app-import/src/main/java/eu/etaxonomy/cdm/io/mexico/MexicoConabioDistributionImport.java

   1 /**
   2 * Copyright (C) 2016 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9 package eu.etaxonomy.cdm.io.mexico;
  10
  11 import eu.etaxonomy.cdm.common.URI;
  12 import java.util.Map;
  13 import java.util.Set;
  14 import java.util.UUID;
  15
  16 import org.apache.commons.lang3.StringUtils;
  17 import org.apache.log4j.Logger;
  18 import org.springframework.stereotype.Component;
  19
  20 import eu.etaxonomy.cdm.ext.geo.GeoServiceArea;
  21 import eu.etaxonomy.cdm.ext.geo.GeoServiceAreaAnnotatedMapping;
  22 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  23 import eu.etaxonomy.cdm.model.common.CdmBase;
  24 import eu.etaxonomy.cdm.model.common.Language;
  25 import eu.etaxonomy.cdm.model.description.Distribution;
  26 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  27 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  28 import eu.etaxonomy.cdm.model.location.NamedArea;
  29 import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
  30 import eu.etaxonomy.cdm.model.location.NamedAreaType;
  31 import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
  32 import eu.etaxonomy.cdm.model.reference.Reference;
  33 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  34 import eu.etaxonomy.cdm.model.taxon.Taxon;
  35 import eu.etaxonomy.cdm.model.term.OrderedTermVocabulary;
  36 import eu.etaxonomy.cdm.model.term.Representation;
  37 import eu.etaxonomy.cdm.model.term.TermType;
  38
  39 /**
  40  * @author a.mueller
  41  * @since 16.06.2016
  42  *
  43  */
  44 @Component
  45 public class MexicoConabioDistributionImport<CONFIG extends MexicoConabioImportConfigurator>
  46             extends SimpleExcelTaxonImport<CONFIG> {
  47
  48     private static final long serialVersionUID = -1733208053395372094L;
  49
  50     private static final Logger logger = Logger.getLogger(MexicoConabioDistributionImport.class);
  51
  52     private OrderedTermVocabulary<NamedArea> stateAreasVoc;
  53     private NamedArea mexico;
  54
  55     private Map<String, Taxon> taxonIdMap;
  56
  57
  58     @Override
  59     protected String getWorksheetName(CONFIG config) {
  60         return "DistribucionEstatal";
  61     }
  62
  63     private void initTaxa() {
  64         if (taxonIdMap == null){
  65             Set<String> existingKeys = MexicoConabioTaxonImport.taxonIdMap.keySet();
  66             taxonIdMap = getCommonService().getSourcedObjectsByIdInSourceC(Taxon.class,
  67                     existingKeys, MexicoConabioTaxonImport.TAXON_NAMESPACE);
  68         }
  69     }
  70
  71     @Override
  72     protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {
  73         initAreaVocabulary(state);
  74         initTaxa();
  75
  76         String line = state.getCurrentLine() + ": ";
  77         Map<String, String> record = state.getOriginalRecord();
  78
  79         String idCat = getValue(record, "IdCAT");
  80         Taxon taxon = taxonIdMap.get(idCat);
  81         if (taxon == null){
  82             logger.warn(line + "Taxon could not be found: " + idCat);
  83         }else{
  84             TaxonDescription desc = getTaxonDescription(taxon);
  85
  86             String distrStatusStr = getValue(record, "TipoDistribucion");
  87             try {
  88                 if (distrStatusStr != null){
  89                     PresenceAbsenceTerm mexicanDistributionStatus = state.getTransformer().getPresenceTermByKey(distrStatusStr);
  90                     if (mexicanDistributionStatus == null){
  91                         UUID statusUuid = state.getTransformer().getPresenceTermUuid(distrStatusStr);
  92                         mexicanDistributionStatus = getPresenceTerm(state, statusUuid,
  93                                 distrStatusStr, distrStatusStr, null, false);
  94                     }
  95                     if (mexicanDistributionStatus != null){
  96                         NamedArea mexicoCountry = getMexico();
  97                         Distribution mexicanDistribution = Distribution.NewInstance(mexicoCountry, mexicanDistributionStatus);
  98                         desc.addElement(mexicanDistribution);
  99                         String refStr = getValue(record, "ReferenciaTipoDistribucion");
 100                         Reference ref = getReference(state, refStr);
