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.berlinModel.in;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

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.hibernate.HibernateProxyHelper;

import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;

import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelOccurrenceImportValidator;

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

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

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

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.IdentifiableSource;

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.term.OrderedTermVocabulary;

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

/**

 * @author a.mueller

 * @since 20.03.2008

 */

@Component

public class BerlinModelOccurrenceImport  extends BerlinModelImportBase {

    private static final long serialVersionUID = -7918122767284077183L;

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

	public static final String NAMESPACE = "Occurrence";

	private static int modCount = 5000;

	private static final String pluralString = "occurrences";

	private static final String dbTableName = "emOccurrence";  //??

	public BerlinModelOccurrenceImport(){

		super(dbTableName, pluralString);

	}

	@Override

	protected String getIdQuery(BerlinModelImportState state) {

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

		if (StringUtils.isNotBlank(state.getConfig().getOccurrenceFilter())){

			result += " WHERE " +  state.getConfig().getOccurrenceFilter();

		}

		return result;

	}

	@Override

	protected String getRecordQuery(BerlinModelImportConfigurator config) {

			String emCode = config.isIncludesAreaEmCode()? ", ar.EMCode" : "";

			String strQuery =   //DISTINCT because otherwise emOccurrenceSource creates multiple records for a single distribution

                " SELECT DISTINCT pt.RIdentifier AS taxonId, occ.OccurrenceId, occ.Native, occ.Introduced, " +

            		" occ.Cultivated, occ.StatusUnknown, occ.WorldDistCompl, occ.Notes occNotes, " +

            		" sumcat.emOccurSumCatId, sumcat.Short, sumcat.Description, " +

                	" sumcat.OutputCode, ar.AreaId, ar.TDWGCode " + emCode +

                " FROM emOccurrence occ " +

                	" INNER JOIN emArea ar ON occ.AreaFk = ar.AreaId " +

                	" INNER JOIN PTaxon pt ON occ.PTNameFk = pt.PTNameFk AND occ.PTRefFk = pt.PTRefFk " +

                	" LEFT OUTER JOIN emOccurSumCat sumcat ON occ.SummaryStatus = sumcat.emOccurSumCatId " +

                	" LEFT OUTER JOIN emOccurrenceSource ocs ON occ.OccurrenceId = ocs.OccurrenceFk " +

                " WHERE (occ.OccurrenceId IN (" + ID_LIST_TOKEN + ")  )" +

                " ORDER BY pt.RIdentifier";

		return strQuery;

	}

	@Override

	public void doInvoke(BerlinModelImportState state) {

		super.doInvoke(state);

	}

    private NamedArea getAreaByAreaId(int areaId) {

        NamedArea result = null;

        String areaIdStr = String.valueOf(areaId);

        OrderedTermVocabulary<NamedArea> voc = getAreaVoc();

        for (NamedArea area : voc.getTerms()){

            for (IdentifiableSource source : area.getSources()){

                if (areaIdStr.equals(source.getIdInSource()) && BerlinModelAreaImport.NAMESPACE.equals(source.getIdNamespace())){

                    if (result != null){

                        logger.warn("Result for areaId already exists. areaId: " + areaId);

                    }

                    result = area;

                }

            }

        }

        return result;

    }

    private OrderedTermVocabulary<NamedArea> areaVoc;

    @SuppressWarnings("unchecked")

    private OrderedTermVocabulary<NamedArea> getAreaVoc(){

        if (areaVoc == null){

            areaVoc = (OrderedTermVocabulary<NamedArea>)getVocabularyService().find(BerlinModelTransformer.uuidVocEuroMedAreas);

        }

        return areaVoc;

    }

	private String nullSafeTrim(String string) {

		if (string == null){

			return null;

		}else{

			return string.trim();

		}

	}

	@Override

	public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, BerlinModelImportState state) {

		boolean success = true;

		@SuppressWarnings("rawtypes")

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

		@SuppressWarnings("unchecked")

        Map<String, TaxonBase<?>> taxonMap = partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);

		ResultSet rs = partitioner.getResultSet();

		try {

			//map to store the mapping of duplicate berlin model occurrences to their real distributions

			//duplicated may occur due to area mappings from BM areas to TDWG areas

			Map<Integer, String> duplicateMap = new HashMap<>();

			int oldTaxonId = -1;

			TaxonDescription oldDescription = null;

			int i = 0;

			int countDescriptions = 0;

			int countDistributions = 0;

			int countDuplicates = 0;

			//for each reference

            while (rs.next()){

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

                int occurrenceId = rs.getInt("OccurrenceId");

                int newTaxonId = rs.getInt("taxonId");

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

                Integer emStatusId = nullSafeInt(rs, "emOccurSumCatId");

                try {

                    //area(s)

                    List<NamedArea> areas = makeAreaList(state, partitioner, rs, occurrenceId);

                    if (areas.size() != 1){

                        logger.warn("Exactly 1 area expected but was " + areas.size() + ". OccId: " + occurrenceId);

                        if (areas.isEmpty()){

                            continue;

                        }

                    }

                    //status

                	PresenceAbsenceTerm status = null;

