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.app.cyprus;

import java.io.FileNotFoundException;

import eu.etaxonomy.cdm.common.URI;

import java.net.URISyntaxException;

import java.util.HashSet;

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.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.api.application.CdmApplicationController;

import eu.etaxonomy.cdm.app.common.CdmDestinations;

import eu.etaxonomy.cdm.common.ExcelUtils;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.io.api.application.CdmIoApplicationController;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/**

 * @author a.mueller

 * @since 16.12.2010

 */

public class CyprusAltitudeActivator {

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

	//database validation status (create, update, validate ...)

	static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;

	static final URI source = cyprus_altitude();

	static final ICdmDataSource cdmDestination = CdmDestinations.localH2();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_cyprus();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_production();

	//feature tree uuid

	public static final UUID featureTreeUuid = UUID.fromString("14d1e912-5ec2-4d10-878b-828788b70a87");

	//classification

	static final UUID classificationUuid = UUID.fromString("0c2b5d25-7b15-4401-8b51-dd4be0ee5cab");

	private static final String sourceReferenceTitle = "Cyprus Excel Altitude Import";

	private static final UUID uuidAltitudeFeature = Feature.uuidAltitude;

	//check - import

	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

	private void doImport(ICdmDataSource cdmDestination){

		List<Map<String, String>> excel;

		try {

			excel = ExcelUtils.parseXLS(source, "coreTax");

		} catch (FileNotFoundException e) {

			e.printStackTrace();

			return;

		}

		CdmApplicationController app = CdmIoApplicationController.NewInstance(cdmDestination, hbm2dll);

		@SuppressWarnings("rawtypes")

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

		TransactionStatus tx = app.startTransaction();

		UUID uuidMikle77 = UUID.fromString("9f5fa7ee-538b-4ae5-bd82-2a9503fea1d6");

		UUID uuidMikle85 = UUID.fromString("994403c4-c400-413d-9a1a-8531a40bfd8c");

		Reference mikle77 = app.getReferenceService().find(uuidMikle77);

		Reference mikle85 = app.getReferenceService().find(uuidMikle85);

		Feature altitudeFeature = (Feature) app.getTermService().find(uuidAltitudeFeature);

		if (altitudeFeature == null){

			throw new RuntimeException("Could not find altitudinal range feature");

		}

		MeasurementUnit meter = (MeasurementUnit)app.getTermService().find(UUID.fromString("8bef5055-789c-41e5-bea2-8dc2ea8ecdf6"));

		int count =1;

		for (Map<String, String> row : excel){

			count++;

			UUID baseUuid = makeUuid(row, "uuid");

			UUID acceptedUuid = makeUuid(row, "acceptedNameUuid");

			UUID parentUuid = makeUuid(row, "parentUuid");

			String altitudeMin = row.get("Min");

			String altitudeMax = row.get("Max");

			String acceptedName = row.get("AcceptedName");

			String source = row.get("Source");

			if (StringUtils.isBlank(altitudeMin)){

				continue;

			}

			boolean hasAltitude = false;

			Reference sourceRef = getSource(source, mikle77, mikle85);

			Taxon taxon = getTaxon(app, baseUuid, acceptedUuid, parentUuid, acceptedName, count);

			if (taxon != null){

				TaxonDescription desc = getDescription(taxon, sourceRef);

				hasAltitude = makeAltitude(altitudeMin, altitudeMax, altitudeFeature, sourceRef, desc, meter, count);

				if (hasAltitude){

					if(desc.getTaxon() == null){

						taxon.addDescription(desc);

					}

					taxaToSave.add(taxon);

				}else{

					logger.warn("HasALtitude is false in " + count);

				}

			}else{

				logger.warn("Taxon not recognized in line " + count);

			}

		}

		app.getTaxonService().saveOrUpdate(taxaToSave);

		app.commitTransaction(tx);

	}

	private Taxon getTaxon(CdmApplicationController app, UUID baseUuid, UUID acceptedUuid, UUID parentUuid, String acceptedName, int row) {

		TaxonBase<?> base = app.getTaxonService().find(baseUuid);

		Taxon result = null;

		if (base.isInstanceOf(Taxon.class)){

			Taxon t = CdmBase.deproxy(base, Taxon.class);

			if (t.getTaxonNodes().size() == 1 && t.getTaxonNodes().iterator().next().getClassification().getUuid().equals(classificationUuid)){

				result = t;

