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.algaterra;

import java.net.URI;

import java.sql.Date;

import java.sql.ResultSet;

import java.sql.SQLException;

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.facade.DerivedUnitFacade;

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

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

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

import eu.etaxonomy.cdm.model.agent.Team;

import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

/**

 * @author a.mueller

 * @created 12.09.2012

 */

public abstract class AlgaTerraSpecimenImportBase extends BerlinModelImportBase{

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

	public static final String ECO_FACT_FIELD_OBSERVATION_NAMESPACE = "EcoFact_FieldObservation";

	public static final String ECO_FACT_DERIVED_UNIT_NAMESPACE = "EcoFact_DerivedUnit";

	public static final String TYPE_SPECIMEN_FIELD_OBSERVATION_NAMESPACE = "TypeSpecimen_FieldObservation";

	public static final String TYPE_SPECIMEN_DERIVED_UNIT_NAMESPACE = "TypeSpecimen_DerivedUnit";

	public static final String FACT_ECOLOGY_NAMESPACE = "Fact(Ecology)";

	public static final String TERMS_NAMESPACE = "ALGA_TERRA_TERMS";

	//TODO move to transformrer

	final static UUID uuidMarkerAlkalinity = UUID.fromString("e52d0ea2-0c1f-4d95-ae6d-e21ab317c594");  

	final static UUID uuidRefSystemGps = UUID.fromString("c23e4928-c137-4e4a-b6ab-b430da3d0b94");  

	public final static UUID uuidFeatureSpecimenCommunity = UUID.fromString("3ff5b1ab-3999-4b5a-b8f7-01fd2f6c12c7");

	public final static UUID uuidFeatureAdditionalData = UUID.fromString("0ac82ab8-2c2b-4953-98eb-a9f718eb9c57");

	public final static UUID uuidFeatureHabitatExplanation = UUID.fromString("6fe32295-61a3-44fc-9fcf-a85790ea888f");

	final static UUID uuidVocAlgaTerraClimate = UUID.fromString("b0a677c6-8bb6-43f4-b1b8-fc377a10feb5");

	final static UUID uuidVocAlgaTerraHabitat = UUID.fromString("06f30114-e19c-4e7d-a8e5-5488c41fcbc5");

	final static UUID uuidVocAlgaTerraLifeForm = UUID.fromString("3c0b194e-809c-4b42-9498-6ff034066ed7");

	public final static UUID uuidFeatureAlgaTerraClimate = UUID.fromString("8754674c-9ab9-4f28-95f1-91eeee2314ee");

	public final static UUID uuidFeatureAlgaTerraHabitat = UUID.fromString("7def3fc2-cdc5-4739-8e13-62edbd053415");

	public final static UUID uuidFeatureAlgaTerraLifeForm = UUID.fromString("9b657901-1b0d-4a2a-8d21-dd8c1413e2e6");

	final static UUID uuidVocParameter = UUID.fromString("45888b40-5bbb-4293-aa1e-02479796cd7c");

	final static UUID uuidStatMeasureSingleValue = UUID.fromString("eb4c3d98-4d4b-4c37-8eb4-17315ce79920");

	final static UUID uuidMeasurementValueModifier = UUID.fromString("0218a7a3-f6c0-4d06-a4f8-6b50b73aef5e");

	final static UUID uuidModifierLowerThan = UUID.fromString("2b500085-6bef-4003-b6ea-e0ad0237d79d");

	final static UUID uuidModifierGreaterThan = UUID.fromString("828df49d-c745-48f7-b083-0ada43356c34");

	public AlgaTerraSpecimenImportBase(String tableName, String pluralString) {

		super(tableName, pluralString);

	}

	/**

	 * Creates the vocabularies and the features for Climate, Habitat and Lifeform

	 * @param state

	 * @throws SQLException

	 */

	protected void makeVocabulariesAndFeatures(AlgaTerraImportState state) throws SQLException {

		String abbrevLabel = null;

		URI uri = null;

		if (! state.isSpecimenVocabulariesCreated()){

			TransactionStatus txStatus = this.startTransaction();

			boolean isOrdered = true;