 101                         if (ref != null){
 102                             mexicanDistribution.addSource(OriginalSourceType.PrimaryTaxonomicSource,
 103                                     null, null, ref, null);
 104                         }
 105                     }
 106                 }
 107             } catch (UndefinedTransformerMethodException e) {}
 108
 109             handleDistribution(state, desc, "AGUASCALIENTES", MexicoConabioTransformer.uuidAguascalientes, line);
 110             handleDistribution(state, desc, "BAJA CALIFORNIA", MexicoConabioTransformer.uuidBaja_california, line);
 111             handleDistribution(state, desc, "BAJA CALIFORNIA SUR", MexicoConabioTransformer.uuidBaja_california_sur, line);
 112             handleDistribution(state, desc, "CAMPECHE", MexicoConabioTransformer.uuidCampeche, line);
 113             handleDistribution(state, desc, "COAHUILA DE ZARAGOZA", MexicoConabioTransformer.uuidCoahuila_de_zaragoza, line);
 114             handleDistribution(state, desc, "COLIMA", MexicoConabioTransformer.uuidColima, line);
 115             handleDistribution(state, desc, "CHIAPAS", MexicoConabioTransformer.uuidChiapas, line);
 116             handleDistribution(state, desc, "CHIHUAHUA", MexicoConabioTransformer.uuidChihuahua, line);
 117             handleDistribution(state, desc, "DISTRITO FEDERAL", MexicoConabioTransformer.uuidDistrito_federal, line);
 118             handleDistribution(state, desc, "DURANGO", MexicoConabioTransformer.uuidDurango, line);
 119             handleDistribution(state, desc, "GUANAJUATO", MexicoConabioTransformer.uuidGuanajuato, line);
 120             handleDistribution(state, desc, "GUERRERO", MexicoConabioTransformer.uuidGuerrero, line);
 121             handleDistribution(state, desc, "HIDALGO", MexicoConabioTransformer.uuidHidalgo, line);
 122             handleDistribution(state, desc, "JALISCO", MexicoConabioTransformer.uuidJalisco, line);
 123             handleDistribution(state, desc, "MEXICO", MexicoConabioTransformer.uuidMexico, line);
 124             handleDistribution(state, desc, "MICHOACAN DE OCAMPO", MexicoConabioTransformer.uuidMichoacan_de_ocampo, line);
 125             handleDistribution(state, desc, "MORELOS", MexicoConabioTransformer.uuidMorelos, line);
 126             handleDistribution(state, desc, "NAYARIT", MexicoConabioTransformer.uuidNayarit, line);
 127             handleDistribution(state, desc, "NUEVO LEON", MexicoConabioTransformer.uuidNuevo_leon, line);
 128             handleDistribution(state, desc, "OAXACA", MexicoConabioTransformer.uuidOaxaca, line);
 129             handleDistribution(state, desc, "PUEBLA", MexicoConabioTransformer.uuidPuebla, line);
 130             handleDistribution(state, desc, "QUERETARO DE ARTEAGA", MexicoConabioTransformer.uuidQueretaro_de_arteaga, line);
 131             handleDistribution(state, desc, "QUINTANA ROO", MexicoConabioTransformer.uuidQuintana_roo, line);
 132             handleDistribution(state, desc, "SAN LUIS POTOSI", MexicoConabioTransformer.uuidSan_luis_potosi, line);
 133             handleDistribution(state, desc, "SINALOA", MexicoConabioTransformer.uuidSinaloa, line);
 134             handleDistribution(state, desc, "SONORA", MexicoConabioTransformer.uuidSonora, line);
 135             handleDistribution(state, desc, "TABASCO", MexicoConabioTransformer.uuidTabasco, line);
 136             handleDistribution(state, desc, "TAMAULIPAS", MexicoConabioTransformer.uuidTamaulipas, line);
 137             handleDistribution(state, desc, "TLAXCALA", MexicoConabioTransformer.uuidTlaxcala, line);
 138             handleDistribution(state, desc, "VERACRUZ DE IGNACIO DE LA LLAVE", MexicoConabioTransformer.uuidVeracruz_de_ignacio_de_la_llave, line);
 139             handleDistribution(state, desc, "YUCATAN", MexicoConabioTransformer.uuidYucatan, line);
 140             handleDistribution(state, desc, "ZACATECAS", MexicoConabioTransformer.uuidZacatecas, line);
 141
 142             getTaxonService().save(taxon);
 143         }
 144     }
 145
 146     private NamedArea getMexico() {
 147         if (mexico == null){
 148             mexico = CdmBase.deproxy(getTermService().find(MexicoConabioTransformer.uuidMexicoCountry), NamedArea.class);
 149             if (mexico == null){
 150                 logger.warn("Mexico country not found");
 151             }
 152         }
 153         return mexico;
