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.wp6;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import org.hibernate.criterion.Criterion;

import org.springframework.stereotype.Component;

import eu.etaxonomy.cdm.common.CdmUtils;

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

import eu.etaxonomy.cdm.io.excel.common.ExcelImporterBase;

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.persistence.query.OrderHint;

/**

 * @author a.babadshanjan

 * @created 08.01.2009

 * @version 1.0

 */

@Component

public class CommonNameExcelImport extends ExcelImporterBase<CichorieaeCommonNameImportState> {

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

	protected static final String SPECIES_COLUMN = "Art";

	protected static final String COMMON_NAME_COLUMN = "common name";

	protected static final String REFERENCE_COLUMN = "Literaturnummer";

	protected static final String DISTIRBUTION_COLUMN = "Verbreitung";

	protected static final String AREA_COLUMN = "Vorschlag Bezeichnung L?nder/Regionen";

	private Map<String, NamedArea> areaStore = new HashMap<String, NamedArea>();

	private Map<String, Language> languageStore = new HashMap<String, Language>();

	@Override

	protected boolean isIgnore(CichorieaeCommonNameImportState state) {

		return false;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)

	 */

	@Override

	protected boolean doCheck(CichorieaeCommonNameImportState state) {

		logger.warn("DoCheck not yet implemented for CommonNameExcelImport");

		return true;

	}

	@Override

    protected void analyzeRecord(HashMap<String, String> record, CichorieaeCommonNameImportState state) {

		Set<String> keys = record.keySet();

    	CommonNameRow row = new CommonNameRow();

    	state.setCommonNameRow(row);

    	for (String originalKey: keys) {

    		String indexedKey = CdmUtils.removeDuplicateWhitespace(originalKey.trim()).toString();

    		String[] split = indexedKey.split("_");

    		String key = split[0];

    		if (split.length > 1){

    			String indexString = split[1];

    			try {

    				Integer.valueOf(indexString);

				} catch (NumberFormatException e) {

					String message = "Index must be integer";

					logger.error(message);

					continue;

				}

    		}

    		String value = (String) record.get(indexedKey);

    		if (! StringUtils.isBlank(value)) {

    			if (logger.isDebugEnabled()) { logger.debug(key + ": " + value); }

        		value = CdmUtils.removeDuplicateWhitespace(value.trim()).toString();

    		}else{

    			continue;

    		}

    		if (key.equalsIgnoreCase(SPECIES_COLUMN)) {

    			row.parseSpecies(value);

			} else if(key.equalsIgnoreCase(COMMON_NAME_COLUMN)) {

				row.setCommonNames(value);

			} else if(key.equalsIgnoreCase(REFERENCE_COLUMN)) {

				row.setReference(value);

			} else if(key.equalsIgnoreCase(DISTIRBUTION_COLUMN)) {

				//do nothing

			} else if(key.equalsIgnoreCase(AREA_COLUMN)) {

				row.setArea(value);

 			} else {

				state.setUnsuccessfull();

				logger.error("Unexpected column header " + key);

			}

    	}

    	return;

    }

	/** 

	 *  Stores taxa records in DB

	 */

	@Override

    protected void firstPass(CichorieaeCommonNameImportState state) {

		CommonNameRow taxonLight = state.getCommonNameRow();

		//species name

		String speciesStr = taxonLight.getSpecies();

		TaxonDescription taxonDesc = getTaxon(state, speciesStr);

		Reference ref = getReference(state, taxonLight);

		NamedArea area = getArea(state, taxonLight.getArea());

		makeCommonNames(state, taxonLight.getCommonNames(), taxonDesc, ref, area, taxonLight.getNameUsedInSource());

//		OLD 

//		TaxonNameBase nameUsedInSource = getNameUsedInSource(state, taxonLight.getNameUsedInSource());

		getTaxonService().save(taxonDesc.getTaxon());

		return;

    }

	private Map<String, Reference> referenceStore = new HashMap<String, Reference>();

	private Reference getReference(CichorieaeCommonNameImportState state, CommonNameRow taxonLight) {

		String reference = taxonLight.getReference();

		Reference result = referenceStore.get(reference);

		if (result == null){

			result = (Reference)getCommonService().getSourcedObjectByIdInSource(Reference.class, reference, "import to Berlin Model");

			if (result == null){

				logger.warn("Reference not found: " + reference + " for taxon " + taxonLight.getSpecies());

//				result = ReferenceFactory.newGeneric();

//				result.setTitleCache(reference);

			}else{

				referenceStore.put(reference, result);

			}

		}

		return result;

	}

	private NamedArea getArea(CichorieaeCommonNameImportState state, String area) {

		NamedArea result;

		List<OrderHint> orderHints = null;

		List<Criterion> criteria = null;

		result = areaStore.get(area);

		if (result == null){

			try {

				result = state.getTransformer().getNamedAreaByKey(area);

			} catch (UndefinedTransformerMethodException e) {

				e.printStackTrace();

			}

			if (result == null){

				List<DefinedTermBase> candidates = getTermService().findByTitle(WaterbodyOrCountry.class, area, null, criteria, null, null, orderHints, null).getRecords();

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

					candidates = getTermService().findByTitle(NamedArea.class, area, null, criteria, null, null, orderHints, null).getRecords();

