app-import/src/main/java/eu/etaxonomy/cdm/app/caryophyllales/KewNyctaginaceaeActivator.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 package eu.etaxonomy.cdm.app.caryophyllales;
  10
  11 import java.io.File;
  12 import java.util.UUID;
  13
  14 import org.apache.logging.log4j.LogManager;
  15 import org.apache.logging.log4j.Logger;
  16
  17 import eu.etaxonomy.cdm.app.berlinModelImport.SourceBase;
  18 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  19 import eu.etaxonomy.cdm.common.URI;
  20 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  21 import eu.etaxonomy.cdm.database.ICdmDataSource;
  22 import eu.etaxonomy.cdm.io.caryo.KewExcelTaxonImportConfigurator;
  23 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  24 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  25 import eu.etaxonomy.cdm.model.reference.Reference;
  26 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  27
  28 /**
  29  * Import Kew WCVP Nyctabinaceae data to CDM Caryophyllales.
  30  *
  31  * @author a.mueller
  32  * @since 12.01.2023
  33  */
  34 public class KewNyctaginaceaeActivator extends SourceBase{
  35
  36         @SuppressWarnings("unused")
  37     private static final Logger logger = LogManager.getLogger();
  38
  39         //database validation status (create, update, validate ...)
  40         private static final DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;
  41         private static final URI source = nyctaginaceae();
  42
  43         private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_caryo_spp();
  44 //    private static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_caryophyllales_spp();
  45
  46
  47         //classification
  48         static final UUID classificationUuid = UUID.fromString("9edc58b5-de3b-43aa-9f31-1ede7c009c2b");
  49
  50         static final UUID rootTaxonUuid = UUID.fromString("7040cc71-4f0d-4fd9-9384-eb4d003274aa"); //taxon.uuid not taxonNode.uuid , here Nyctaginaceae
  51         //for taxa/names declared as unplaced
  52         static final UUID unplacedTaxonUuid = UUID.fromString("9835a6e5-3b8a-49b5-a692-5da531ef8634");
  53         //for orphaned synonyms
  54         static final UUID orphanedPlaceholderTaxonUuid = UUID.fromString("cc5cec9b-b0c7-432a-8d10-31cbb3685d35");
  55
  56
  57         //check - import
  58         static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  59
  60         //taxa
  61         static final boolean doTaxa = true;
  62
  63         private void doImport(ICdmDataSource cdmDestination){
  64
  65                 //make Source
  66             KewExcelTaxonImportConfigurator config= KewExcelTaxonImportConfigurator.NewInstance(source, cdmDestination);
  67                 config.setClassificationUuid(classificationUuid);
  68                 config.setRootTaxonUuid(rootTaxonUuid);
  69                 config.setUnplacedTaxonUuid(unplacedTaxonUuid);
  70                 config.setOrphanedPlaceholderTaxonUuid(orphanedPlaceholderTaxonUuid);
  71                 config.setCheck(check);
  72 //              config.setDoTaxa(doTaxa);
  73                 config.setDbSchemaValidation(hbm2dll);
  74                 config.setSourceReferenceTitle("Nyctaginaceae_Export_Kew4CDM-Import.xlsx");
  75
  76                 CdmDefaultImport<KewExcelTaxonImportConfigurator> myImport = new CdmDefaultImport<>();
  77
  78                 //...
  79                 if (true){
  80                         System.out.println("Start import from ("+ source.toString() + ") ...");
  81                         config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));
  82                         myImport.invoke(config);
  83                         System.out.println("End import from ("+ source.toString() + ")...");
  84                 }
  85         }
  86
  87         private Reference getSourceReference(String string) {
  88                 Reference result = ReferenceFactory.newGeneric();
  89                 result.setTitleCache(string, true);
  90                 return result;
  91         }
  92
  93
  94         public static URI nyctaginaceae(){
  95       String fileName = "Nyctaginaceae_Export_Kew4CDM-Import.xlsx";
  96 //      URI uri = URI.create("file:////BGBM-PESIHPC/Caryophyllales/Kew/" +  fileName);
  97       File file = new File("E://data/Caryophyllales/Kew/" +  fileName);
  98       if (!file.exists()) {
  99           System.exit(0);
 100       }
 101       URI uri = URI.fromFile(file);
 102 //      URI uri = URI.create("file://E:/Caryophyllales/Kew/" +  fileName);
 103       return uri;
 104         }
 105
 106         public static void main(String[] args) {
 107                 KewNyctaginaceaeActivator me = new KewNyctaginaceaeActivator();
 108                 me.doImport(cdmDestination);
 109                 System.exit(0);
 110         }
 111 }