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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.algaterra;
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import java.net.URI;
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import java.sql.Date;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
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import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.common.TimePeriod;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.SpecimenDescription;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.location.Point;
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import eu.etaxonomy.cdm.model.location.ReferenceSystem;
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import eu.etaxonomy.cdm.model.location.TdwgArea;
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import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
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/**
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* @author a.mueller
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* @created 12.09.2012
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*/
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public abstract class AlgaTerraSpecimenImportBase extends BerlinModelImportBase{
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private static final Logger logger = Logger.getLogger(AlgaTerraSpecimenImportBase.class);
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public static final String ECO_FACT_NAMESPACE = "EcoFact";
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public static final String TYPE_SPECIMEN_NAMESPACE = "TypeSpecimen";
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public static final String TERMS_NAMESPACE = "ALGA_TERRA_TERMS";
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//TODO move to transformrer
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final static UUID uuidMarkerAlkalinity = UUID.fromString("e52d0ea2-0c1f-4d95-ae6d-e21ab317c594");
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final static UUID uuidRefSystemGps = UUID.fromString("c23e4928-c137-4e4a-b6ab-b430da3d0b94");
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final static UUID uuidFeatureSpecimenCommunity = UUID.fromString("3ff5b1ab-3999-4b5a-b8f7-01fd2f6c12c7");
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final static UUID uuidFeatureAdditionalData = UUID.fromString("0ac82ab8-2c2b-4953-98eb-a9f718eb9c57");
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final static UUID uuidFeatureHabitatExplanation = UUID.fromString("6fe32295-61a3-44fc-9fcf-a85790ea888f");
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final static UUID uuidVocAlgaTerraClimate = UUID.fromString("b0a677c6-8bb6-43f4-b1b8-fc377a10feb5");
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final static UUID uuidVocAlgaTerraHabitat = UUID.fromString("06f30114-e19c-4e7d-a8e5-5488c41fcbc5");
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final static UUID uuidVocAlgaTerraLifeForm = UUID.fromString("3c0b194e-809c-4b42-9498-6ff034066ed7");
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final static UUID uuidFeatureAlgaTerraClimate = UUID.fromString("8754674c-9ab9-4f28-95f1-91eeee2314ee");
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final static UUID uuidFeatureAlgaTerraHabitat = UUID.fromString("7def3fc2-cdc5-4739-8e13-62edbd053415");
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final static UUID uuidFeatureAlgaTerraLifeForm = UUID.fromString("9b657901-1b0d-4a2a-8d21-dd8c1413e2e6");
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final static UUID uuidVocParameter = UUID.fromString("45888b40-5bbb-4293-aa1e-02479796cd7c");
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final static UUID uuidStatMeasureSingleValue = UUID.fromString("eb4c3d98-4d4b-4c37-8eb4-17315ce79920");
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final static UUID uuidMeasurementValueModifier = UUID.fromString("0218a7a3-f6c0-4d06-a4f8-6b50b73aef5e");
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final static UUID uuidModifierLowerThan = UUID.fromString("2b500085-6bef-4003-b6ea-e0ad0237d79d");
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final static UUID uuidModifierGreaterThan = UUID.fromString("828df49d-c745-48f7-b083-0ada43356c34");
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/**
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* Creates the vocabularies and the features for Climate, Habitat and Lifeform
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* @param state
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* @throws SQLException
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*/
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protected void makeVocabulariesAndFeatures(AlgaTerraImportState state) throws SQLException {
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String abbrevLabel = null;
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URI uri = null;
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if (! state.isSpecimenVocabulariesCreated()){
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TransactionStatus txStatus = this.startTransaction();
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boolean isOrdered = true;
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OrderedTermVocabulary<State> climateVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraClimate, "Climate", "Climate", abbrevLabel, uri, isOrdered, null);
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OrderedTermVocabulary<State> habitatVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraHabitat, "Habitat", "Habitat", abbrevLabel, uri, isOrdered, null);
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OrderedTermVocabulary<State> lifeformVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraLifeForm, "Lifeform", "Lifeform", abbrevLabel, uri, isOrdered, null);
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Feature feature = getFeature(state, uuidFeatureAlgaTerraClimate, "Climate","Climate", null, null);
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feature.setSupportsCategoricalData(true);
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feature = getFeature(state, uuidFeatureAlgaTerraLifeForm, "LifeForm","LifeForm", null, null);
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feature.setSupportsCategoricalData(true);
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feature = Feature.HABITAT();
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feature.setSupportsCategoricalData(true);
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getTermService().saveOrUpdate(feature);
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Source source = state.getAlgaTerraConfigurator().getSource();
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String climateSql = "SELECT * FROM EcoClimate";
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ResultSet rs = source.getResultSet(climateSql);
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while (rs.next()){
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String climate = rs.getString("Climate");
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String description = rs.getString("Description");
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Integer id = rs.getInt("ClimateId");
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UUID uuid = UUID.fromString(rs.getString("UUID"));
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State stateTerm = getStateTerm(state, uuid, climate, description, null, climateVoc);
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addOriginalSource(stateTerm, id.toString(), "EcoClimate", state.getTransactionalSourceReference());
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getTermService().saveOrUpdate(stateTerm);
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}
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String habitatSql = "SELECT * FROM EcoHabitat";