				}

				if (candidates.size()>0){

					//TODO

					result = (NamedArea)candidates.get(0);

				}else{

					UUID uuidArea;

					try {

						uuidArea = state.getTransformer().getNamedAreaUuid(area);

						if (uuidArea == null){

							logger.warn("Area not defined: " + area)  ;

						}

						result = getNamedArea(state, uuidArea, area, area, null, null, null);

					} catch (UndefinedTransformerMethodException e) {

						e.printStackTrace();

					}

					if (result == null){

						logger.warn("Area not defined: " + area)  ;

					}

				}

			}

			areaStore.put(area, result);

		}

		return result;

	}

	Map<String, TaxonDescription> taxonStore = new HashMap<String, TaxonDescription>();

	private TaxonDescription getTaxon(CichorieaeCommonNameImportState state, String taxonNameStr) {

		TaxonDescription desc;

		Taxon taxon;

		if (taxonStore.get(taxonNameStr) != null){

			desc = taxonStore.get(taxonNameStr);

		}else{

			taxon = getTaxonService().findBestMatchingTaxon(taxonNameStr);

//			TaxonNameBase name = BotanicalName.NewInstance(Rank.SPECIES());

//			name.setTitleCache(taxonNameStr, true);

//			

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

			if (taxon == null){

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

				desc = null;

			}else{

				desc = getNewDescription(state, taxon);

				taxonStore.put(taxonNameStr, desc);

			}

		}

		return desc;

	}

	private TaxonDescription getNewDescription(CichorieaeCommonNameImportState state, Taxon taxon) {

		Reference excelRef = state.getConfig().getSourceReference();

		TaxonDescription desc = TaxonDescription.NewInstance(taxon, false);

		desc.setTitleCache("Common Names Excel import", true);

		desc.addSource(null, null, excelRef, null);

		return desc;

	}

	private void makeCommonNames(CichorieaeCommonNameImportState state, Map<String, List<String>> commonNamesMap, TaxonDescription description, Reference ref, NamedArea area, String nameUsedInSource) {

		//Common Names

//		TaxonDescription td = this.getTaxonDescription(mainTaxon, false, true);

		for (String languageKey : commonNamesMap.keySet()){

			Language language = getLanguage(state, languageKey);

			List<String> commonNamesList = commonNamesMap.get(languageKey);

			for (String strCommonName : commonNamesList){

				CommonTaxonName commonName = CommonTaxonName.NewInstance(strCommonName, language, area);

				if (ref != null || StringUtils.isNotBlank(nameUsedInSource)){

					DescriptionElementSource source = DescriptionElementSource.NewInstance(ref, null);

					source.setOriginalNameString(nameUsedInSource);

					commonName.addSource(source);

				}else{

					logger.debug("No reference defined");

				}

				description.addElement(commonName);

			}

		}

	}

	private Language getLanguage(CichorieaeCommonNameImportState state, String languageKey) {

		if (languageKey.equals("*")){

			return null;

		}

		Language result;

		languageKey = languageKey.replace(", no ISO-Code", "");

		result = languageStore.get(languageKey);

		if (result == null){

			try{

				if (languageKey.length()<4){

					try {

						result = getTermService().getLanguageByIso(languageKey);

					} catch (Exception e) {

						// TODO Auto-generated catch block

						e.printStackTrace();

					}

				}else{

					UUID uuid = state.getTransformer().getLanguageUuid(languageKey);

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

				}

				if (result == null){

					result = state.getTransformer().getLanguageByKey(languageKey);

					if (result == null){

						UUID uuidLanguage;

						uuidLanguage = state.getTransformer().getLanguageUuid(languageKey);

						if (uuidLanguage == null){

							logger.warn("Language not defined: " + languageKey)  ;

						}

						result = getLanguage(state, uuidLanguage, languageKey, languageKey, null);

						if (result == null){

							logger.warn("Language not defined: " + languageKey)  ;

						}

					}else if (result.getId() == 0){

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

						UUID uuidLanguageVoc = UUID.fromString("434cea89-9052-4567-b2db-ff77f42e9084"); 

						TermVocabulary<Language> voc = getVocabulary(uuidLanguageVoc, "User Defined Languages", "User Defined Languages", null, null, false, result);

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

						voc.addTerm(result);

						getTermService().saveOrUpdate(result);

						state.putLanguage(result);

					}

				}

				languageStore.put(languageKey, result);

			} catch (UndefinedTransformerMethodException e) {

				e.printStackTrace();

			}

		}

		return result;

	}

	/** 

	 *  Stores parent-child, synonym and common name relationships

	 */

	@Override

    protected void secondPass(CichorieaeCommonNameImportState state) {

		//no second pass

		return;

	}

//	private TaxonNameBase getNameUsedInSource(CichorieaeCommonNameImportState state, String nameUsedInSource) {

//		if (StringUtils.isBlank(nameUsedInSource)){

//			return null;

//		}else{

//			Pager<TaxonNameBase> list = getNameService().findByName(BotanicalName.class, nameUsedInSource, null, null, null, null, null, null);

//			if (list.getCount() > 0){

//				return list.getRecords().get(0);

//			}else{

//				return null;

//			}

//		}

//		

//	}

}