app-import/src/main/java/eu/etaxonomy/cdm/app/cyprus/CyprusAltitudeActivator.java

   1 /**
   2 * Copyright (C) 2007 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
  10 package eu.etaxonomy.cdm.app.cyprus;
  11
  12 import java.io.FileNotFoundException;
  13 import java.net.URISyntaxException;
  14 import java.util.HashSet;
  15 import java.util.List;
  16 import java.util.Map;
  17 import java.util.Set;
  18 import java.util.UUID;
  19
  20 import org.apache.commons.lang3.StringUtils;
  21 import org.apache.logging.log4j.LogManager;
  22 import org.apache.logging.log4j.Logger;
  23 import org.springframework.transaction.TransactionStatus;
  24
  25 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  26 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  27 import eu.etaxonomy.cdm.common.ExcelUtils;
  28 import eu.etaxonomy.cdm.common.URI;
  29 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  30 import eu.etaxonomy.cdm.database.ICdmDataSource;
  31 import eu.etaxonomy.cdm.io.api.application.CdmIoApplicationController;
  32 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  33 import eu.etaxonomy.cdm.model.common.CdmBase;
  34 import eu.etaxonomy.cdm.model.description.Feature;
  35 import eu.etaxonomy.cdm.model.description.MeasurementUnit;
  36 import eu.etaxonomy.cdm.model.description.QuantitativeData;
  37 import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
  38 import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
  39 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  40 import eu.etaxonomy.cdm.model.name.TaxonName;
  41 import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
  42 import eu.etaxonomy.cdm.model.reference.Reference;
  43 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  44 import eu.etaxonomy.cdm.model.taxon.Synonym;
  45 import eu.etaxonomy.cdm.model.taxon.Taxon;
  46 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  47
  48 /**
  49  * @author a.mueller
  50  * @since 16.12.2010
  51  */
  52 public class CyprusAltitudeActivator {
  53
  54     private static final Logger logger = LogManager.getLogger();
  55
  56         //database validation status (create, update, validate ...)
  57         static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
  58         static final URI source = cyprus_altitude();
  59
  60
  61         static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  62 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql_test();
  63 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_cyprus();
  64 //      static final ICdmDataSource cdmDestination = CdmDestinations.cdm_cyprus_production();
  65
  66
  67         //feature tree uuid
  68         public static final UUID featureTreeUuid = UUID.fromString("14d1e912-5ec2-4d10-878b-828788b70a87");
  69
  70         //classification
  71         static final UUID classificationUuid = UUID.fromString("0c2b5d25-7b15-4401-8b51-dd4be0ee5cab");
  72
  73         private static final String sourceReferenceTitle = "Cyprus Excel Altitude Import";
  74
  75         private static final UUID uuidAltitudeFeature = Feature.uuidAltitude;
  76
  77         //check - import
  78         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  79
  80         private void doImport(ICdmDataSource cdmDestination){
  81
  82                 List<Map<String, String>> excel;
  83                 try {
  84                         excel = ExcelUtils.parseXLS(source, "coreTax");
  85                 } catch (FileNotFoundException e) {
  86                         e.printStackTrace();
  87                         return;
  88                 }
  89
  90                 CdmApplicationController app = CdmIoApplicationController.NewInstance(cdmDestination, hbm2dll);
  91
  92                 @SuppressWarnings("rawtypes")
  93         Set<TaxonBase> taxaToSave = new HashSet<>();
  94
  95                 TransactionStatus tx = app.startTransaction();
  96
  97                 UUID uuidMikle77 = UUID.fromString("9f5fa7ee-538b-4ae5-bd82-2a9503fea1d6");
  98                 UUID uuidMikle85 = UUID.fromString("994403c4-c400-413d-9a1a-8531a40bfd8c");
  99
 100                 Reference mikle77 = app.getReferenceService().find(uuidMikle77);
 101                 Reference mikle85 = app.getReferenceService().find(uuidMikle85);
 102
 103                 Feature altitudeFeature = (Feature) app.getTermService().find(uuidAltitudeFeature);
 104                 if (altitudeFeature == null){
 105                         throw new RuntimeException("Could not find altitudinal range feature");
 106                 }
 107
 108                 MeasurementUnit meter = (MeasurementUnit)app.getTermService().find(UUID.fromString("8bef5055-789c-41e5-bea2-8dc2ea8ecdf6"));
