EDIT

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsAreaImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsDrImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsImageImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsImportBase.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsImportConfigurator.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsImportRankMap.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsImportState.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsLinkImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsNotesImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsNotesSourcesImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsReferenceImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsSourceUsesImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsTaxonImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsTaxonRelationImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsTransformer.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsVernacularImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsVernacularSourcesImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/validation/ErmsAreaImportValidator.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/validation/ErmsGeneralImportValidator.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/validation/ErmsImageImportValidator.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/validation/ErmsLinkImportValidator.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/validation/ErmsNoteImportValidator.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/validation/ErmsRankImportValidator.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/validation/ErmsReferenceImportValidator.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/validation/ErmsSourceUsesImportValidator.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/validation/ErmsTaxonImportValidator.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/validation/ErmsVernacularSourceImportValidator.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaAdditionalTaxonDataImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaAuthorImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaDistribution.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaDistributionImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaDistributionTaxon.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaHeterotypicSynonymImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaImportBase.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaImportConfigurator.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaImportState.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaRefImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaReference.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaReferenceTaxon.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaRelTaxonIncludeImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaTaxon.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaTaxonNameImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaTransformer.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaUsersImport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/merging/FaunaEuErmsMerging.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiAdditionalTaxonSourceExport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiCollectionExportMapping.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiExportBase.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiExportConfigurator.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiExportMapping.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiExportState.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiImageExport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiNoteExport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiNoteSourceExport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiOccurrenceExport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiOccurrenceSourceExport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiRelTaxonExport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiSourceExport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTaxonExport.java -text

cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/out/PesiTransformer.java -text

cdm-pesi/src/test/java/eu/etaxonomy/cdm/io/erms/ermsErrors.txt -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.pesi.erms;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashMap;

import java.util.Map;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.io.pesi.erms.validation.ErmsAreaImportValidator;

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

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

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

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

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

/**

 * @author a.mueller

 * @created 20.02.2010

 * @version 1.0

 */

@Component

public class ErmsAreaImport  extends ErmsImportBase<NamedArea> implements IMappingImport<NamedArea, ErmsImportState>{

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

	private DbImportMapping mapping;

	private int modCount = 10000;

	private static final String pluralString = "areas";

	private static final String dbTableName = "gu";

	private static final Class cdmTargetClass = NamedArea.class;

	public ErmsAreaImport(){

		super(pluralString, dbTableName, cdmTargetClass);

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected String getRecordQuery(ErmsImportConfigurator config) {

		String strRecordQuery = 

			" SELECT * " + 

			" FROM gu " +

			" WHERE ( gu.id IN (" + ID_LIST_TOKEN + ") )";

		return strRecordQuery;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getMapping()

	 */

	protected DbImportMapping getMapping() {

		if (mapping == null){

			mapping = new DbImportMapping();

			mapping.addMapper(DbImportObjectCreationMapper.NewInstance(this, "id", AREA_NAMESPACE)); //id

			mapping.addMapper(DbImportStringMapper.NewInstance("gu_name", "titleCache"));

			mapping.addMapper(DbImportExtensionMapper.NewInstance("gazetteer_id", ErmsTransformer.GAZETTEER_UUID, "Gazetteer ID", "Gazetteer ID", "G-ID"));

			mapping.addMapper(DbImportAnnotationMapper.NewInstance("note", AnnotationType.EDITORIAL()));

		}

		return mapping;

	}

	/* (non-Javadoc)

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

	 */

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

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

		return result;  //not needed

	}

	/* (non-Javadoc)

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

	 */

	public NamedArea createObject(ResultSet rs, ErmsImportState state) throws SQLException {

		int id = rs.getInt("id");

		String strGuName = rs.getString("gu_name");

		UUID uuid = ErmsTransformer.uuidFromGuName(strGuName);

		String label = strGuName;

		String text = strGuName;

		//TODO

		String labelAbbrev = String.valueOf(id);

		NamedAreaType areaType = null;

		NamedAreaLevel level = null;

		NamedArea area = getNamedArea(state, uuid, label, text, labelAbbrev, areaType, level);

		return area;

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected boolean doCheck(ErmsImportState state){