                	String alternativeStatusString = null;

					if (emStatusId != null){

						status = BerlinModelTransformer.occStatus2PresenceAbsence(emStatusId);

					}else{

						//EM

					    if (state.getConfig().isEuroMed() && areas.get(0).getUuid().equals(BerlinModelTransformer.uuidEM)){

						    String complete = rs.getString("WorldDistCompl");

						    if (complete == null){

						        //FIXME

                                status = PresenceAbsenceTerm.ENDEMISM_UNKNOWN();

                                alternativeStatusString = getStatusAnnotation(rs);

						    }else if (complete.equals("C")){

                                status = PresenceAbsenceTerm.ENDEMIC_FOR_THE_RELEVANT_AREA();

                                logger.warn("EmStatusId undefined though WorldDistCompl is 'C'. This is an unexpected state. OccID: " + occurrenceId);

						    }else if (complete.equals("I")){

						        status = PresenceAbsenceTerm.NOT_ENDEMIC_FOR_THE_RELEVANT_AREA();

                            }else{

                                status = PresenceAbsenceTerm.ENDEMISM_UNKNOWN();

                                alternativeStatusString = getStatusAnnotation(rs);

                            }

						}else{ //other areas

						    alternativeStatusString = getStatusAnnotation(rs);

						    status = getPresenceTerm(state, BerlinModelTransformer.uuidStatusUndefined, "Undefined", "Undefined status as status was not computed in Berlin Model", "none", false, null);

						}

					}

					Reference sourceRef = state.getTransactionalSourceReference();

                    //create description(elements)

                    TaxonDescription taxonDescription = getTaxonDescription(newTaxonId, oldTaxonId, oldDescription, taxonMap, occurrenceId, sourceRef);

                    for (NamedArea area : areas){

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

                        if (StringUtils.isNotBlank(alternativeStatusString)){

                            AnnotationType type = getAnnotationType(state, BerlinModelTransformer.uuidAnnoTypeDistributionStatus, "Original distribution status", "Original distribution status", null, null);

                            Annotation annotation = Annotation.NewInstance(alternativeStatusString, type, null);

                            distribution.addAnnotation(annotation);

                        }

//                      distribution.setCitation(sourceRef);

                        if (taxonDescription != null) {

                        	Distribution duplicate = checkIsNoDuplicate(taxonDescription, distribution, duplicateMap , occurrenceId);

                            if (duplicate == null){

                            	taxonDescription.addElement(distribution);

	                            distribution.addImportSource(String.valueOf(occurrenceId), NAMESPACE, state.getTransactionalSourceReference(), null);

	                        	countDistributions++;

	                            if (taxonDescription != oldDescription){

	                            	taxaToSave.add(taxonDescription.getTaxon());

	                                oldDescription = taxonDescription;

	                                countDescriptions++;

	                            }

                            }else{

                            	countDuplicates++;

                            	duplicate.addImportSource(String.valueOf(occurrenceId), NAMESPACE, state.getTransactionalSourceReference(), null);

                            	logger.info("Distribution is duplicate");	                           }

                        } else {

                        	logger.warn("Distribution " + area.getLabel() + " ignored. OccurrenceId = " + occurrenceId);

	                       	success = false;

	                    }

                        //notes

                        if (isNotBlank(notes)){

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

                        	distribution.addAnnotation(annotation);

                        }

                    }

                } catch (UnknownCdmTypeException e) {

                     logger.error("Unknown presenceAbsence status id: " + emStatusId);

                	e.printStackTrace();

                     success = false;

                }

            }

            logger.info("Distributions: " + countDistributions + ", Descriptions: " + countDescriptions );

			logger.info("Duplicate occurrences: "  + (countDuplicates));

			logger.info("Taxa to save: " + taxaToSave.size());

			getTaxonService().save(taxaToSave);

			return success;

		} catch (SQLException e) {

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

			return false;

		}

	}

    /**

     * @param rs

     * @return

     * @throws SQLException

     */

    protected String getStatusAnnotation(ResultSet rs) throws SQLException {

        String alternativeStatusString;

        String[] stringArray = new String[]{"Native: " + rs.getString("Native"), "Introduced: "+ rs.getString("Introduced"),

                "Cultivated: " + rs.getString("Cultivated"), "StatusUnknown: " + rs.getString("StatusUnknown"),

                "WorldDistCompl: " + rs.getString("WorldDistCompl")};

        alternativeStatusString = CdmUtils.concat("; ", stringArray);

        return alternativeStatusString;

    }

	/**

	 * @param state

	 * @param partitioner

	 * @param rs

	 * @param occurrenceId

	 * @param tdwgCodeString

	 * @param emCodeString

	 * @return

	 * @throws SQLException

	 */

	//Create area list

	private List<NamedArea> makeAreaList(BerlinModelImportState state,

	        @SuppressWarnings("rawtypes") ResultSetPartitioner partitioner,

	        ResultSet rs, int occurrenceId) throws SQLException {

	    List<NamedArea> areas = new ArrayList<>();

		if (state.getConfig().isUseEmAreaVocabulary()){

		    Integer areaId = rs.getInt("AreaId");