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rs = source.getResultSet(habitatSql);
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while (rs.next()){
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String habitat = rs.getString("Habitat");
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String description = rs.getString("Description");
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Integer id = rs.getInt("HabitatId");
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UUID uuid = UUID.fromString(rs.getString("UUID"));
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State stateTerm = getStateTerm(state, uuid, habitat, description, null, habitatVoc);
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addOriginalSource(stateTerm, id.toString(), "EcoHabitat", state.getTransactionalSourceReference());
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getTermService().saveOrUpdate(stateTerm);
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}
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String lifeformSql = "SELECT * FROM EcoLifeForm";
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rs = source.getResultSet(lifeformSql);
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while (rs.next()){
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String lifeform = rs.getString("LifeForm");
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String description = rs.getString("Description");
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Integer id = rs.getInt("LifeFormId");
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UUID uuid = UUID.fromString(rs.getString("UUID"));
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State stateTerm = getStateTerm(state, uuid, lifeform, description, null, lifeformVoc);
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addOriginalSource(stateTerm, id.toString(), "EcoLifeForm", state.getTransactionalSourceReference());
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getTermService().saveOrUpdate(stateTerm);
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}
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this.commitTransaction(txStatus);
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state.setSpecimenVocabulariesCreated(true);
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}
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}
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protected String getLocalityString(){
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return "Locality";
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}
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protected void handleSingleSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state) throws SQLException {
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//FIXME missing fields #3084, #3085, #3080
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try {
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String locality = rs.getString(getLocalityString());
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Double latitude = nullSafeDouble(rs, "Latitude");
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Double longitude = nullSafeDouble(rs, "Longitude");
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Integer errorRadius = nullSafeInt(rs,"Prec");
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String geoCodeMethod = rs.getString("GeoCodeMethod");
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Integer altitude = nullSafeInt(rs, "Altitude");
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Integer lowerAltitude = nullSafeInt(rs,"AltitudeLowerValue");
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String altitudeUnit = rs.getString("AltitudeUnit");
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Double depth = nullSafeDouble(rs, "Depth");
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Double depthLow = nullSafeDouble(rs, "DepthLow");
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String collectorsNumber = rs.getString("CollectorsNumber");
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Date collectionDateStart = rs.getDate("CollectionDate");
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Date collectionDateEnd = rs.getDate("CollectionDateEnd");
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//location
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facade.setLocality(locality);
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//exact location
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ReferenceSystem referenceSystem = makeRefrenceSystem(geoCodeMethod, state);
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if (longitude != null || latitude != null || referenceSystem != null || errorRadius != null){
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Point exactLocation = Point.NewInstance(longitude, latitude, referenceSystem, errorRadius);
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facade.setExactLocation(exactLocation);
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}
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//altitude, depth
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if (StringUtils.isNotBlank(altitudeUnit) && ! altitudeUnit.trim().equalsIgnoreCase("m")){
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logger.warn("Altitude unit is not [m] but: " + altitudeUnit);
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}
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if ( altitude != null){
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if (lowerAltitude == null){
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facade.setAbsoluteElevation(altitude);
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}else{
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if (! facade.isEvenDistance(lowerAltitude, altitude)){
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//FIXME there is a ticket for this
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altitude = altitude + 1;
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logger.info("Current implementation of altitude does not allow uneven distances");
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}
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facade.setAbsoluteElevationRange(lowerAltitude,altitude);
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}
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}
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if ( depth != null){
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//FIXME needs model change to accept double #3072
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Integer intDepth = depth.intValue();
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if (depthLow == null){
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facade.setDistanceToWaterSurface(intDepth);
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}else{
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//FIXME range not yet in model #3074
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facade.setDistanceToWaterSurface(intDepth);
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}
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}
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//field
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facade.setFieldNumber(collectorsNumber);
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TimePeriod gatheringPeriod = TimePeriod.NewInstance(collectionDateStart, collectionDateEnd);
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facade.setGatheringPeriod(gatheringPeriod);
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handleCollectorTeam(state, facade, rs);
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//areas
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makeAreas(state, rs, facade);
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//notes
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//TODO is this an annotation on field observation or on the derived unit?