 109
 110                 int count =1;
 111                 for (Map<String, String> row : excel){
 112                         count++;
 113                         UUID baseUuid = makeUuid(row, "uuid");
 114                         UUID acceptedUuid = makeUuid(row, "acceptedNameUuid");
 115                         UUID parentUuid = makeUuid(row, "parentUuid");
 116
 117                         String altitudeMin = row.get("Min");
 118                         String altitudeMax = row.get("Max");
 119                         String acceptedName = row.get("AcceptedName");
 120
 121                         String source = row.get("Source");
 122
 123                         if (StringUtils.isBlank(altitudeMin)){
 124                                 continue;
 125                         }
 126
 127                         boolean hasAltitude = false;
 128                         Reference sourceRef = getSource(source, mikle77, mikle85);
 129                         Taxon taxon = getTaxon(app, baseUuid, acceptedUuid, parentUuid, acceptedName, count);
 130                         if (taxon != null){
 131                                 TaxonDescription desc = getDescription(taxon, sourceRef);
 132
 133                                 hasAltitude = makeAltitude(altitudeMin, altitudeMax, altitudeFeature, sourceRef, desc, meter, count);
 134                                 if (hasAltitude){
 135                                         if(desc.getTaxon() == null){
 136                                                 taxon.addDescription(desc);
 137                                         }
 138                                         taxaToSave.add(taxon);
 139                                 }else{
 140                                         logger.warn("HasALtitude is false in " + count);
 141                                 }
 142                         }else{
 143                                 logger.warn("Taxon not recognized in line " + count);
 144                         }
 145                 }
 146
 147                 app.getTaxonService().saveOrUpdate(taxaToSave);
 148
 149                 app.commitTransaction(tx);
 150         }
 151
 152
 153         private Taxon getTaxon(CdmApplicationController app, UUID baseUuid, UUID acceptedUuid, UUID parentUuid, String acceptedName, int row) {
 154                 TaxonBase<?> base = app.getTaxonService().find(baseUuid);
 155
 156                 Taxon result = null;
 157                 if (base.isInstanceOf(Taxon.class)){
 158                         Taxon t = CdmBase.deproxy(base, Taxon.class);
 159                         if (t.getTaxonNodes().size() == 1 && t.getTaxonNodes().iterator().next().getClassification().getUuid().equals(classificationUuid)){
 160                                 result = t;
 161                         }else{
 162                                 logger.warn("Base taxon (uuid) not in classification. Row: " + row +  ", Taxon: " + base.getTitleCache());
 163                         }
 164                 }
 165                 if (result == null){
 166                         TaxonBase<?> accepted = app.getTaxonService().find(acceptedUuid);
 167                         Taxon t = CdmBase.deproxy(accepted, Taxon.class);;
 168                         if (t.getTaxonNodes().size() == 1 && t.getTaxonNodes().iterator().next().getClassification().getUuid().equals(classificationUuid)){
 169                                 if (hasSynonym(t, base)){
 170                                         result = t;
 171                                 }else{
 172                                         logger.warn("Synonym relation has changed somehow. Row: " + row +  ", Taxon: " + base.getTitleCache());
 173                                 }
 174
 175                         }else{
 176                                 logger.warn("Accepted taxon not in classification. Row: " + row +  ", Taxon: " + base.getTitleCache());
 177                         }
 178                 }
 179
 180                 if (result != null){
 181                         if (! result.getName().getTitleCache().equals(acceptedName)){
 182                                 logger.warn("AcceptedName and taxon name is not equal in " + row + ".\n" +
 183                                                 " Accepted Name: " + acceptedName + ";\n" +
 184                                                 " Taxon    Name: " + result.getName().getTitleCache());
 185                         }
 186                 }
 187
 188                 return result;
 189         }
 190