 154     }
 155
 156     /**
 157      * @param state
 158      * @param refStr
 159      * @return
 160      */
 161     private Reference getReference(SimpleExcelTaxonImportState<CONFIG> state, String refStr) {
 162         if (StringUtils.isBlank(refStr)){
 163             return null;
 164         }
 165         Reference ref = state.getReference(refStr);
 166         if (ref == null){
 167             ref = ReferenceFactory.newBook();
 168             ref.setTitleCache(refStr, true);
 169             state.putReference(refStr, ref);
 170         }
 171         return ref;
 172     }
 173
 174     /**
 175      * @param desc
 176      * @param string
 177      * @param uuidUserDefinedAnnotationTypeVocabulary
 178      */
 179     private void handleDistribution(SimpleExcelTaxonImportState<CONFIG> state, TaxonDescription desc, String key,
 180             UUID uuid, String line) {
 181         Map<String, String> record = state.getOriginalRecord();
 182         String value = getValue(record, key);
 183         if ("1".equals(value)){
 184             NamedArea area = getNamedArea(state, uuid, null, null, null, null, null);
 185             Distribution dist = Distribution.NewInstance(area, PresenceAbsenceTerm.PRESENT());
 186             desc.addElement(dist);
 187         }else if (value != null){
 188             logger.warn(line + "Unrecognized distribution status '" + value + "' for " + key);
 189         }
 190     }
 191
 192     /**
 193      * @param taxon
 194      * @return
 195      */
 196     private TaxonDescription getTaxonDescription(Taxon taxon) {
 197         if (!taxon.getDescriptions().isEmpty()){
 198             return taxon.getDescriptions().iterator().next();
 199         }else{
 200             TaxonDescription desc = TaxonDescription.NewInstance(taxon);
 201             return desc;
 202         }
 203     }
 204
 205     /**
 206      * @param state
 207      */
 208     @SuppressWarnings("unchecked")
 209     private void initAreaVocabulary(SimpleExcelTaxonImportState<CONFIG> state) {
 210         if (stateAreasVoc == null){
 211             stateAreasVoc = (OrderedTermVocabulary<NamedArea>)this.getVocabularyService().find(MexicoConabioTransformer.uuidMexicanStatesVoc);
 212             if (stateAreasVoc == null){
 213                 createStateAreasVoc(state);
 214             }
 215         }
 216     }
 217
 218     /**
 219      * @param state
 220      * @return
 221      */
 222     @SuppressWarnings("unchecked")
 223     private void createStateAreasVoc(SimpleExcelTaxonImportState<CONFIG> state) {
 224         //voc
 225         URI termSourceUri = null;
 226         String label = "Mexican States";
 227         String description = "Mexican States as used by the CONABIO Rubiaceae database";
 228         stateAreasVoc = OrderedTermVocabulary.NewInstance(TermType.NamedArea,
 229                 description, label, null, termSourceUri);
 230         stateAreasVoc.setUuid(MexicoConabioTransformer.uuidMexicanStatesVoc);
 231         Representation rep = Representation.NewInstance("Estados Méxicanos", "Estados Méxicanos", null, Language.SPANISH_CASTILIAN());
 232         stateAreasVoc.addRepresentation(rep);
 233
 234         //mexico country
 235         String mexicoLabel = "Mexico (Country)";
 236         mexico = NamedArea.NewInstance(
 237                 mexicoLabel, mexicoLabel, null);
 238         mexico.setUuid(MexicoConabioTransformer.uuidMexicoCountry);
 239         stateAreasVoc.addTerm(mexico);
 240          addMapping(mexico, "mex_adm0", "iso", "MEX");
 241
 242          //Example with almost all areas is Chiococca alba
 243          addArea(state, "Aguascalientes", MexicoConabioTransformer.uuidAguascalientes);
 244          addArea(state, "Baja California", MexicoConabioTransformer.uuidBaja_california);
 245          addArea(state, "Baja California Sur", MexicoConabioTransformer.uuidBaja_california_sur);
 246          addArea(state, "Campeche", MexicoConabioTransformer.uuidCampeche);
 247          addArea(state, "Coahuila de Zaragoza", MexicoConabioTransformer.uuidCoahuila_de_zaragoza, "Coahuila");
 248          addArea(state, "Colima", MexicoConabioTransformer.uuidColima);
 249          addArea(state, "Chiapas", MexicoConabioTransformer.uuidChiapas);
 250          addArea(state, "Chihuahua", MexicoConabioTransformer.uuidChihuahua);
