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 java.net.URI;
  12 import java.util.HashMap;
  13 import java.util.Map;
  14 import java.util.Set;
  15 import java.util.UUID;
  16
  17 import org.apache.commons.lang3.StringUtils;
  18 import org.apache.log4j.Logger;
  19 import org.springframework.stereotype.Component;
  20
  21 import eu.etaxonomy.cdm.ext.geo.GeoServiceArea;
  22 import eu.etaxonomy.cdm.ext.geo.GeoServiceAreaAnnotatedMapping;
  23 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  24 import eu.etaxonomy.cdm.model.common.Language;
  25 import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
  26 import eu.etaxonomy.cdm.model.common.OriginalSourceType;
  27 import eu.etaxonomy.cdm.model.common.Representation;
  28 import eu.etaxonomy.cdm.model.common.TermType;
  29 import eu.etaxonomy.cdm.model.description.Distribution;
  30 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  31 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  32 import eu.etaxonomy.cdm.model.location.NamedArea;
  33 import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
  34 import eu.etaxonomy.cdm.model.location.NamedAreaType;
  35 import eu.etaxonomy.cdm.model.reference.Reference;
  36 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  37 import eu.etaxonomy.cdm.model.taxon.Taxon;
  38
  39 /**
  40  * @author a.mueller
  41  * @date 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() {
  60         return "DistribucionEstatal";
  61     }
  62
  63     @SuppressWarnings("unchecked")
  64     private void initTaxa() {
  65         if (taxonIdMap == null){
  66             Set<String> existingKeys = MexicoConabioTaxonImport.taxonIdMap.keySet();
  67             taxonIdMap = (Map<String, Taxon>)getCommonService().getSourcedObjectsByIdInSource(Taxon.class,
  68                     existingKeys, MexicoConabioTaxonImport.TAXON_NAMESPACE);
  69         }
  70     }
  71
  72     @Override
  73     protected void firstPass(SimpleExcelTaxonImportState<CONFIG> state) {
  74         initAreaVocabulary(state);
  75         initTaxa();
  76
  77         String line = state.getCurrentLine() + ": ";
  78         HashMap<String, String> record = state.getOriginalRecord();
  79
  80         String idCat = getValue(record, "IdCAT");
  81         Taxon taxon = taxonIdMap.get(idCat);
  82         if (taxon == null){
  83             logger.warn(line + "Taxon could not be found: " + idCat);
  84         }else{
  85             TaxonDescription desc = getTaxonDescription(taxon);
  86
  87             String distrStatusStr = getValue(record, "TipoDistribucion");
  88             try {
  89                 if (distrStatusStr != null){
  90                     PresenceAbsenceTerm mexicanDistributionStatus = state.getTransformer().getPresenceTermByKey(distrStatusStr);
  91                     if (mexicanDistributionStatus == null){
  92                         UUID statusUuid = state.getTransformer().getPresenceTermUuid(distrStatusStr);
  93                         mexicanDistributionStatus = getPresenceTerm(state, statusUuid,
  94                                 distrStatusStr, distrStatusStr, null, false);
  95                     }
  96                     if (mexicanDistributionStatus != null){
  97                         Distribution mexicanDistribution = Distribution.NewInstance(mexico, 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     }
 147
 148     /**
 149      * @param state
 150      * @param refStr
 151      * @return
 152      */
 153     private Reference getReference(SimpleExcelTaxonImportState<CONFIG> state, String refStr) {
 154         if (StringUtils.isNoneBlank(refStr)){
 155             return null;
 156         }
 157         Reference ref = state.getReference(refStr);
 158         if (ref == null){
 159             ref = ReferenceFactory.newBook();
 160             ref.setTitleCache(refStr, true);
 161             state.putReference(refStr, ref);
 162         }
 163         return ref;
 164     }
 165
 166     /**
 167      * @param desc
 168      * @param string