			OrderedTermVocabulary<State> climateVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraClimate, "Climate", "Climate", abbrevLabel, uri, isOrdered, null);

			OrderedTermVocabulary<State> habitatVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraHabitat, "Habitat", "Habitat", abbrevLabel, uri, isOrdered, null);

			OrderedTermVocabulary<State> lifeformVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraLifeForm, "Lifeform", "Lifeform", abbrevLabel, uri, isOrdered, null);

			Feature feature = getFeature(state, uuidFeatureAlgaTerraClimate, "Climate","Climate", null, null);

			feature.setSupportsCategoricalData(true);

			feature = getFeature(state, uuidFeatureAlgaTerraLifeForm, "LifeForm","LifeForm", null, null);

			feature.setSupportsCategoricalData(true);

			feature = Feature.HABITAT();

			feature.setSupportsCategoricalData(true);

			getTermService().saveOrUpdate(feature);

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

			String climateSql = "SELECT * FROM EcoClimate";

			ResultSet rs = source.getResultSet(climateSql);

			while (rs.next()){

				String climate = rs.getString("Climate");

				String description = rs.getString("Description");

				Integer id = rs.getInt("ClimateId");

				UUID uuid = UUID.fromString(rs.getString("UUID"));

				State stateTerm = getStateTerm(state, uuid, climate, description, null, climateVoc);

				addOriginalSource(stateTerm, id.toString(), "EcoClimate", state.getTransactionalSourceReference());

				getTermService().saveOrUpdate(stateTerm);

			}

			String habitatSql = "SELECT * FROM EcoHabitat";

			rs = source.getResultSet(habitatSql);

			while (rs.next()){

				String habitat = rs.getString("Habitat");

				String description = rs.getString("Description");

				Integer id = rs.getInt("HabitatId");

				UUID uuid = UUID.fromString(rs.getString("UUID"));

				State stateTerm = getStateTerm(state, uuid, habitat, description, null, habitatVoc);

				addOriginalSource(stateTerm, id.toString(), "EcoHabitat", state.getTransactionalSourceReference());

				getTermService().saveOrUpdate(stateTerm);

			}

			String lifeformSql = "SELECT * FROM EcoLifeForm";

			rs = source.getResultSet(lifeformSql);

			while (rs.next()){

				String lifeform = rs.getString("LifeForm");

				String description = rs.getString("Description");

				Integer id = rs.getInt("LifeFormId");

				UUID uuid = UUID.fromString(rs.getString("UUID"));

				State stateTerm = getStateTerm(state, uuid, lifeform, description, null, lifeformVoc);

				addOriginalSource(stateTerm, id.toString(), "EcoLifeForm", state.getTransactionalSourceReference());

				getTermService().saveOrUpdate(stateTerm);

			}

			this.commitTransaction(txStatus);

			state.setSpecimenVocabulariesCreated(true);

		}

	}

	protected String getLocalityString(){

		return "Locality";

	}

	protected void handleFieldObservationSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state, ResultSetPartitioner partitioner) throws SQLException {

		//FIXME missing fields #3084, #3085, #3080

		try {

			Integer unitId = nullSafeInt(rs, "unitId");

			String locality = rs.getString(getLocalityString());

			Double latitude = nullSafeDouble(rs, "Latitude");

			Double longitude = nullSafeDouble(rs, "Longitude");

			Integer errorRadius = nullSafeInt(rs,"Prec");

			String geoCodeMethod = rs.getString("GeoCodeMethod");

			Integer altitude = nullSafeInt(rs, "Altitude");

			Integer lowerAltitude = nullSafeInt(rs,"AltitudeLowerValue");

			String altitudeUnit = rs.getString("AltitudeUnit");

			Double depth = nullSafeDouble(rs, "Depth");

			Double depthLow = nullSafeDouble(rs, "DepthLow");

			String collectorsNumber = rs.getString("CollectorsNumber");

			Date collectionDateStart = rs.getDate("CollectionDate");

			Date collectionDateEnd = rs.getDate("CollectionDateEnd");

			//location

			facade.setLocality(locality);