		IOValidator<ErmsImportState> validator = new ErmsAreaImportValidator();

		return validator.validate(state);

	}

	/* (non-Javadoc)

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

	 */

	protected boolean isIgnore(ErmsImportState state){

		//TODO

//		return ! state.getConfig().isDoAreas();

		return false;

	}

}

/**

* 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.pesi.erms;

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.log4j.Logger;

import org.springframework.stereotype.Component;

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.io.pesi.erms.validation.ErmsReferenceImportValidator;

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

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

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

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

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

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

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

/**

 * @author a.mueller

 * @created 20.02.2010

 * @version 1.0

 */

@Component

public class ErmsDrImport  extends ErmsImportBase<Distribution> {

	@SuppressWarnings("unused")

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

	private DbImportMapping mapping;

	private int modCount = 10000;

	private static final String pluralString = "distributions";

	private static final String dbTableName = "dr";

	private static final Class cdmTargetClass = Distribution.class;

	public ErmsDrImport(){

		super(pluralString, dbTableName, cdmTargetClass);

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected String getRecordQuery(ErmsImportConfigurator config) {

		String strRecordQuery = 

			" SELECT dr.*, tu.tu_acctaxon, tu.id " + 

			" FROM dr INNER JOIN tu ON dr.tu_id = tu.id " +

			" WHERE ( dr.id IN (" + ID_LIST_TOKEN + ") )";

		return strRecordQuery;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getMapping()

	 */

	protected DbImportMapping getMapping() {

		if (mapping == null){

			mapping = new DbImportMapping();

			PresenceTerm status = PresenceTerm.PRESENT();

			DbImportDistributionCreationMapper<?> distributionMapper = DbImportDistributionCreationMapper.NewFixedStatusInstance("id", DR_NAMESPACE, "tu_acctaxon", ErmsTaxonImport.TAXON_NAMESPACE, status);

			distributionMapper.setSource("source_id", REFERENCE_NAMESPACE, null);

			mapping.addMapper(distributionMapper);

			mapping.addMapper(DbImportObjectMapper.NewInstance("gu_id", "area", ErmsAreaImport.AREA_NAMESPACE));

			mapping.addMapper(DbImportAnnotationMapper.NewInstance("note", AnnotationType.EDITORIAL()));

			mapping.addMapper(DbIgnoreMapper.NewInstance("unacceptsource_id"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("unacceptreason"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("valid_flag"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("certain_flag"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("map_flag"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("endemic_flag"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("exotic_flag"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("typelocality_flag"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("specimenflag"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("lat"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("long"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("depthshallow"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("depthdeep"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("beginyear"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("beginmonth"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("beginday"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("endyear"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("endmonth"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("endday"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("min_abundance"));

			mapping.addMapper(DbIgnoreMapper.NewInstance("max_abundance"));

		}

		return mapping;

	}

	/* (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>();

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

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

			while (rs.next()){

				handleForeignKey(rs, taxonIdSet,"tu_acctaxon" );

				handleForeignKey(rs, areaIdSet, "gu_id");

				handleForeignKey(rs, sourceIdSet, "source_id");

			}

			//taxon map

			nameSpace = ErmsTaxonImport.TAXON_NAMESPACE;

			cdmClass = TaxonBase.class;

			idSet = taxonIdSet;

			Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, taxonMap);

			//areas

			nameSpace = ErmsAreaImport.AREA_NAMESPACE;

			cdmClass = NamedArea.class;

			idSet = areaIdSet;

			Map<String, NamedArea> areaMap = (Map<String, NamedArea>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, areaMap);

			//reference map

			nameSpace = ErmsReferenceImport.REFERENCE_NAMESPACE;

			cdmClass = Reference.class;

			idSet = sourceIdSet;

			Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, referenceMap);

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

		return result;

	}

	/**

	 * @param distribution

	 * @param source_id

	 * @param state 

	 */

	private void addSource(Distribution distribution, Integer source_id, ErmsImportState state) {

		Reference ref = (Reference)state.getRelatedObject(ErmsReferenceImport.REFERENCE_NAMESPACE, String.valueOf(source_id));

		distribution.addSource(null, null, ref, null);