 169      * @param uuidUserDefinedAnnotationTypeVocabulary
 170      */
 171     private void handleDistribution(SimpleExcelTaxonImportState<CONFIG> state, TaxonDescription desc, String key,
 172             UUID uuid, String line) {
 173         HashMap<String, String> record = state.getOriginalRecord();
 174         String value = getValue(record, key);
 175         if ("1".equals(value)){
 176             NamedArea area = getNamedArea(state, uuid, null, null, null, null, null);
 177             Distribution dist = Distribution.NewInstance(area, PresenceAbsenceTerm.PRESENT());
 178             desc.addElement(dist);
 179         }else if (value != null){
 180             logger.warn(line + "Unrecognized distribution status '" + value + "' for " + key);
 181         }
 182     }
 183
 184     /**
 185      * @param taxon
 186      * @return
 187      */
 188     private TaxonDescription getTaxonDescription(Taxon taxon) {
 189         if (!taxon.getDescriptions().isEmpty()){
 190             return taxon.getDescriptions().iterator().next();
 191         }else{
 192             TaxonDescription desc = TaxonDescription.NewInstance(taxon);
 193             return desc;
 194         }
 195     }
 196
 197     /**
 198      * @param state
 199      */
 200     @SuppressWarnings("unchecked")
 201     private void initAreaVocabulary(SimpleExcelTaxonImportState<CONFIG> state) {
 202         if (stateAreasVoc == null){
 203             stateAreasVoc = (OrderedTermVocabulary<NamedArea>)this.getVocabularyService().find(MexicoConabioTransformer.uuidMexicanStatesVoc);
 204             if (stateAreasVoc == null){
 205                 createStateAreasVoc(state);
 206             }
 207         }
 208     }
 209
 210     /**
 211      * @param state
 212      * @return
 213      */
 214     @SuppressWarnings("unchecked")
 215     private void createStateAreasVoc(SimpleExcelTaxonImportState<CONFIG> state) {
 216         //voc
 217         URI termSourceUri = null;
 218         String label = "Mexican States";
 219         String description = "Mexican States as used by the CONABIO Rubiaceae database";
 220         stateAreasVoc = OrderedTermVocabulary.NewInstance(TermType.NamedArea,
 221                 description, label, null, termSourceUri);
 222         stateAreasVoc.setUuid(MexicoConabioTransformer.uuidMexicanStatesVoc);
 223         Representation rep = Representation.NewInstance("Estados Méxicanos", "Estados Méxicanos", null, Language.SPANISH_CASTILIAN());
 224         stateAreasVoc.addRepresentation(rep);
 225
 226         //mexico country
 227         String mexicoLabel = "Mexico (Country)";
 228         mexico = NamedArea.NewInstance(
 229                 mexicoLabel, mexicoLabel, null);
 230         mexico.setUuid(MexicoConabioTransformer.uuidMexicoCountry);
 231         stateAreasVoc.addTerm(mexico);
 232          addMapping(mexico, "mex_adm0", "iso", "MEX");
 233
 234          //Example with almost all areas is Chiococca alba
 235          addArea(state, "Aguascalientes", MexicoConabioTransformer.uuidAguascalientes);
 236          addArea(state, "Baja California", MexicoConabioTransformer.uuidBaja_california);
 237          addArea(state, "Baja California Sur", MexicoConabioTransformer.uuidBaja_california_sur);
 238          addArea(state, "Campeche", MexicoConabioTransformer.uuidCampeche);
 239          addArea(state, "Coahuila de Zaragoza", MexicoConabioTransformer.uuidCoahuila_de_zaragoza, "Coahuila");
 240          addArea(state, "Colima", MexicoConabioTransformer.uuidColima);
 241          addArea(state, "Chiapas", MexicoConabioTransformer.uuidChiapas);
 242          addArea(state, "Chihuahua", MexicoConabioTransformer.uuidChihuahua);
 243          addArea(state, "Distrito Federal", MexicoConabioTransformer.uuidDistrito_federal);
 244          addArea(state, "Durango", MexicoConabioTransformer.uuidDurango);
 245          addArea(state, "Guanajuato", MexicoConabioTransformer.uuidGuanajuato);
 246          addArea(state, "Guerrero", MexicoConabioTransformer.uuidGuerrero);
 247          addArea(state, "Hidalgo", MexicoConabioTransformer.uuidHidalgo);
