app-import/src/main/java/eu/etaxonomy/cdm/app/euromed/CaucasusAreaVocabularyMigrationActivator.java

   1 /**
   2 * Copyright (C) 2019 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.app.euromed;
  10
  11 import java.util.HashSet;
  12 import java.util.Set;
  13 import java.util.UUID;
  14 import java.util.function.Function;
  15 import java.util.stream.Collectors;
  16
  17 import org.apache.logging.log4j.LogManager;
  18 import org.apache.logging.log4j.Logger;
  19
  20 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  21 import eu.etaxonomy.cdm.common.DoubleResult;
  22 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  23 import eu.etaxonomy.cdm.database.ICdmDataSource;
  24 import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
  25 import eu.etaxonomy.cdm.filter.VocabularyFilter;
  26 import eu.etaxonomy.cdm.io.cdm2cdm.Cdm2CdmImportConfigurator;
  27 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  28 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  29 import eu.etaxonomy.cdm.model.description.Distribution;
  30 import eu.etaxonomy.cdm.model.description.Feature;
  31 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  32 import eu.etaxonomy.cdm.model.location.NamedArea;
  33 import eu.etaxonomy.cdm.model.reference.Reference;
  34 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  35 import eu.etaxonomy.cdm.model.taxon.Taxon;
  36 import eu.etaxonomy.cdm.model.term.DefinedTermBase;
  37
  38 /**
  39  * Import for area vocabularies in the caucasus context.
  40  * For imports from a preliminary to a final (or more recent preliminary) version.
  41  * Usually running after {@link EuroMedCaucasusChecklistExportActivator}.
  42  *
  43  * @author a.mueller
  44  * @since 2023-12-13
  45  */
  46 public class CaucasusAreaVocabularyMigrationActivator {
  47
  48     @SuppressWarnings("unused")
  49     private static final Logger logger = LogManager.getLogger();
  50
  51 //    static final ICdmDataSource source = CdmDestinations.cdm_local_azerbaijan_old();
  52     static final ICdmDataSource source = CdmDestinations.cdm_production_azerbaijan_old();
  53
  54     static boolean isProduction = true;
  55     static final DB db = DB.AZERBAIJAN;
  56
  57     static final UUID areaVocabulary = UUID.fromString("c839f88f-c04b-481e-badc-384773b649d0");
  58
  59     static ICdmDataSource cdmDestination = !isProduction ?
  60             (db == DB.GEORGIA ? CdmDestinations.cdm_local_georgia() :
  61              db == DB.ARMENIA ? CdmDestinations.cdm_local_armenia() :
  62                                 CdmDestinations.cdm_local_azerbaijan()
  63           ):(db == DB.GEORGIA ? CdmDestinations.cdm_production_georgia() :
  64              db == DB.ARMENIA ? CdmDestinations.cdm_production_armenia() :
  65                                 CdmDestinations.cdm_production_azerbaijan());
  66
  67     //check - import
  68     static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  69
  70     private enum DB{GEORGIA, ARMENIA,AZERBAIJAN}
  71
  72     static final int partitionSize = 5000;
  73
  74     static final boolean includeAbsentDistributions = true;
  75
  76     static final DbSchemaValidation schemaValidation = DbSchemaValidation.VALIDATE;
  77
  78     static final boolean removeImportSources = true;
  79     static final boolean addSource = false;
  80     //TODO needed?
  81     static final String sourceRefTitle = "Azerbaijan area trees";
  82     static final UUID sourceRefUuid = UUID.fromString("30583931-5f5d-40cb-8198-10dc9e7fb9ef");
  83
  84     //auditing
  85     static final boolean registerAuditing = true;
  86
  87 // ***************** ALL ************************************************//
  88
  89
  90     private void doImportVocs(ICdmDataSource source, ICdmDataSource destination, DbSchemaValidation hbm2dll){
  91         String importFrom = " import from "+ source.getDatabase() + " to "+ destination.getDatabase() + " ...";
  92         System.out.println("Start" + importFrom);
  93
  94         Cdm2CdmImportConfigurator config = Cdm2CdmImportConfigurator.NewInstace(source, destination);
  95         config.setDoTaxa(false);
  96         config.setDoDescriptions(false);
  97         config.setDoVocabularies(true);
  98         config.setSourceReference(getSourceRef());
  99
 100         config.setRemoveImportSources(removeImportSources);
 101         config.setAddSources(addSource);
 102
 103         VocabularyFilter vocFilter = VocabularyFilter.NewInstance();
 104         vocFilter.orVocabulary(areaVocabulary);
 105         config.setVocabularyFilter(vocFilter);
 106
 107 //    }else {
 108 //            //vocFilter.orVocabulary(UUID.fromString("625a4962-c211-4597-816e-5804083efe26"));  //E+M areas
 109 //            List<UUID> trees = Arrays.asList(new UUID[] {
 110 //                    UUID.fromString("23970e4d-9da3-4416-86f7-5ae4f4307065"), //Caucasus area tree
 111 //                    UUID.fromString("6a5e1c2b-ec0d-46c8-9c7d-a2059267ffb7")});  //feature tree
 112 //            config.setGraphFilter(trees);
 113 //        }
 114
 115         // invoke import
 116         CdmDefaultImport<Cdm2CdmImportConfigurator> myImport = new CdmDefaultImport<>();
 117         myImport.invoke(config);
 118     }
 119
 120     private void doImport(ICdmDataSource source, ICdmDataSource destination, DbSchemaValidation hbm2dll) throws NoSuchMethodException, SecurityException{
 121
 122         String importFrom = " import from "+ source.getDatabase() + " to "+ destination.getDatabase() + " ...";
 123         System.out.println("Start" + importFrom);