	}

	/* (non-Javadoc)

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

	 */

	public Distribution createObject(ResultSet rs, ErmsImportState state)

			throws SQLException {

		return null;  //not needed

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected boolean doCheck(ErmsImportState state){

		IOValidator<ErmsImportState> validator = new ErmsReferenceImportValidator();

		return validator.validate(state);

	}

	/* (non-Javadoc)

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

	 */

	protected boolean isIgnore(ErmsImportState state){

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

	}

}

/**

* 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.pesi.erms;

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.log4j.Logger;

import org.springframework.stereotype.Component;

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

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

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

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

import eu.etaxonomy.cdm.io.pesi.erms.validation.ErmsImageImportValidator;

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

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

import eu.etaxonomy.cdm.model.media.Media;

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

/**

 * @author a.mueller

 * @created 20.02.2010

 * @version 1.0

 */

@Component

public class ErmsImageImport  extends ErmsImportBase<TextData> {

	@SuppressWarnings("unused")

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

	private DbImportMapping mapping;

	private int modCount = 10000;

	private static final String pluralString = "images";

	private static final String dbTableName = "images";

	private static final Class cdmTargetClass = Media.class;

	public ErmsImageImport(){

		super(pluralString, dbTableName, cdmTargetClass);

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getIdQuery()

	 */

	@Override

	protected String getIdQuery() {

		String strIdQuery = 

			" SELECT tu_id, img_thumb " +   //tu_id is not a key

			" FROM images " + 

			" ORDER BY tu_id, img_thumb, img_url ";

		return strIdQuery;

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected String getRecordQuery(ErmsImportConfigurator config) {

		String strRecordQuery = 

			" SELECT * " + 

			" FROM images " +

			" WHERE ( images.tu_id IN (" + ID_LIST_TOKEN + ") AND " +

				"  images.img_thumb IN (" + ID_LIST_TOKEN + ")  )";

		return strRecordQuery;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getMapping()

	 */

	protected DbImportMapping getMapping() {

		if (mapping == null){

			mapping = new DbImportMapping();

			//TODO do we need to add to TaxonNameBase too?

			String idAttribute = null;

			boolean isOneTextData = true;

			mapping.addMapper(DbImportImageCreationMapper.NewInstance(idAttribute, IMAGE_NAMESPACE, "tu_id", ErmsTaxonImport.TAXON_NAMESPACE, isOneTextData));

			mapping.addMapper(DbImportMediaMapper.NewInstance("img_url", "img_thumb"));

		}

		return mapping;

	}

	/* (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>();

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

			while (rs.next()){

				handleForeignKey(rs, taxonIdSet, "tu_id");

			}

			//taxon map

			nameSpace = ErmsTaxonImport.TAXON_NAMESPACE;

			cdmClass = TaxonBase.class;

			idSet = taxonIdSet;

			Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, taxonMap);

		} 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(ErmsImportState state){

		IOValidator<ErmsImportState> validator = new ErmsImageImportValidator();

		return validator.validate(state);

	}

	/* (non-Javadoc)

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

	 */

	protected boolean isIgnore(ErmsImportState state){

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

	}

}

/**

* 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.pesi.erms;

import java.lang.reflect.Method;

import java.sql.ResultSet;

import java.sql.ResultSetMetaData;

import java.sql.SQLException;

import java.sql.Timestamp;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.joda.time.DateTime;

import eu.etaxonomy.cdm.common.CdmUtils;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/**

 * @author a.mueller

 * @created 20.03.2008

 * @version 1.0

 */

public abstract class ErmsImportBase<CDM_BASE extends CdmBase> extends CdmImportBase<ErmsImportConfigurator, ErmsImportState> implements ICdmIO<ErmsImportState>, IPartitionedIO<ErmsImportState> {

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

	public static final UUID ID_IN_SOURCE_EXT_UUID = UUID.fromString("23dac094-e793-40a4-bad9-649fc4fcfd44");

