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.globis;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Map;

import java.util.Set;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import com.yourkit.util.Strings;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.io.algaterra.AlgaTerraCollectionImport;

import eu.etaxonomy.cdm.io.algaterra.AlgaTerraSpecimenImport;

import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonImport;

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

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

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

import eu.etaxonomy.cdm.io.globis.validation.GlobisCurrentSpeciesImportValidator;

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

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

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

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

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

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

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.name.Rank;

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

import eu.etaxonomy.cdm.model.occurrence.Collection;

import eu.etaxonomy.cdm.model.occurrence.FieldObservation;

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

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

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

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

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

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

import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser;

import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;

/**

 * @author a.mueller

 * @created 20.02.2010

 * @version 1.0

 */

@Component

public class GlobisCurrentSpeciesImport  extends GlobisImportBase<Taxon> {

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

	private int modCount = 10000;

	private static final String pluralString = "current taxa";

	private static final String dbTableName = "current_species";

	private static final Class cdmTargetClass = Taxon.class;  //not needed

	public GlobisCurrentSpeciesImport(){

		super(pluralString, dbTableName, cdmTargetClass);

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.globis.GlobisImportBase#getIdQuery()

	 */

	@Override

	protected String getIdQuery() {

		String strRecordQuery = 

			" SELECT IDcurrentspec " + 

			" FROM " + dbTableName; 

		return strRecordQuery;	

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)

	 */

	@Override

	protected String getRecordQuery(GlobisImportConfigurator config) {

		String strRecordQuery = 

			" SELECT cs.*, cs.dtSpcEingabedatum as Created_When, cs.dtSpcErfasser as Created_Who," +

				"  cs.dtSpcBearbeiter as Updated_who, cs.dtSpcAendrgdatum as Updated_When, cs.dtSpcBemerkung as Notes " + 

			" FROM " + getTableName() + " cs " +

			" WHERE ( cs.IDcurrentspec IN (" + ID_LIST_TOKEN + ") )";

		return strRecordQuery;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.globis.GlobisImportBase#doPartition(eu.etaxonomy.cdm.io.common.ResultSetPartitioner, eu.etaxonomy.cdm.io.globis.GlobisImportState)

	 */

	@Override

	public boolean doPartition(ResultSetPartitioner partitioner, GlobisImportState state) {

		boolean success = true;

		Set<TaxonBase> objectsToSave = new HashSet<TaxonBase>();

		Map<String, Taxon> taxonMap = (Map<String, Taxon>) partitioner.getObjectMap(TAXON_NAMESPACE);

//		Map<String, DerivedUnit> ecoFactDerivedUnitMap = (Map<String, DerivedUnit>) partitioner.getObjectMap(ECO_FACT_DERIVED_UNIT_NAMESPACE);

		ResultSet rs = partitioner.getResultSet();

		Classification classification = getClassification(state);

		try {

			int i = 0;

			//for each reference

            while (rs.next()){

        		if ((i++ % modCount) == 0 && i!= 1 ){ logger.info(pluralString + " handled: " + (i-1));}

        		Integer taxonId = rs.getInt("IDcurrentspec");

        		//String dtSpcJahr -> ignore !

        		//empty: fiSpcLiteratur

        		//TODO

        		//fiSpcspcgrptax

				try {

					//source ref

					Reference<?> sourceRef = state.getTransactionalSourceReference();

					Taxon nextHigherTaxon = null;

					boolean hasNewParent = false; //true if any parent is new

					//species

					Taxon species = createObject(rs, state);

					String familyStr = rs.getString("dtSpcFamakt");

					String subFamilyStr = rs.getString("dtSpcSubfamakt");

					String tribeStr = rs.getString("dtSpcTribakt");

					//family

					Taxon family = getTaxon(state, rs, familyStr, null, Rank.FAMILY(), null, taxonMap);

					//subfamily

					Taxon subFamily = getTaxon(state, rs, subFamilyStr, null, Rank.SUBFAMILY(), null, taxonMap);

					Taxon subFamilyParent = getParent(subFamily, classification);

					if (subFamilyParent != null){

						if (! compareTaxa(family, subFamilyParent)){

							logger.warn("Current family and parent of subfamily are not equal: " + taxonId);

						}

					}else{

						classification.addParentChild(family, subFamily, sourceRef, null);

					}

					nextHigherTaxon = subFamily;

					//tribe

					Taxon tribe = getTaxon(state, rs, tribeStr, null, Rank.TRIBE(), null, taxonMap);

					if (tribe != null){

						Taxon tribeParent = getParent(tribe, classification);

						if (tribeParent != null){

							if (! compareTaxa(subFamily, tribeParent)){

								logger.warn("Current subFamily and parent of tribe are not equal: " + taxonId);