 251          addArea(state, "Distrito Federal", MexicoConabioTransformer.uuidDistrito_federal);
 252          addArea(state, "Durango", MexicoConabioTransformer.uuidDurango);
 253          addArea(state, "Guanajuato", MexicoConabioTransformer.uuidGuanajuato);
 254          addArea(state, "Guerrero", MexicoConabioTransformer.uuidGuerrero);
 255          addArea(state, "Hidalgo", MexicoConabioTransformer.uuidHidalgo);
 256          addArea(state, "Jalisco", MexicoConabioTransformer.uuidJalisco);
 257         //id_1
 258         addArea(state, "México", MexicoConabioTransformer.uuidMexico, null, 15);
 259         //id_1
 260         addArea(state, "Michoacan de Ocampo", MexicoConabioTransformer.uuidMichoacan_de_ocampo, "Michoacán", 16);
 261          addArea(state, "Morelos", MexicoConabioTransformer.uuidMorelos);
 262          addArea(state, "Nayarit", MexicoConabioTransformer.uuidNayarit);
 263         //gibt beim mapping vielleicht Probleme wg. des Accents
 264         //id_1
 265         addArea(state, "Nuevo Leon", MexicoConabioTransformer.uuidNuevo_leon, "Nuevo León", 19);
 266          addArea(state, "Oaxaca", MexicoConabioTransformer.uuidOaxaca);
 267          addArea(state, "Puebla", MexicoConabioTransformer.uuidPuebla);
 268         //id_1
 269         addArea(state, "Queretaro de Arteaga", MexicoConabioTransformer.uuidQueretaro_de_arteaga, "Querétaro", 22);
 270          addArea(state, "Quintana Roo", MexicoConabioTransformer.uuidQuintana_roo);
 271         //id_1
 272         addArea(state, "San Luis Potosí", MexicoConabioTransformer.uuidSan_luis_potosi,null ,24);
 273          addArea(state, "Sinaloa", MexicoConabioTransformer.uuidSinaloa);
 274          addArea(state, "Sonora", MexicoConabioTransformer.uuidSonora);
 275          addArea(state, "Tabasco", MexicoConabioTransformer.uuidTabasco);
 276          addArea(state, "Tamaulipas", MexicoConabioTransformer.uuidTamaulipas);
 277          addArea(state, "Tlaxcala", MexicoConabioTransformer.uuidTlaxcala);
 278          addArea(state, "Veracruz de Ignacio de la Llave", MexicoConabioTransformer.uuidVeracruz_de_ignacio_de_la_llave, "Veracruz");
 279         //??
 280         addArea(state, "Yucatán", MexicoConabioTransformer.uuidYucatan, null, 31);
 281          addArea(state, "Zacatecas", MexicoConabioTransformer.uuidZacatecas);
 282
 283         this.getVocabularyService().save(stateAreasVoc);
 284
 285         return;
 286     }
 287
 288
 289     private void addArea(SimpleExcelTaxonImportState<CONFIG> state, String areaLabel, UUID uuid) {
 290         addArea(state, areaLabel, uuid, areaLabel);  //short cut if label and mapping label are equal
 291     }
 292
 293     private void addArea(SimpleExcelTaxonImportState<CONFIG> state, String areaLabel, UUID uuid, String mappingLabel) {
 294         addArea(state, areaLabel, uuid, mappingLabel, null);  //short cut if label and mapping label are equal
 295     }
 296
 297
 298     /**
 299      * @param state
 300      * @param string
 301      * @param uuidaguascalientes
 302      */
 303     private void addArea(SimpleExcelTaxonImportState<CONFIG> state, String areaLabel, UUID uuid, String mappingLabel, Integer id1) {
 304         String abbrev = null;
 305         NamedArea newArea = NamedArea.NewInstance(
 306                 areaLabel, areaLabel, abbrev);
 307         newArea.setUuid(uuid);
 308         newArea.setPartOf(mexico);
 309         newArea.setLevel(NamedAreaLevel.STATE());
 310         newArea.setType(NamedAreaType.ADMINISTRATION_AREA());
 311         stateAreasVoc.addTerm(newArea);
 312         if (id1 != null){
 313             addMapping(newArea, "mex_adm1", "id_1", String.valueOf(id1));
 314         }else if (mappingLabel != null){
 315             addMapping(newArea, "mex_adm1", "name_1", mappingLabel);
 316         }
 317     }
 318
 319     private void addMapping(NamedArea area, String mapping_layer, String mapping_field, String abbrev) {
 320         GeoServiceAreaAnnotatedMapping mapping = (GeoServiceAreaAnnotatedMapping)this.getBean("geoServiceAreaAnnotatedMapping");
 321         GeoServiceArea geoServiceArea = new GeoServiceArea();
 322         geoServiceArea.add(mapping_layer, mapping_field, abbrev);
 323         mapping.set(area, geoServiceArea);
 324     }
 325
 326     @Override
 327     protected boolean isIgnore(SimpleExcelTaxonImportState<CONFIG> state) {
 328         return ! state.getConfig().isDoDistributions();
 329     }
 330
 331 }