	//NAMESPACES

	protected static final String AREA_NAMESPACE = "gu";

	protected static final String DR_NAMESPACE = "dr";

	protected static final String IMAGE_NAMESPACE = "Images";

	protected static final String LINKS_NAMESPACE = "Links";

	protected static final String NOTES_NAMESPACE = "Notes";

	protected static final String LANGUAGE_NAMESPACE = "Language";

	protected static final String REFERENCE_NAMESPACE = "Source";

	protected static final String SOURCEUSE_NAMESPACE = "tu_sources";

	protected static final String TAXON_NAMESPACE = "Taxon";

	protected static final String NAME_NAMESPACE = "TaxonName";

	protected static final String VERNACULAR_NAMESPACE = "Vernaculars";

	protected static final String FEATURE_NAMESPACE = "note.type";

	protected static final String EXTENSION_TYPE_NAMESPACE = "ExtensionType";

	private String pluralString;

	private String dbTableName;

	//TODO needed?

	private Class cdmTargetClass;

	/**

	 * @param dbTableName

	 * @param dbTableName2 

	 */

	public ErmsImportBase(String pluralString, String dbTableName, Class cdmTargetClass) {

		this.pluralString = pluralString;

		this.dbTableName = dbTableName;

		this.cdmTargetClass = cdmTargetClass;

	}

	protected void doInvoke(ErmsImportState state){

		logger.info("start make " + getPluralString() + " ...");

		ErmsImportConfigurator config = state.getConfig();

		Source source = config.getSource();

		String strIdQuery = getIdQuery();

		String strRecordQuery = getRecordQuery(config);

		int recordsPerTransaction = config.getRecordsPerTransaction();

		try{

			ResultSetPartitioner partitioner = ResultSetPartitioner.NewInstance(source, strIdQuery, strRecordQuery, recordsPerTransaction);

			while (partitioner.nextPartition()){

				partitioner.doPartition(this, state);

			}

		} catch (SQLException e) {

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

			state.setUnsuccessfull();

			return;

		}

		logger.info("end make " + getPluralString() + " ... " + getSuccessString(true));

		return;

	}

	public boolean doPartition(ResultSetPartitioner partitioner, ErmsImportState state) {

		boolean success = true ;

		Set objectsToSave = new HashSet();

 		DbImportMapping<?, ?> mapping = getMapping();

		mapping.initialize(state, cdmTargetClass);

		ResultSet rs = partitioner.getResultSet();

		try{

			while (rs.next()){

				success &= mapping.invoke(rs,objectsToSave);

			}

		} catch (SQLException e) {

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

			return false;

		}

		partitioner.startDoSave();

		getCommonService().save(objectsToSave);

		return success;

	}

	/**

	 * @return

	 */

	protected abstract DbImportMapping<?, ?> getMapping();

	/**

	 * @return

	 */

	protected abstract String getRecordQuery(ErmsImportConfigurator config);

	/**

	 * @return

	 */

	protected String getIdQuery(){

		String result = " SELECT id FROM " + getTableName();

		return result;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getPluralString()

	 */

	public String getPluralString(){

		return pluralString;

	}

	/**

	 * @return

	 */

	protected String getTableName(){

		return this.dbTableName;

	}

	protected boolean doIdCreatedUpdatedNotes(ErmsImportState state, IdentifiableEntity identifiableEntity, ResultSet rs, long id, String namespace)

			throws SQLException{

		boolean success = true;

		//id

		success &= ImportHelper.setOriginalSource(identifiableEntity, state.getConfig().getSourceReference(), id, namespace);

		//createdUpdateNotes

		success &= doCreatedUpdatedNotes(state, identifiableEntity, rs, namespace);

		return success;

	}

	protected boolean doCreatedUpdatedNotes(ErmsImportState state, AnnotatableEntity annotatableEntity, ResultSet rs, String namespace)

			throws SQLException{

		ErmsImportConfigurator config = state.getConfig();

		Object createdWhen = rs.getObject("Created_When");

		String createdWho = rs.getString("Created_Who");

		Object updatedWhen = null;

		String updatedWho = null;

		try {

			updatedWhen = rs.getObject("Updated_When");

			updatedWho = rs.getString("Updated_who");

		} catch (SQLException e) {

			//Table "Name" has no updated when/who

		}

		String notes = rs.getString("notes");

		boolean success  = true;