			}else{

				logger.warn("Base taxon (uuid) not in classification. Row: " + row +  ", Taxon: " + base.getTitleCache());

			}

		}

		if (result == null){

			TaxonBase<?> accepted = app.getTaxonService().find(acceptedUuid);

			Taxon t = CdmBase.deproxy(accepted, Taxon.class);;

			if (t.getTaxonNodes().size() == 1 && t.getTaxonNodes().iterator().next().getClassification().getUuid().equals(classificationUuid)){

				if (hasSynonym(t, base)){

					result = t;

				}else{

					logger.warn("Synonym relation has changed somehow. Row: " + row +  ", Taxon: " + base.getTitleCache());

				}

			}else{

				logger.warn("Accepted taxon not in classification. Row: " + row +  ", Taxon: " + base.getTitleCache());

			}

		}

		if (result != null){

			if (! result.getName().getTitleCache().equals(acceptedName)){

				logger.warn("AcceptedName and taxon name is not equal in " + row + ".\n" +

						" Accepted Name: " + acceptedName + ";\n" +

						" Taxon    Name: " + result.getName().getTitleCache());

			}

		}

		return result;

	}

	private boolean hasSynonym(Taxon t, TaxonBase<?> base) {

		if (base.isInstanceOf(Synonym.class)){

			for (Synonym syn : t.getSynonyms()){

				if (syn.equals(base)){

					return true;

				}

			}

		}

		return false;

	}

//	private static final Pattern altitudePattern = Pattern.compile("\\d{1,4}(-\\d{1,4})?");

	private boolean makeAltitude(String altitudeMin, String altitudeMax, Feature altitudeFeature,

			Reference sourceRef, TaxonDescription desc, MeasurementUnit meter, int row) {

		QuantitativeData data = QuantitativeData.NewInstance(altitudeFeature);

		//Meikle

		if (source != null){

			TaxonName nameUsedInSource = null;  //TODO

			data.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, sourceRef, null, nameUsedInSource, null);

		}

		data.setUnit(meter);

		Integer min = Integer.valueOf(altitudeMin);

		StatisticalMeasurementValue minValue = StatisticalMeasurementValue.NewInstance(StatisticalMeasure.MIN(), min);

		data.addStatisticalValue(minValue);

		Integer max = Integer.valueOf(altitudeMax);

		StatisticalMeasurementValue maxValue = StatisticalMeasurementValue.NewInstance(StatisticalMeasure.MAX(), max);

		data.addStatisticalValue(maxValue);

		desc.addElement(data);

		return true;

	}

	private TaxonDescription getDescription(Taxon taxon, Reference sourceRef) {

		if (taxon != null){

			//TODO Mikle currently does not exist as Source

			TaxonDescription desc = TaxonDescription.NewInstance();

			desc.setTitleCache("Import from " + getSourceReference().getTitleCache(), true);

			desc.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, sourceRef,null);

			desc.addSource(OriginalSourceType.Import, null, null, getSourceReference(), null);

			return desc;

		}

		return null;

	}

	private Reference getSource(String source, Reference m77, Reference m85) {

		if(StringUtils.isNotBlank(source)){

			if (source.equals("Meikle 1977")){

				return m77;

			}else if (source.equals("Meikle 1985")){

				return m85;

			}else{

				logger.warn("Source not recognized: " + source);

			}

		}

		return null;

	}

	private UUID makeUuid(Map<String, String> row, String colName) {

		if (StringUtils.isBlank(row.get(colName))){

			return null;

		}else{

			return UUID.fromString(row.get(colName));

		}

	}

	Reference sourceReference;

	private Reference getSourceReference() {

		if (sourceReference == null){

			sourceReference = ReferenceFactory.newGeneric();

			sourceReference.setTitleCache(sourceReferenceTitle, true);

		}

		return sourceReference;

	}

	//Cyprus

	public static URI cyprus_altitude() {

		URI sourceUrl;

		try {

			sourceUrl = new URI("file:/F:/data/cyprus/Cyprus-altitude-import-neu.xls");

//			sourceUrl = new URI("file:/F:/data/cyprus/Zypern-Altitude.xls");

			return sourceUrl;

		} catch (URISyntaxException e) {

			e.printStackTrace();

			return null;

		}

	}

	public static void main(String[] args) {

		CyprusAltitudeActivator me = new CyprusAltitudeActivator();

		me.doImport(cdmDestination);

	}

}