			//exact location

			ReferenceSystem referenceSystem = makeRefrenceSystem(geoCodeMethod, state);

			if (longitude != null || latitude != null || referenceSystem != null || errorRadius != null){

				Point exactLocation = Point.NewInstance(longitude, latitude, referenceSystem, errorRadius);

				facade.setExactLocation(exactLocation);

			}

			//altitude, depth

			if (StringUtils.isNotBlank(altitudeUnit) && ! altitudeUnit.trim().equalsIgnoreCase("m")){

				logger.warn("Altitude unit is not [m] but: " +  altitudeUnit);

			}

			if ( altitude != null){

				if (lowerAltitude == null){

					facade.setAbsoluteElevation(altitude);

				}else{

			   		if (! facade.isEvenDistance(lowerAltitude, altitude)){

			   			//FIXME there is a ticket for this

			   			altitude = altitude + 1;

			   			logger.info("Current implementation of altitude does not allow uneven distances");

			   		}

					facade.setAbsoluteElevationRange(lowerAltitude,altitude);

			   	}

			}

			if ( depth != null){

				//FIXME needs model change to accept double #3072

				Integer intDepth = depth.intValue();

				if (depthLow == null){

					facade.setDistanceToWaterSurface(intDepth);

				}else{

					//FIXME range not yet in model #3074

			   		facade.setDistanceToWaterSurface(intDepth);

			   	}

			}

			//field

			facade.setFieldNumber(collectorsNumber);

			TimePeriod gatheringPeriod = TimePeriod.NewInstance(collectionDateStart, collectionDateEnd);

			facade.setGatheringPeriod(gatheringPeriod);

			handleCollectorTeam(state, facade, rs);

			//areas

			makeAreas(state, rs, facade);

			//notes

			//TODO is this an annotation on field observation or on the derived unit?

			//id, created, updated, notes

			if (unitId != null){

				this.doIdCreatedUpdatedNotes(state, facade.innerFieldObservation(), rs, unitId, getFieldObservationNameSpace());

			}else{

				logger.warn("FieldObservation has no unitId: " +  facade.innerFieldObservation() + ": " + getFieldObservationNameSpace());

			}

		} catch (Exception e) {

			throw new RuntimeException(e);

		}

	}

	protected void handleFirstDerivedSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state, ResultSetPartitioner partitioner) throws SQLException {

		Integer unitId = nullSafeInt(rs, "unitId");

		Integer collectionFk = nullSafeInt(rs,"CollectionFk");

		//collection

		if (collectionFk != null){

			Collection subCollection = state.getRelatedObject(AlgaTerraCollectionImport.NAMESPACE_SUBCOLLECTION, String.valueOf(collectionFk), Collection.class);

			if (subCollection != null){

				facade.setCollection(subCollection);

			}else{

				Collection collection = state.getRelatedObject(AlgaTerraCollectionImport.NAMESPACE_COLLECTION, String.valueOf(collectionFk), Collection.class);

				facade.setCollection(collection);

			}

		}

		//TODO id, created for fact +  ecoFact

		//    	this.doIdCreatedUpdatedNotes(state, descriptionElement, rs, id, namespace);

		if (unitId != null){

			this.doIdCreatedUpdatedNotes(state, facade.innerDerivedUnit(), rs, unitId, getDerivedUnitNameSpace());

		}else{

			logger.warn("Specimen has no unitId: " +  facade.innerDerivedUnit() + ": " + getDerivedUnitNameSpace());

		}

	}

	protected abstract String getDerivedUnitNameSpace();

	protected abstract String getFieldObservationNameSpace();

	protected DescriptionBase getFieldObservationDescription(DerivedUnitFacade facade) {

		Set<DescriptionBase> descriptions = facade.innerFieldObservation().getDescriptions();

		for (DescriptionBase desc : descriptions){

			if (desc.isImageGallery() == false){

				return desc;

			}

		}

		SpecimenDescription specDesc = SpecimenDescription.NewInstance(facade.innerFieldObservation());

		descriptions.add(specDesc);

		return specDesc;

	}

	private void makeAreas(AlgaTerraImportState state, ResultSet rs, DerivedUnitFacade facade) throws SQLException {