		//Created When, Who, Updated When Who

		if (config.getEditor() == null || config.getEditor().equals(EDITOR.NO_EDITORS)){

			//do nothing

		}else if (config.getEditor().equals(EDITOR.EDITOR_AS_ANNOTATION)){

			String createdAnnotationString = "Berlin Model record was created By: " + String.valueOf(createdWho) + " (" + String.valueOf(createdWhen) + ") ";

			if (updatedWhen != null && updatedWho != null){

				createdAnnotationString += " and updated By: " + String.valueOf(updatedWho) + " (" + String.valueOf(updatedWhen) + ")";

			}

			Annotation annotation = Annotation.NewInstance(createdAnnotationString, Language.DEFAULT());

			annotation.setCommentator(config.getCommentator());

			annotation.setAnnotationType(AnnotationType.TECHNICAL());

			annotatableEntity.addAnnotation(annotation);

		}else if (config.getEditor().equals(EDITOR.EDITOR_AS_EDITOR)){

			User creator = getUser(createdWho, state);

			User updator = getUser(updatedWho, state);

			DateTime created = getDateTime(createdWhen);

			DateTime updated = getDateTime(updatedWhen);

			annotatableEntity.setCreatedBy(creator);

			annotatableEntity.setUpdatedBy(updator);

			annotatableEntity.setCreated(created);

			annotatableEntity.setUpdated(updated);

		}else {

			logger.warn("Editor type not yet implemented: " + config.getEditor());

		}

		//notes

		if (CdmUtils.isNotEmpty(notes)){

			String notesString = String.valueOf(notes);

			if (notesString.length() > 65530 ){

				notesString = notesString.substring(0, 65530) + "...";

				logger.warn("Notes string is longer than 65530 and was truncated: " + annotatableEntity);

			}

			Annotation notesAnnotation = Annotation.NewInstance(notesString, null);

			//notesAnnotation.setAnnotationType(AnnotationType.EDITORIAL());

			//notes.setCommentator(bmiConfig.getCommentator());

			annotatableEntity.addAnnotation(notesAnnotation);

		}

		return success;

	}

	private User getUser(String userString, ErmsImportState state){

		if (CdmUtils.isEmpty(userString)){

			return null;

		}

		userString = userString.trim();

		User user = state.getUser(userString);

		if (user == null){

			user = getTransformedUser(userString,state);

		}

		if (user == null){

			user = makeNewUser(userString, state);

		}

		if (user == null){

			logger.warn("User is null");

		}

		return user;

	}

	private User getTransformedUser(String userString, ErmsImportState state){

		Method method = state.getConfig().getUserTransformationMethod();

		if (method == null){

			return null;

		}

		try {

			userString = (String)state.getConfig().getUserTransformationMethod().invoke(null, userString);

		} catch (Exception e) {

			logger.warn("Error when trying to transform userString " +  userString + ". No transformation done.");

		}

		User user = state.getUser(userString);

		return user;

	}

	private User makeNewUser(String userString, ErmsImportState state){

		String pwd = getPassword(); 

		User user = User.NewInstance(userString, pwd);

		state.putUser(userString, user);

		getUserService().save(user);

		logger.info("Added new user: " + userString);

		return user;

	}

	private String getPassword(){

		String result = UUID.randomUUID().toString();

		return result;

	}

	private DateTime getDateTime(Object timeString){

		if (timeString == null){

			return null;

		}

		DateTime dateTime = null;

		if (timeString instanceof Timestamp){

			Timestamp timestamp = (Timestamp)timeString;

			dateTime = new DateTime(timestamp);

		}else{

			logger.warn("time ("+timeString+") is not a timestamp. Datetime set to current date. ");

			dateTime = new DateTime();

		}

		return dateTime;

	}

	protected boolean resultSetHasColumn(ResultSet rs, String columnName){

		try {

			ResultSetMetaData metaData = rs.getMetaData();

			for (int i = 0; i < metaData.getColumnCount(); i++){

				if (metaData.getColumnName(i + 1).equalsIgnoreCase(columnName)){

					return true;

				}

			}

			return false;

		} catch (SQLException e) {

            logger.warn("Exception in resultSetHasColumn");

            return false;

		}

	}

	protected boolean checkSqlServerColumnExists(Source source, String tableName, String columnName){