			NamedArea area = getAreaByAreaId(areaId);

			if (area == null){

			    logger.warn("Area for areaId " + areaId + " not found.");

			}

			areas.add(area);

		}else{

	        String tdwgCodeString = rs.getString("TDWGCode");

	        String emCodeString = state.getConfig().isIncludesAreaEmCode() ? rs.getString("EMCode") : null;

			if (tdwgCodeString != null){

				String[] tdwgCodes = new String[]{tdwgCodeString};

				if (state.getConfig().isSplitTdwgCodes()){

					tdwgCodes = tdwgCodeString.split(";");

				}

				for (String tdwgCode : tdwgCodes){

					NamedArea area = TdwgAreaProvider.getAreaByTdwgAbbreviation(tdwgCode.trim());

			    	if (area == null){

			    		area = getOtherAreas(state, emCodeString, tdwgCodeString);

			    	}

			    	if (area != null){

			    		areas.add(area);

			    	}

				}

			 }

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

				 NamedArea area = getOtherAreas(state, emCodeString, tdwgCodeString);

				 if (area != null){

			         areas.add(area);

			   }

			 }

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

				 String areaId = rs.getString("AreaId");

				 logger.warn("No areas defined for occurrence " + occurrenceId + ". EMCode: " + CdmUtils.Nz(emCodeString).trim() + ". AreaId: " + areaId );

			 }

		}

		return areas;

	}

	@Override

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

		try{

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

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

			while (rs.next()){

				handleForeignKey(rs, taxonIdSet, "taxonId");

			}

			//taxon map

			String nameSpace = BerlinModelTaxonImport.NAMESPACE;

			Class<?> cdmClass = TaxonBase.class;

			Set<String> idSet = taxonIdSet;

			@SuppressWarnings("unchecked")

            Map<String, ? extends CdmBase> objectMap = (Map<String, TaxonBase<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, objectMap);

			return result;

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

	}

	/**

     * Tests if a distribution with the same tdwgArea and the same status already exists in the description.

     * If so the old distribution is returned

     * @param description

     * @param tdwgArea

     * @return false, if dupplicate exists. True otherwise.

     */

    private Distribution checkIsNoDuplicate(TaxonDescription description, Distribution distribution, Map<Integer, String> duplicateMap, Integer bmDistributionId){

    	for (DescriptionElementBase descElBase : description.getElements()){

    		if (descElBase.isInstanceOf(Distribution.class)){

    			Distribution oldDistr = HibernateProxyHelper.deproxy(descElBase, Distribution.class);

    			NamedArea oldArea = oldDistr.getArea();

    			if (oldArea != null && oldArea.equals(distribution.getArea())){

    				PresenceAbsenceTerm oldStatus = oldDistr.getStatus();

    				if (oldStatus != null && oldStatus.equals(distribution.getStatus())){

    					duplicateMap.put(bmDistributionId, oldDistr.getSources().iterator().next().getIdInSource());

    					return oldDistr;

    				}

    			}

    		}

    	}

    	return null;

    }

	/**

	 * Use same TaxonDescription if two records belong to the same taxon

	 * @param newTaxonId

	 * @param oldTaxonId

	 * @param oldDescription

	 * @param taxonMap

	 * @return

	 */

	private TaxonDescription getTaxonDescription(int newTaxonId, int oldTaxonId, TaxonDescription oldDescription, Map<String, TaxonBase<?>> taxonMap, int occurrenceId, Reference sourceSec){

		TaxonDescription result = null;

		if (oldDescription == null || newTaxonId != oldTaxonId){

			TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(newTaxonId));

			//TODO for testing

			//TaxonBase taxonBase = Taxon.NewInstance(TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()), null);

			Taxon taxon;

			if ( taxonBase instanceof Taxon ) {

				taxon = (Taxon) taxonBase;

			} else if (taxonBase != null) {

				logger.warn("TaxonBase for Occurrence " + occurrenceId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());

				return null;

			} else {

				logger.warn("TaxonBase for Occurrence " + occurrenceId + " is null.");

				return null;

			}

			Set<TaxonDescription> descriptionSet= taxon.getDescriptions();

			if (descriptionSet.size() > 0) {

				result = descriptionSet.iterator().next();

			}else{

				result = TaxonDescription.NewInstance();

				result.setTitleCache(sourceSec.getTitleCache(), true);

				taxon.addDescription(result);

			}

		}else{

			result = oldDescription;

		}

		return result;

	}

	@Override

	protected boolean doCheck(BerlinModelImportState state){

		IOValidator<BerlinModelImportState> validator = new BerlinModelOccurrenceImportValidator();

		return validator.validate(state);

	}

	@Override

	protected boolean isIgnore(BerlinModelImportState state){

		if (! state.getConfig().isDoOccurrence()){

			return true;

		}else{

			if (!this.checkSqlServerColumnExists(state.getConfig().getSource(), "emOccurrence", "OccurrenceId")){

				logger.error("emOccurrence table or emOccurrenceId does not exist. Must ignore occurrence import");

				return true;

			}else{

				return false;

			}

		}

	}

}