 248          addArea(state, "Jalisco", MexicoConabioTransformer.uuidJalisco);
 249         //id_1
 250         addArea(state, "México", MexicoConabioTransformer.uuidMexico, null, 15);
 251         //id_1
 252         addArea(state, "Michoacan de Ocampo", MexicoConabioTransformer.uuidMichoacan_de_ocampo, "Michoacán", 16);
 253          addArea(state, "Morelos", MexicoConabioTransformer.uuidMorelos);
 254          addArea(state, "Nayarit", MexicoConabioTransformer.uuidNayarit);
 255         //gibt beim mapping vielleicht Probleme wg. des Accents
 256         //id_1
 257         addArea(state, "Nuevo Leon", MexicoConabioTransformer.uuidNuevo_leon, "Nuevo León", 19);
 258          addArea(state, "Oaxaca", MexicoConabioTransformer.uuidOaxaca);
 259          addArea(state, "Puebla", MexicoConabioTransformer.uuidPuebla);
 260         //id_1
 261         addArea(state, "Queretaro de Arteaga", MexicoConabioTransformer.uuidQueretaro_de_arteaga, "Querétaro", 22);
 262          addArea(state, "Quintana Roo", MexicoConabioTransformer.uuidQuintana_roo);
 263         //id_1
 264         addArea(state, "San Luis Potosí", MexicoConabioTransformer.uuidSan_luis_potosi,null ,24);
 265          addArea(state, "Sinaloa", MexicoConabioTransformer.uuidSinaloa);
 266          addArea(state, "Sonora", MexicoConabioTransformer.uuidSonora);
 267          addArea(state, "Tabasco", MexicoConabioTransformer.uuidTabasco);
 268          addArea(state, "Tamaulipas", MexicoConabioTransformer.uuidTamaulipas);
 269          addArea(state, "Tlaxcala", MexicoConabioTransformer.uuidTlaxcala);
 270          addArea(state, "Veracruz de Ignacio de la Llave", MexicoConabioTransformer.uuidVeracruz_de_ignacio_de_la_llave, "Veracruz");
 271         //??
 272         addArea(state, "Yucatán", MexicoConabioTransformer.uuidYucatan, null, 31);
 273          addArea(state, "Zacatecas", MexicoConabioTransformer.uuidZacatecas);
 274
 275         this.getVocabularyService().save(stateAreasVoc);
 276
 277         return;
 278     }
 279
 280
 281     private void addArea(SimpleExcelTaxonImportState<CONFIG> state, String areaLabel, UUID uuid) {
 282         addArea(state, areaLabel, uuid, areaLabel);  //short cut if label and mapping label are equal
 283     }
 284
 285     private void addArea(SimpleExcelTaxonImportState<CONFIG> state, String areaLabel, UUID uuid, String mappingLabel) {
 286         addArea(state, areaLabel, uuid, mappingLabel, null);  //short cut if label and mapping label are equal
 287     }
 288
 289
 290     /**
 291      * @param state
 292      * @param string
 293      * @param uuidaguascalientes
 294      */
 295     private void addArea(SimpleExcelTaxonImportState<CONFIG> state, String areaLabel, UUID uuid, String mappingLabel, Integer id1) {
 296         String abbrev = null;
 297         NamedArea newArea = NamedArea.NewInstance(
 298                 areaLabel, areaLabel, abbrev);
 299         newArea.setUuid(uuid);
 300         newArea.setPartOf(mexico);
 301         newArea.setLevel(NamedAreaLevel.STATE());
 302         newArea.setType(NamedAreaType.ADMINISTRATION_AREA());
 303         stateAreasVoc.addTerm(newArea);
 304         if (id1 != null){
 305             addMapping(newArea, "mex_adm1", "id_1", String.valueOf(id1));
 306         }else if (mappingLabel != null){
 307             addMapping(newArea, "mex_adm1", "name_1", mappingLabel);
 308         }
 309     }
 310
 311     private void addMapping(NamedArea area, String mapping_layer, String mapping_field, String abbrev) {
 312         GeoServiceAreaAnnotatedMapping mapping = (GeoServiceAreaAnnotatedMapping)this.getBean("geoServiceAreaAnnotatedMapping");
 313         GeoServiceArea geoServiceArea = new GeoServiceArea();
 314         geoServiceArea.add(mapping_layer, mapping_field, abbrev);
 315         mapping.set(area, geoServiceArea);
 316     }
 317
 318     @Override
 319     protected boolean isIgnore(SimpleExcelTaxonImportState<CONFIG> state) {
 320         return ! state.getConfig().isDoDistributions();
 321     }
 322
 323 }