		String strQuery = "SELECT  Count(t.id) as n " +

				" FROM sysobjects AS t " +

				" INNER JOIN syscolumns AS c ON t.id = c.id " +

				" WHERE (t.xtype = 'U') AND " + 

				" (t.name = '" + tableName + "') AND " + 

				" (c.name = '" + columnName + "')";

		ResultSet rs = source.getResultSet(strQuery) ;		

		int n;

		try {

			rs.next();

			n = rs.getInt("n");

			return n>0;

		} catch (SQLException e) {

			e.printStackTrace();

			return false;

		}

	}

	/**

	 * Returns a map that holds all values of a ResultSet. This is needed if a value needs to

	 * be accessed twice

	 * @param rs

	 * @return

	 * @throws SQLException

	 */

	protected Map<String, Object> getValueMap(ResultSet rs) throws SQLException{

		try{

			Map<String, Object> valueMap = new HashMap<String, Object>();

			int colCount = rs.getMetaData().getColumnCount();

			for (int c = 0; c < colCount ; c++){

				Object value = rs.getObject(c+1);

				String label = rs.getMetaData().getColumnLabel(c+1).toLowerCase();

				if (value != null && ! CdmUtils.Nz(value.toString()).trim().equals("")){

					valueMap.put(label, value);

				}

			}

			return valueMap;

		}catch(SQLException e){

			throw e;

		}

	}

	protected ExtensionType getExtensionType(UUID uuid, String label, String text, String labelAbbrev){

		ExtensionType extensionType = (ExtensionType)getTermService().find(uuid);

		if (extensionType == null){

			extensionType = ExtensionType.NewInstance(text, label, labelAbbrev);

			extensionType.setUuid(uuid);

			getTermService().save(extensionType);

		}

		return extensionType;

	}

	protected MarkerType getMarkerType(UUID uuid, String label, String text, String labelAbbrev){

		MarkerType markerType = (MarkerType)getTermService().find(uuid);

		if (markerType == null){

			markerType = MarkerType.NewInstance(label, text, labelAbbrev);

			markerType.setUuid(uuid);

			getTermService().save(markerType);

		}

		return markerType;

	}

	/**

	 * Reads a foreign key field from the result set and adds its value to the idSet.

	 * @param rs

	 * @param teamIdSet

	 * @throws SQLException

	 */

	protected void handleForeignKey(ResultSet rs, Set<String> idSet, String attributeName)

			throws SQLException {

		Object idObj = rs.getObject(attributeName);

		if (idObj != null){

			String id  = String.valueOf(idObj);

			idSet.add(id);

		}

	}

	/**

	 * Returns true if i is a multiple of recordsPerTransaction

	 * @param i

	 * @param recordsPerTransaction

	 * @return

	 */

	protected boolean loopNeedsHandling(int i, int recordsPerLoop) {

		startTransaction();

		return (i % recordsPerLoop) == 0;

	}

	protected void doLogPerLoop(int count, int recordsPerLog, String pluralString){

		if ((count % recordsPerLog ) == 0 && count!= 0 ){ logger.info(pluralString + " handled: " + (count));}

	}

}

/**

* 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.pesi.erms;

import java.lang.reflect.Method;

import org.apache.log4j.Logger;

import eu.etaxonomy.cdm.database.ICdmDataSource;

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

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

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

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

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

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

import eu.etaxonomy.cdm.io.pesi.erms.validation.ErmsGeneralImportValidator;

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

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

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

/**

 * @author a.mueller

 * @created 20.03.2008

 * @version 1.0

 */

public class ErmsImportConfigurator extends ImportConfiguratorBase<ErmsImportState, Source> implements IImportConfigurator{

	@SuppressWarnings("unused")

	private static Logger logger = Logger.getLogger(ErmsImportConfigurator.class);

	public static ErmsImportConfigurator NewInstance(Source ermsSource, ICdmDataSource destination){

			return new ErmsImportConfigurator(ermsSource, destination);

	}

	/* Max number of records to be saved with one service call */

	private int recordsPerTransaction = 1000;  //defaultValue

	//TODO needed ??