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//TODO id, created for fact + ecoFact
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// this.doIdCreatedUpdatedNotes(state, descriptionElement, rs, id, namespace);
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} catch (Exception e) {
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throw new RuntimeException(e);
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}
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}
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protected DescriptionBase getFieldObservationDescription(DerivedUnitFacade facade) {
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Set<DescriptionBase> descriptions = facade.innerFieldObservation().getDescriptions();
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for (DescriptionBase desc : descriptions){
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if (desc.isImageGallery() == false){
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return desc;
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}
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}
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SpecimenDescription specDesc = SpecimenDescription.NewInstance(facade.innerFieldObservation());
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descriptions.add(specDesc);
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return specDesc;
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}
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private void makeAreas(AlgaTerraImportState state, ResultSet rs, DerivedUnitFacade facade) throws SQLException {
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Object gazetteerId = rs.getObject("GazetteerId");
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if (gazetteerId != null){
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//TDWG
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NamedArea tdwgArea;
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String tdwg4 = rs.getString("L4Code");
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if (isNotBlank(tdwg4)){
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tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(tdwg4);
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}else{
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String tdwg3 = rs.getString("L3Code");
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if (isNotBlank(tdwg3)){
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tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(tdwg3);
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}else{
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Integer tdwg2 = rs.getInt("L2Code");
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tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(String.valueOf(tdwg2));
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}
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}
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if (tdwgArea == null){
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logger.warn("TDWG area could not be defined for gazetterId: " + gazetteerId);
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}else{
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facade.addCollectingArea(tdwgArea);
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}
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//Countries
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WaterbodyOrCountry country = null;
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String isoCountry = rs.getString("ISOCountry");
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String countryStr = rs.getString("Country");
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if (isNotBlank(isoCountry)){
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country = WaterbodyOrCountry.getWaterbodyOrCountryByIso3166A2(isoCountry);
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}else if (isNotBlank(countryStr)){
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logger.warn("Country exists but no ISO code");
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}
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if (country == null){
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logger.warn("Country does not exist for GazetteerID " + gazetteerId);
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}else{
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facade.setCountry(country);
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}
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}
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//Waterbody
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WaterbodyOrCountry waterbody = null;
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String waterbodyStr = rs.getString("WaterBody");
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if (isNotBlank(waterbodyStr)){
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if (waterbodyStr.equals("Atlantic Ocean")){
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waterbody = WaterbodyOrCountry.ATLANTICOCEAN();
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}else{
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logger.warn("Waterbody not recognized: " + waterbody);
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}
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if (waterbody != null){
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facade.addCollectingArea(waterbody);
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}
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}
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//countries sub
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//TODO -> SpecimenImport (not existing in TypeSpecimen)
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}
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private ReferenceSystem makeRefrenceSystem(String geoCodeMethod, AlgaTerraImportState state) {
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if (StringUtils.isBlank(geoCodeMethod)){
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return null;
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}else if(geoCodeMethod.startsWith("GPS")){
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getReferenceSystem(state, uuidRefSystemGps, "GPS", "GPS", "GPS", ReferenceSystem.GOOGLE_EARTH().getVocabulary());
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return ReferenceSystem.WGS84();
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}else if(geoCodeMethod.startsWith("Google")){
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return ReferenceSystem.GOOGLE_EARTH();
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}else if(geoCodeMethod.startsWith("Map")){
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logger.warn("Reference system " + geoCodeMethod + " not yet supported.");
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return null;
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}else if(geoCodeMethod.startsWith("WikiProjekt Georeferenzierung") || geoCodeMethod.startsWith("http://toolserver.org/~geohack/geohack.php") ){
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return ReferenceSystem.WGS84();
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}else {
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logger.warn("Reference system " + geoCodeMethod + " not yet supported.");
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return null;
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}
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}
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private void handleCollectorTeam(AlgaTerraImportState state, DerivedUnitFacade facade, ResultSet rs) throws SQLException {
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// FIXME parsen
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String collector = rs.getString("Collector");
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|
331
|
Team team = Team.NewTitledInstance(collector, collector);
|
|
332
|
facade.setCollector(team);
|
|
333
|
}
|
|
334
|
|
|
335
|
|
|
336
|
|
|
337
|
|
|
338
|
}
|