							}

						}else{

							classification.addParentChild(subFamily, tribe, sourceRef, null);

						}

						nextHigherTaxon = tribe;

					}					

					//genus

					String genusStr = rs.getString("dtSpcGenusakt");

					String genusAuthorStr = rs.getString("dtSpcGenusaktauthor");

					Taxon genus = getTaxon(state, rs, genusStr, null, Rank.GENUS(), genusAuthorStr, taxonMap);

					Taxon genusParent = getParent(genus, classification);

					if (genusParent != null){

						if (! compareTaxa(genusParent, nextHigherTaxon)){

							logger.warn("Current tribe/subfamily and parent of genus are not equal: " + taxonId);

						}

					}else{

						classification.addParentChild(nextHigherTaxon, genus, sourceRef, null);

					}

					nextHigherTaxon = genus;

					//subgenus

					String subGenusStr = CdmBase.deproxy(species.getName(), ZoologicalName.class).getInfraGenericEpithet();

					String subGenusAuthorStr = rs.getString("dtSpcSubgenaktauthor");

					boolean hasSubgenus = StringUtils.isNotBlank(subGenusStr) || StringUtils.isNotBlank(subGenusAuthorStr);

					if (hasSubgenus){

						Taxon subGenus = getTaxon(state, rs, genusStr, subGenusStr, Rank.SUBGENUS(), subGenusAuthorStr, taxonMap);

						classification.addParentChild(nextHigherTaxon, subGenus, sourceRef, null);

						nextHigherTaxon = subGenus;

					}

					classification.addParentChild(nextHigherTaxon, species, sourceRef, null);

					handleCountries(state, rs, species);

					handleCommonNames(state, rs, species);

					this.doIdCreatedUpdatedNotes(state, species, rs, taxonId, TAXON_NAMESPACE);

					objectsToSave.add(species); 

				} catch (Exception e) {

					logger.warn("Exception in current_species: IDcurrentspec " + taxonId + ". " + e.getMessage());

//					e.printStackTrace();

				} 

            }

//            logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );

			logger.warn(pluralString + " to save: " + objectsToSave.size());

			getTaxonService().save(objectsToSave);	

			return success;

		} catch (SQLException e) {

			logger.error("SQLException:" +  e);

			return false;

		}

	}

	private void handleCountries(GlobisImportState state, ResultSet rs, Taxon species) throws SQLException {

		String countriesStr = rs.getString("dtSpcCountries");

		if (isBlank(countriesStr)){

			return;

		}

		String[] countriesSplit = countriesStr.split(";");

		for (String countryStr : countriesSplit){

			if (isBlank(countryStr)){

				continue;

			}

			countryStr = countryStr.trim();

			//TODO use isComplete

			boolean isComplete = countryStr.endsWith(".");

			if (isComplete){

				countryStr = countryStr.substring(0,countryStr.length() - 1).trim();

			}

			boolean isDoubtful = countryStr.endsWith("[?]");

			if (isDoubtful){

				countryStr = countryStr.substring(0,countryStr.length() - 3).trim();

			}

			if (countryStr.startsWith("?")){

				isDoubtful = true;

				countryStr = countryStr.substring(1).trim();

			}

			countryStr = normalizeCountry(countryStr);

			WaterbodyOrCountry country = getCountry(state, countryStr);

			PresenceTerm status;

			if (isDoubtful){

				status = PresenceTerm.PRESENT_DOUBTFULLY();

			}else{

				status = PresenceTerm.PRESENT();

			}

			if (country != null){

				TaxonDescription desc = getTaxonDescription(species, state.getTransactionalSourceReference(), false, true);

				Distribution distribution = Distribution.NewInstance(country, status);

				desc.addElement(distribution);

			}else{

				logger.warn("Country string not recognized: " + countryStr);

			}

		}

	}

	/**

	 * @param countryStr

	 * @return

	 */

	private String normalizeCountry(String countryStr) {

		String result = countryStr.trim();

		if (result.endsWith(".")){

			result = result.substring(0,result.length() - 1);

		}

		return result; 

	}

	private void handleCommonNames(GlobisImportState state, ResultSet rs, Taxon species) throws SQLException {

		//DON't use, use seperate common name tables instead

//		String commonNamesStr = rs.getString("vernacularnames");

//		if (isBlank(commonNamesStr)){

//			return;

//		}

//		String[] commonNamesSplit = commonNamesStr.split(";");