	private Method userTransformationMethod;

	private boolean doVernaculars = true;

	private boolean doLinks = true;

	private boolean doNotes = true;

	private boolean doImages = true;

	private boolean doOccurrence = true;

	private DO_REFERENCES doReferences = DO_REFERENCES.ALL;

	private boolean doTaxa = true;

	private boolean doRelTaxa = true;

	private static IInputTransformer defaultTransformer = new ErmsTransformer();

	protected void makeIoClassList(){

		ioClassList = new Class[]{

				ErmsGeneralImportValidator.class

				, ErmsImportRankMap.class

				, ErmsReferenceImport.class

				, ErmsTaxonImport.class

				, ErmsTaxonRelationImport.class

				, ErmsVernacularImport.class

				, ErmsNotesImport.class

				, ErmsVernacularSourcesImport.class

				, ErmsNotesSourcesImport.class

				, ErmsAreaImport.class

				, ErmsDrImport.class

				, ErmsSourceUsesImport.class

				, ErmsLinkImport.class  //kann weiter hoch

				, ErmsImageImport.class

		};	

	}

	/* (non-Javadoc)

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

	 */

	public ImportStateBase getNewState() {

		return new ErmsImportState(this);

	}

	/**

	 * @param berlinModelSource

	 * @param sourceReference

	 * @param destination

	 */

	private ErmsImportConfigurator(Source ermsSource, ICdmDataSource destination) {

	   super(defaultTransformer);

	   setNomenclaturalCode(NomenclaturalCode.ICZN); //default for ERMS

	   setSource(ermsSource);

	   setDestination(destination);

	}

	public Source getSource() {

		return (Source)super.getSource();

	}

	public void setSource(Source berlinModelSource) {

		super.setSource(berlinModelSource);

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.tcsrdf.IImportConfigurator#getSourceReference()

	 */

	public Reference getSourceReference() {

		ReferenceFactory refFactory = ReferenceFactory.newInstance();

		if (sourceReference == null){

			sourceReference =  refFactory.newDatabase();

			if (getSource() != null){

				sourceReference.setTitleCache(getSource().getDatabase(), true);

			}

		}

		return sourceReference;

	}

	/* (non-Javadoc)

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

	 */

	public String getSourceNameString() {

		if (this.getSource() == null){

			return null;

		}else{

			return this.getSource().getDatabase();

		}

	}

	/**

	 * @return the userTransformationMethod

	 */

	public Method getUserTransformationMethod() {

		return userTransformationMethod;

	}

	/**

	 * @param userTransformationMethod the userTransformationMethod to set

	 */

	public void setUserTransformationMethod(Method userTransformationMethod) {

		this.userTransformationMethod = userTransformationMethod;

	}

	/**

	 * @return the limitSave

	 */

	public int getRecordsPerTransaction() {

		return recordsPerTransaction;

	}

	/**

	 * @param limitSave the limitSave to set

	 */

	public void setRecordsPerTransaction(int recordsPerTransaction) {

		this.recordsPerTransaction = recordsPerTransaction;

	}

	/**

	 * @param doVernaculars the doVernaculars to set

	 */

	public void setDoVernaculars(boolean doVernaculars) {

		this.doVernaculars = doVernaculars;

	}

	/**

	 * @return the doVernaculars

	 */

	public boolean isDoVernaculars() {

		return doVernaculars;

	}

	/**

	 * @param doLinks the doLinks to set

	 */

	public void setDoLinks(boolean doLinks) {

		this.doLinks = doLinks;

	}

	/**

	 * @return the doLinks

	 */

	public boolean isDoLinks() {

		return doLinks;

	}

	/**

	 * @param doNotes the doNotes to set

	 */

	public void setDoNotes(boolean doNotes) {

		this.doNotes = doNotes;

	}

	/**

	 * @return the doNotes

	 */

	public boolean isDoNotes() {

		return doNotes;

	}

	/**

	 * @param doImages the doImages to set

	 */

	public void setDoImages(boolean doImages) {

		this.doImages = doImages;

	}

	/**

	 * @return the doImages

	 */

	public boolean isDoImages() {

		return doImages;

	}

	public boolean isDoOccurrence() {

		return doOccurrence;

	}

	public void setDoOccurrence(boolean doOccurrence) {

		this.doOccurrence = doOccurrence;

