app-import/src/main/java/eu/etaxonomy/cdm/app/lichenes/CoraImportActivator.java

   1 /**
   2 * Copyright (C) 2023 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.lichenes;
  10
  11 import java.util.UUID;
  12
  13 import org.apache.logging.log4j.LogManager;
  14 import org.apache.logging.log4j.Logger;
  15
  16 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  17 import eu.etaxonomy.cdm.common.URI;
  18 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  19 import eu.etaxonomy.cdm.database.ICdmDataSource;
  20 import eu.etaxonomy.cdm.io.common.CdmDefaultImport;
  21 import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;
  22 import eu.etaxonomy.cdm.io.lichenes.CoraImportConfigurator;
  23 import eu.etaxonomy.cdm.model.agent.Person;
  24 import eu.etaxonomy.cdm.model.agent.Team;
  25 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  26 import eu.etaxonomy.cdm.model.reference.Reference;
  27 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
  28 import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
  29
  30 /**
  31  *
  32  * Import for species of lichenes genus Cora.
  33  *
  34  * https://dev.e-taxonomy.eu/redmine/issues/10432
  35  *
  36  * @author a.mueller
  37  * @since 2023-11-23
  38  */
  39 public class CoraImportActivator {
  40
  41     @SuppressWarnings("unused")
  42     private static final Logger logger = LogManager.getLogger();
  43
  44     //database validation status (create, update, validate ...)
  45     static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;
  46
  47     static final ICdmDataSource cdmDestination = CdmDestinations.localH2();
  48 //    static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_cdmtest_mysql();
  49 //    static final ICdmDataSource cdmDestination = CdmDestinations.cdm_production_lichenes_cora();
  50
  51     //classification
  52     static final UUID classificationUuid = UUID.fromString("43183724-1919-4036-84ee-3e0e84938f8d");
  53     private static final String classificationName = "Lichenes";
  54
  55     static final UUID secRefUuid = UUID.fromString("5c2e5198-6cbd-4d30-97d5-ee2abb1f422c");
  56     static final UUID sourceRefUuid = UUID.fromString("ac67197e-8668-45cf-82bf-3682d21b3e69");
  57
  58     static final String fileName = "cora_names_EDIT.xlsx";
  59
  60     //check - import
  61     static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;
  62
  63     private void doImport(ICdmDataSource cdmDestination){
  64
  65         //make Source
  66         URI source = coraChecklist();
  67 //        URI source = lichenesChecklist_local();
  68
  69         CoraImportConfigurator config = CoraImportConfigurator.NewInstance(source, cdmDestination);
  70         config.setClassificationUuid(classificationUuid);
  71         config.setClassificationName(classificationName);
  72         config.setCheck(check);
  73         config.setDbSchemaValidation(hbm2dll);
  74 //        config.setUuidFeatureTree(featureTreeUuid);
  75 //        config.setFeatureTreeTitle(featureTreeTitle);
  76         config.setSecReference(getSecReference());
  77         config.setSourceReference(getSourceReference());
  78         config.setNomenclaturalCode(NomenclaturalCode.Fungi);
  79
  80         CdmDefaultImport<CoraImportConfigurator> myImport = new CdmDefaultImport<>();
  81         myImport.invoke(config);
  82     }
  83
  84
  85     private URI coraChecklist(){
  86         return URI.create("file:////BGBM-PESIHPC/Lichenes/" + fileName);
  87     }
  88
  89     private Reference secRef;
  90     private Reference getSecReference(){
  91         if (secRef != null){
  92             return secRef;
  93         }
  94         System.out.println("Sec Ref data still need to be updated");
  95         Reference result = ReferenceFactory.newArticle();
  96         result.setTitle("Corrections and amendments to the 2016 classification of lichenized fungi in the Ascomycota and Basidiomycota");
  97         result.setDatePublished(TimePeriodParser.parseStringVerbatim("2016"));
  98
  99         Team team = Team.NewInstance();
 100
 101         Person person = Person.NewInstance();
 102         person.setInitials("R.");
 103         person.setFamilyName("Lücking");
 104         team.addTeamMember(person);
 105
 106         person = Person.NewInstance();
 107         person.setInitials("B.P.");
 108         person.setFamilyName("Hodkinson");
 109         team.addTeamMember(person);
 110
 111         person = Person.NewInstance();
 112         person.setInitials("S.D.");
 113         person.setFamilyName("Leavitt");
 114         team.addTeamMember(person);
 115
 116         result.setAuthorship(team);
 117
 118 //        result.setPublisher("Berlin: Botanic Garden and Botanical Museum Berlin-Dahlem; Athens: Hellenic Botanical Society.");
 119
 120         result.setVolume("120(1)");
 121         Reference journal = ReferenceFactory.newJournal();
 122         journal.setTitle("The Bryologist");
 123         result.setInReference(journal);
 124         secRef = result;
 125
 126         secRef.setUuid(secRefUuid);
 127         return result;
 128     }
 129
 130     private Reference getSourceReference(){
 131         Reference result = ReferenceFactory.newGeneric();
 132         result.setTitle("Excelfile (LichenesGeneraImport.xlsx) derived from ");
 133         result.setInReference(getSecReference());
 134         result.setUuid(sourceRefUuid);
 135
 136         return result;
 137     }
 138
 139     public static void main(String[] args) {
 140         CoraImportActivator me = new CoraImportActivator();
 141         me.doImport(cdmDestination);
 142         System.exit(0);
 143     }
 144 }