equals(oneFeature.getRepresentation(Language.DEFAULT() ).getText() )){

				feature = oneFeature;

			}

		}

		if (feature == null){

			feature = Feature.NewInstance(strType, strType, null);

			featureVoc.addTerm(feature);

			getTermService().save(feature);

			logger.warn(e.getMessage() + ". Feature was added to the feature vocabulary. " + getBracketSourceName(txConfig));

		}

		return feature;

	}

	private String getText(Element div){

		String result = "";

		Iterator<Content> it =div.getDescendants(); 

		while (it.hasNext()){

			Content next = (Content)it.next();

			if (next instanceof Text){

				result += ((Text)next).getText();

			}

		}

		return result;

	}

	private Taxon getTaxon(TaxonXImportConfigurator config){

		Taxon result;

//		result =  Taxon.NewInstance(BotanicalName.NewInstance(null), null);

		ICommonService commonService = getCommonService();

		String originalSourceId = config.getOriginalSourceId();

		String namespace = config.getOriginalSourceTaxonNamespace();

		result = (Taxon)commonService.getSourcedObjectByIdInSource(Taxon.class, originalSourceId , namespace);

		if (result == null){

			logger.warn("Taxon (id: " + originalSourceId + ", namespace: " + namespace + ") could not be found");

		}

		return result;

	}

	private void unlazyDescription(TaxonXImportConfigurator config, Taxon taxon){

//		logger.warn("Preliminary commented");  //used single Transaction for all import instead !

//		TransactionStatus txStatus = config.getCdmAppController().startTransaction();

//		ITaxonService taxonService = config.getCdmAppController().getTaxonService();

//		taxonService.saveTaxon(taxon);

//		taxon.getDescriptions().size();

//		config.getCdmAppController().commitTransaction(txStatus);

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)

	 */

	protected boolean isIgnore(TaxonXImportState state){

		return ! state.getConfig().isDoFacts();

	}

	private String getBracketSourceName(TaxonXImportConfigurator config){

		return "(" + config.getSourceNameString() + ")";

	}

}