	}

	public DO_REFERENCES getDoReferences() {

		return doReferences;

	}

	public void setDoReferences(DO_REFERENCES doReferences) {

		this.doReferences = doReferences;

	}

	public boolean isDoTaxa() {

		return doTaxa;

	}

	public void setDoTaxa(boolean doTaxa) {

		this.doTaxa = doTaxa;

	}

	public boolean isDoRelTaxa() {

		return doRelTaxa;

	}

	public void setDoRelTaxa(boolean doRelTaxa) {

		this.doRelTaxa = doRelTaxa;

	}

}

// $Id$

/**

* 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.pesi.erms;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashMap;

import java.util.Map;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

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

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

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

import eu.etaxonomy.cdm.io.pesi.erms.validation.ErmsRankImportValidator;

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

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

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

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

/**

 * @author a.mueller

 * @created 01.03.2010

 * @version 1.0

 */

@Component

public class ErmsImportRankMap extends ErmsImportBase<Rank>{

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

	private Map<Integer, Map<Integer,Rank>> rankMap;

	/**

	 * @param pluralString

	 * @param dbTableName

	 */

	public ErmsImportRankMap() {

		super(null, null, null);

	}

	/* (non-Javadoc)

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

	 */

	public boolean invoke (ErmsImportState state){

		rankMap = new HashMap<Integer, Map<Integer,Rank>>();

		Source source = state.getConfig().getSource() ;

		String strSQL = " SELECT * FROM ranks ";

		ResultSet rs = source.getResultSet(strSQL);

		try {

			while (rs.next()){

				Integer kingdomId = rs.getInt("kingdom_id");

				Integer rankId = rs.getInt("rank_id");

				String rankName = rs.getString("rank_name");

				NomenclaturalCode nc = ErmsTransformer.kingdomId2NomCode(kingdomId);

				Map<Integer, Rank> kingdomMap = makeKingdomMap(rankMap, rankId);			

				try {

					rankName = rankName.replace("Forma", "Form").replace("Subforma", "Subform");

					Rank rank = Rank.getRankByEnglishName(rankName, nc, false);

					if (rank == null){

						logger.warn("Rank is null: " + rankName);

					}

					kingdomMap.put(kingdomId, rank);	

				} catch (UnknownCdmTypeException e) {

					String errorMessage = "Rank '" + rankName + "' is not well mapped for code " + nc + ", kingdom_id = " + kingdomId + ". Rank is ignored!";

					logger.warn(errorMessage);

				}

			}

		} catch (SQLException e) {

			logger.error(e.getMessage());

			throw new RuntimeException(e);

		}

		state.setRankMap(rankMap);

		return true;

	}

	/**

	 * Retrieves or creates the kingdom map (mapping kingdom to rank for a defined rank_id) and

	 * adds it to the rank map.

	 * @param rankMap

	 * @param rankId

	 * @return

	 */

	private Map<Integer, Rank> makeKingdomMap(Map<Integer, Map<Integer, Rank>> rankMap, Integer rankId) {

		Map<Integer, Rank> result = rankMap.get(rankId);

		if (result == null){

			result = new HashMap<Integer, Rank>();

			rankMap.put(rankId, result);

		}

		return result;

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected boolean doCheck(ErmsImportState state) {

		IOValidator rankImport = new ErmsRankImportValidator();

		return rankImport.validate(state);

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getRecordQuery(eu.etaxonomy.cdm.io.erms.ErmsImportConfigurator)

	 */

	@Override

	protected String getRecordQuery(ErmsImportConfigurator config) {

		// TODO Auto-generated method stub

		return null;

	}

	/* (non-Javadoc)

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

	 */

	@Override

	protected boolean isIgnore(ErmsImportState state) {

		return false;  //should always be called

	}

	/* (non-Javadoc)

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

	 */

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

		return null;  // not needed

	}

	/* (non-Javadoc)

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

	 */

	public Rank createObject(ResultSet rs, ErmsImportState state)

			throws SQLException {

		return null;  // not needed

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getMapping()

	 */

	@Override

	protected DbImportMapping<?, ?> getMapping() {

		return null;  //not needed

	}

}

// $Id$