 191         private boolean hasSynonym(Taxon t, TaxonBase<?> base) {
 192                 if (base.isInstanceOf(Synonym.class)){
 193                         for (Synonym syn : t.getSynonyms()){
 194                                 if (syn.equals(base)){
 195                                         return true;
 196                                 }
 197                         }
 198                 }
 199                 return false;
 200         }
 201
 202 //      private static final Pattern altitudePattern = Pattern.compile("\\d{1,4}(-\\d{1,4})?");
 203
 204
 205         private boolean makeAltitude(String altitudeMin, String altitudeMax, Feature altitudeFeature,
 206                         Reference sourceRef, TaxonDescription desc, MeasurementUnit meter, int row) {
 207
 208                 QuantitativeData data = QuantitativeData.NewInstance(altitudeFeature);
 209
 210                 //Meikle
 211                 if (source != null){
 212                         TaxonName nameUsedInSource = null;  //TODO
 213                         data.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, sourceRef, null, nameUsedInSource, null);
 214                 }
 215                 data.setUnit(meter);
 216
 217                 Integer min = Integer.valueOf(altitudeMin);
 218                 StatisticalMeasurementValue minValue = StatisticalMeasurementValue.NewInstance(StatisticalMeasure.MIN(), min);
 219                 data.addStatisticalValue(minValue);
 220
 221                 Integer max = Integer.valueOf(altitudeMax);
 222                 StatisticalMeasurementValue maxValue = StatisticalMeasurementValue.NewInstance(StatisticalMeasure.MAX(), max);
 223                 data.addStatisticalValue(maxValue);
 224
 225                 desc.addElement(data);
 226                 return true;
 227         }
 228
 229         private TaxonDescription getDescription(Taxon taxon, Reference sourceRef) {
 230                 if (taxon != null){
 231                         //TODO Mikle currently does not exist as Source
 232
 233                         TaxonDescription desc = TaxonDescription.NewInstance();
 234                         desc.setTitleCache("Import from " + getSourceReference().getTitleCache(), true);
 235                         desc.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, sourceRef,null);
 236                         desc.addSource(OriginalSourceType.Import, null, null, getSourceReference(), null);
 237
 238                         return desc;
 239                 }
 240                 return null;
 241         }
 242
 243         private Reference getSource(String source, Reference m77, Reference m85) {
 244                 if(StringUtils.isNotBlank(source)){
 245                         if (source.equals("Meikle 1977")){
 246                                 return m77;
 247                         }else if (source.equals("Meikle 1985")){
 248                                 return m85;
 249                         }else{
 250                                 logger.warn("Source not recognized: " + source);
 251                         }
 252                 }
 253                 return null;
 254         }
 255
 256         private UUID makeUuid(Map<String, String> row, String colName) {
 257                 if (StringUtils.isBlank(row.get(colName))){
 258                         return null;
 259                 }else{
 260                         return UUID.fromString(row.get(colName));
 261                 }
 262         }
 263
 264         Reference sourceReference;
 265         private Reference getSourceReference() {
 266                 if (sourceReference == null){
 267                         sourceReference = ReferenceFactory.newGeneric();
 268                         sourceReference.setTitleCache(sourceReferenceTitle, true);
 269                 }
 270                 return sourceReference;
 271
 272         }
 273
 274         //Cyprus
 275         public static URI cyprus_altitude() {
 276                 URI sourceUrl;
 277                 try {
 278                         sourceUrl = new URI("file:/F:/data/cyprus/Cyprus-altitude-import-neu.xls");
 279 //                      sourceUrl = new URI("file:/F:/data/cyprus/Zypern-Altitude.xls");
 280                         return sourceUrl;
 281                 } catch (URISyntaxException e) {
 282                         e.printStackTrace();
 283                         return null;
 284                 }
 285         }
 286
 287         public static void main(String[] args) {
 288                 CyprusAltitudeActivator me = new CyprusAltitudeActivator();
 289                 me.doImport(cdmDestination);
 290         }
 291
 292 }