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app-import/src/main/java/eu/etaxonomy/cdm/io/globis/GlobisCommonNameImport.java -text

/**

* 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 eu.etaxonomy.cdm.common.CdmUtils;

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

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

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

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

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

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.WaterbodyOrCountry;

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

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

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;

/**

 * @author a.mueller

 * @created 20.02.2010

 * @version 1.0

 */

@Component

public class GlobisCommonNameImport  extends GlobisImportBase<Taxon> {

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

	private int modCount = 10000;

	private static final String pluralString = "common names";

	private static final String dbTableName = "species_language";

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

	public GlobisCommonNameImport(){

		super(pluralString, dbTableName, cdmTargetClass);

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected String getIdQuery() {

		String strRecordQuery = 

			" SELECT ID " + 

			" 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 * " + 

			" FROM " + getTableName() + " sl " +

			" WHERE ( sl.ID 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();

		try {

			int i = 0;

			//for each common name

            while (rs.next()){

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

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

        		//String dtSpcJahr -> ignore !

        		//empty: fiSpcLiteratur

        		//TODO

        		//fiSpcspcgrptax

				try {

					//source ref

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

					//species

					Taxon species = createObject(rs, state);

					handleCountries(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; 

	}

	/* (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();

	}

}