	   	Object gazetteerId = rs.getObject("GazetteerId");

	   	if (gazetteerId != null){

	   		//TDWG

	   		NamedArea tdwgArea;

	   		String tdwg4 = rs.getString("L4Code");

	   		if (isNotBlank(tdwg4)){

	   			tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(tdwg4);

	   		}else{

	   			String tdwg3 = rs.getString("L3Code");

	   			if (isNotBlank(tdwg3)){

	   				tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(tdwg3);

	   			}else{

	   				Integer tdwg2 = rs.getInt("L2Code");   				

	   				tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(String.valueOf(tdwg2));

		   		}

	   		}

	   		if (tdwgArea == null){

	   			logger.warn("TDWG area could not be defined for gazetterId: " + gazetteerId);

	   		}else{

	   			facade.addCollectingArea(tdwgArea);

	   		}

	   		//Countries

	   		WaterbodyOrCountry country = null;

	   		String isoCountry = rs.getString("ISOCountry");

	   		String countryStr = rs.getString("Country");

	   		if (isNotBlank(isoCountry)){

		   		country = WaterbodyOrCountry.getWaterbodyOrCountryByIso3166A2(isoCountry);

	   		}else if (isNotBlank(countryStr)){

	   			logger.warn("Country exists but no ISO code");

	   		}

	   		if (country == null){

	   			logger.warn("Country does not exist for GazetteerID " + gazetteerId);

	   		}else{

	   			facade.setCountry(country);

	   		}

	   	}

	   	//Waterbody

	   	WaterbodyOrCountry waterbody = null;

	   	String waterbodyStr = rs.getString("WaterBody");

	   	if (isNotBlank(waterbodyStr)){

	   		if (waterbodyStr.equals("Atlantic Ocean")){

	   			waterbody = WaterbodyOrCountry.ATLANTICOCEAN();

	   		}else{

	   			logger.warn("Waterbody not recognized: " + waterbody);

	   		}

	   		if (waterbody != null){

	   			facade.addCollectingArea(waterbody);

	   		}

	   	}

	   	//countries sub

	   	//TODO -> SpecimenImport (not existing in TypeSpecimen)

	}

	private ReferenceSystem makeRefrenceSystem(String geoCodeMethod, AlgaTerraImportState state) {

		if (StringUtils.isBlank(geoCodeMethod)){

			return null;

		}else if(geoCodeMethod.startsWith("GPS")){

			getReferenceSystem(state, uuidRefSystemGps, "GPS", "GPS", "GPS", ReferenceSystem.GOOGLE_EARTH().getVocabulary());

			return ReferenceSystem.WGS84(); 

		}else if(geoCodeMethod.startsWith("Google")){

			return ReferenceSystem.GOOGLE_EARTH();

		}else if(geoCodeMethod.startsWith("Map")){

			logger.warn("Reference system " +  geoCodeMethod +  " not yet supported.");

			return null;

		}else if(geoCodeMethod.startsWith("WikiProjekt Georeferenzierung") || geoCodeMethod.startsWith("http://toolserver.org/~geohack/geohack.php") ){

			return ReferenceSystem.WGS84();

		}else {

			logger.warn("Reference system " +  geoCodeMethod +  " not yet supported.");

			return null;

		}

	}

	private void handleCollectorTeam(AlgaTerraImportState state, DerivedUnitFacade facade, ResultSet rs) throws SQLException {

		String collector = rs.getString("Collector");

		TeamOrPersonBase<?> author = getAuthor(collector);

		facade.setCollector(author);

	}

	/**

	 * @param facade

	 * @param collector

	 */

	protected TeamOrPersonBase<?> getAuthor(String author) {

		// FIXME TODO parsen und deduplizieren

		Team team = Team.NewTitledInstance(author, author);

		return team;

	}

	/**

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

	 * @param state 

	 * @param newTaxonId

	 * @param oldTaxonId

	 * @param oldDescription

	 * @param taxonMap

	 * @return

	 */

	protected TaxonDescription getTaxonDescription(AlgaTerraImportState state, Taxon taxon, Reference<?> sourceSec){

		TaxonDescription result = 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);

		}

		return result;

	}

}