 124
 125         Cdm2CdmImportConfigurator config = Cdm2CdmImportConfigurator.NewInstace(source, destination);
 126         config.setDoTaxa(false);
 127         config.setDoDescriptions(false);
 128         config.setDoVocabularies(false);
 129         config.setSourceReference(getSourceRef());
 130
 131         config.setRemoveImportSources(removeImportSources);
 132         config.setAddSources(addSource);
 133
 134         config.setDbSchemaValidation(hbm2dll);
 135
 136         config.setCheck(check);
 137         config.setRegisterAuditing(registerAuditing);
 138
 139         // invoke import
 140         CdmDefaultImport<Cdm2CdmImportConfigurator> myImport = new CdmDefaultImport<>();
 141         myImport.invoke(config);
 142
 143         System.out.println("End" + importFrom);
 144     }
 145
 146 //    private Reference getEndemismReference() {
 147 //        Reference ref = ReferenceFactory.newWebPage();
 148 //        ref.setTitle("Euro+Med PlantBase");
 149 //        ref.setAccessed(DateTime.now());
 150 //        ref.setUuid(endemismReferenceUuid);
 151 //        return ref;
 152 //    }
 153
 154     private Function<DoubleResult<Taxon,DefinedTermBase<?>[]>,Distribution> getEndemismHandler(TaxonNodeFilter taxonNodeFilter) {
 155         Set<UUID> emAreas = new HashSet<>();
 156         emAreas.add(UUID.fromString("111bdf38-7a32-440a-9808-8af1c9e54b51"));  //EM
 157         emAreas.add(UUID.fromString("865e0fcc-bfb5-4af2-8822-08c90c7ba61e")); //Europe
 158         Set<UUID> largerCaucasusAreas = new HashSet<>();
 159         emAreas.add(UUID.fromString("904c3980-b98d-422e-a195-95f4f41fc734"));  //Tcs
 160         emAreas.add(UUID.fromString("05b0dd06-30f8-477d-bf4c-30d9def56320")); //Cc
 161
 162
 163         Set<UUID> relevantAreas = taxonNodeFilter.getAreaFilter().stream().map(f->f.getUuid()).collect(Collectors.toSet());
 164
 165         Function<DoubleResult<Taxon,DefinedTermBase<?>[]>,Distribution> function = input->{
 166             Taxon t = input.getFirstResult();
 167             DefinedTermBase<?>[] params = input.getSecondResult();
 168             NamedArea relevantArea = (NamedArea)params[0];
 169
 170             PresenceAbsenceTerm endemic = (PresenceAbsenceTerm)params[1];
 171             PresenceAbsenceTerm notEndemic = (PresenceAbsenceTerm)params[2];
 172             PresenceAbsenceTerm unknownEndemic = (PresenceAbsenceTerm)params[3];
 173             Feature distributionFeature = (Feature)params[4];
 174
 175             boolean isNativeInRelevantArea = false;
 176             boolean isEndemicInEuroMed = false;
 177
 178             Distribution result = Distribution.NewInstance(relevantArea, unknownEndemic);
 179             result.setFeature(distributionFeature);
 180             Set<Distribution> distributions = t.getDescriptionItems(Feature.DISTRIBUTION(), Distribution.class);
 181             if (distributions.isEmpty()) {
 182                 return null;
 183             }
 184
 185             for (Distribution distribution : distributions) {
 186                 NamedArea area = distribution.getArea();
 187                 PresenceAbsenceTerm status = distribution.getStatus();
 188                 if (area == null || status == null) {
 189                     continue;
 190                 } else if (emAreas.contains(area.getUuid())) {
 191                     if (status.equals(notEndemic)) {
 192                         result.setStatus(notEndemic);
 193                         return result;
 194                     }else if (status.equals(endemic)) {
 195                         isEndemicInEuroMed = true;
 196                     }
 197                 } else if (relevantAreas.contains(area.getUuid())) {
 198                     if (isNative(status)) {
 199                         isNativeInRelevantArea = true;
 200                     }
 201                 } else if (largerCaucasusAreas.contains(area.getUuid())) {
 202                     System.out.println("Larger Cc area for " + t.getName().getTitleCache() + " with status " + distribution.getStatus().getTitleCache());
 203                 } else {
 204                     //other areas
 205                     if (isNative(status)) {
 206                         result.setStatus(notEndemic);
 207                         return result;
 208                     }
 209                 }
 210             }
 211             if (isNativeInRelevantArea && isEndemicInEuroMed) {
 212                 result.setStatus(endemic);
 213             }
 214
 215             return result;
 216         };
 217         return function;
 218     }
 219
 220     private boolean isNative(PresenceAbsenceTerm status) {
 221         return status.equals(PresenceAbsenceTerm.NATIVE())
 222                 || status.equals(PresenceAbsenceTerm.ENDEMIC_FOR_THE_RELEVANT_AREA()) ;
 223     }
 224
 225     private Reference getSourceRef() {
 226         Reference ref = ReferenceFactory.newDatabase();
 227         ref.setTitle(sourceRefTitle);
 228 //        ref.setDatePublished(VerbatimTimePeriod.NewVerbatimInstance(Calendar.getInstance()));
 229 //        ref.setAccessed(DateTime.now());
 230         ref.setUuid(sourceRefUuid);
 231         return ref;
 232     }
 233
 234     public static void main(String[] args) {
 235         ICdmDataSource cdmDB = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;
 236         CaucasusAreaVocabularyMigrationActivator myImport = new CaucasusAreaVocabularyMigrationActivator();
 237         myImport.doImportVocs(source, cdmDB, schemaValidation);
 238         System.exit(0);
 239     }
 240 }