//		for (String commonNameStr : commonNamesSplit){

//			if (isBlank(commonNameStr)){

//				continue;

//			}

//			Language language = null; //TODO

//			CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameStr, language);

//			TaxonDescription desc = getTaxonDescription(species, state.getTransactionalSourceReference(), false, true);

//			desc.addElement(commonName);

//		}

	}

	/**

	 * Compares 2 taxa, returns true of both taxa look similar

	 * @param genus

	 * @param nextHigherTaxon

	 * @return

	 */

	private boolean compareTaxa(Taxon taxon1, Taxon taxon2) {

		ZoologicalName name1 = CdmBase.deproxy(taxon1.getName(), ZoologicalName.class);

		ZoologicalName name2 = CdmBase.deproxy(taxon2.getName(), ZoologicalName.class);

		if (!name1.getRank().equals(name2.getRank())){

			return false;

		}

		if (! name1.getTitleCache().equals(name2.getTitleCache())){

			return false;

		}

		return true;

	}

	private Taxon getParent(Taxon child, Classification classification) {

		for (TaxonNode node :  child.getTaxonNodes()){

			if (node.getClassification().equals(classification)){

				if (node.getParent() != null){

					return node.getParent().getTaxon();	

				}else{

					return null;

				}

			}

		}

		return null;

	}

	private Taxon getTaxon(GlobisImportState state, ResultSet rs, String uninomial, String infraGenericEpi, Rank rank, String author, Map<String, Taxon> taxonMap) {

		if (isBlank(uninomial)){

			return null;

		}

		String keyEpithet = StringUtils.isNotBlank(infraGenericEpi)? infraGenericEpi : uninomial ;

		String key = keyEpithet + "@" + CdmUtils.Nz(author) + "@" + rank.getTitleCache();

		Taxon taxon = taxonMap.get(key);

		if (taxon == null){

			ZoologicalName name = ZoologicalName.NewInstance(rank);

			name.setGenusOrUninomial(uninomial);

			if (isNotBlank(infraGenericEpi)){

				name.setInfraGenericEpithet(infraGenericEpi);

			}

			taxon = Taxon.NewInstance(name, state.getTransactionalSourceReference());

			taxonMap.put(key, taxon);

			handleAuthorAndYear(author, name);

			getTaxonService().save(taxon);

		}

		return taxon;

	}

	//fast and dirty is enough here

	private Classification classification;

	private Classification getClassification(GlobisImportState state) {

		if (this.classification == null){

			String name = state.getConfig().getClassificationName();

			Reference<?> reference = state.getTransactionalSourceReference();

			this.classification = Classification.NewInstance(name, reference, Language.DEFAULT());

			classification.setUuid(state.getConfig().getClassificationUuid());

			getClassificationService().save(classification);

		}

		return this.classification;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.mapping.IMappingImport#createObject(java.sql.ResultSet, eu.etaxonomy.cdm.io.common.ImportStateBase)

	 */

	public Taxon createObject(ResultSet rs, GlobisImportState state)

			throws SQLException {

		String speciesEpi = rs.getString("dtSpcSpcakt");

		String subGenusEpi = rs.getString("dtSpcSubgenakt");

		String genusEpi = rs.getString("dtSpcGenusakt");

		String author = rs.getString("dtSpcAutor");

		ZoologicalName zooName = ZoologicalName.NewInstance(Rank.SPECIES());

		zooName.setSpecificEpithet(speciesEpi);

		if (StringUtils.isNotBlank(subGenusEpi)){

			zooName.setInfraGenericEpithet(subGenusEpi);

		}

		zooName.setGenusOrUninomial(genusEpi);

		handleAuthorAndYear(author, zooName);

		Taxon taxon = Taxon.NewInstance(zooName, state.getTransactionalSourceReference());

		return taxon;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)

	 */

	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {

		String nameSpace;

		Class cdmClass;

		Set<String> idSet;

		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();

		try{

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

			while (rs.next()){

//				handleForeignKey(rs, taxonIdSet, "taxonId");

			}

			//taxon map

			nameSpace = TAXON_NAMESPACE;

			cdmClass = Taxon.class;

			idSet = taxonIdSet;

			Map<String, Taxon> objectMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, objectMap);

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

		return result;

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected boolean doCheck(GlobisImportState state){

		IOValidator<GlobisImportState> validator = new GlobisCurrentSpeciesImportValidator();

		return validator.validate(state);

	}

	/* (non-Javadoc)

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

	 */

	protected boolean isIgnore(GlobisImportState state){

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

	}

}