app-import/src/main/java/eu/etaxonomy/cdm/io/greece/FloraHellenicaImportBase.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.greece;
  10
  11 import java.util.HashMap;
  12 import java.util.List;
  13 import java.util.Map;
  14 import java.util.UUID;
  15
  16 import org.apache.log4j.Logger;
  17
  18 import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImport;
  19 import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
  20 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  21 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  22 import eu.etaxonomy.cdm.model.name.Rank;
  23 import eu.etaxonomy.cdm.model.name.TaxonName;
  24 import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
  25 import eu.etaxonomy.cdm.model.reference.Reference;
  26 import eu.etaxonomy.cdm.model.taxon.Taxon;
  27
  28 /**
  29  * @author a.mueller
  30  * @since 14.12.2016
  31  */
  32
  33 public abstract class FloraHellenicaImportBase<CONFIG extends FloraHellenicaImportConfigurator>
  34             extends SimpleExcelTaxonImport<CONFIG>{
  35
  36     private static final long serialVersionUID = 2593130403213346396L;
  37     private static final Logger logger = Logger.getLogger(FloraHellenicaImportBase.class);
  38
  39     private Map<UUID, Taxon> acceptedTaxonMap = new HashMap<>();
  40     private Reference sourceReference;
  41     private Reference secReference;
  42     private Reference secReference2;
  43
  44     protected TaxonDescription getTaxonDescription(Taxon taxon) {
  45         if (!taxon.getDescriptions().isEmpty()){
  46             return taxon.getDescriptions().iterator().next();
  47         }else{
  48             TaxonDescription desc = TaxonDescription.NewInstance(taxon);
  49             desc.setDefault(true);
  50             return desc;
  51         }
  52     }
  53
  54     protected Reference getSourceCitation(SimpleExcelTaxonImportState<CONFIG> state) {
  55         if (this.sourceReference == null){
  56             this.sourceReference = getPersistentReference(state.getConfig().getSourceReference());
  57         }
  58         return this.sourceReference;
  59     }
  60
  61     protected Reference getSecReference(SimpleExcelTaxonImportState<CONFIG> state) {
  62         if (this.secReference == null){
  63             this.secReference = getPersistentReference(state.getConfig().getSecReference());
  64         }
  65         return this.secReference;
  66     }
  67
  68     protected Reference getSecReference2(SimpleExcelTaxonImportState<CONFIG> state) {
  69         if (this.secReference2 == null){
  70             this.secReference2 = getPersistentReference(state.getConfig().getSecReference2());
  71         }
  72         return this.secReference2;
  73     }
  74
  75     private Reference getPersistentReference(Reference reference) {
  76         Reference result = getReferenceService().find(reference.getUuid());
  77         if (result == null){
  78             result = reference;
  79         }
  80         return result;
  81     }
  82
  83     protected Taxon getAcceptedTaxon(Map<String, String> record,
  84             SimpleExcelTaxonImportState<CONFIG> state, String key) {
  85
  86         String accStr = getValue(record, key);
  87         if (accStr == null){
  88             return null;
  89         }
  90         accStr = accStr.trim();
  91
  92         Taxon accTaxon = state.getTaxon(accStr);
  93         if (accTaxon == null){
  94             String message = state.getCurrentLine()+  ": Accepted taxon could not be found: " + accStr;
  95             logger.warn(message);
  96             return null;
  97         }else{
  98             initAcceptedTaxonMap();
  99 //            accTaxon = (Taxon)getTaxonService().find(accTaxon.getUuid());
 100             accTaxon = acceptedTaxonMap.get(accTaxon.getUuid());
 101         }
 102         return accTaxon;
 103     }
 104
 105     private void initAcceptedTaxonMap() {
 106         if (acceptedTaxonMap.isEmpty()){
 107             List<Taxon> list = getTaxonService().list(Taxon.class, null, null, null, null);
 108             for (Taxon taxon : list){
 109                 acceptedTaxonMap.put(taxon.getUuid(), taxon);
 110             }
 111         }
 112     }
 113
 114     /**
 115      * @param record
 116      * @param state
 117      * @return
 118      */
 119     protected Taxon getHigherTaxon(Map<String, String> record,
 120             SimpleExcelTaxonImportState<CONFIG> state, String key) {
 121
 122         String accStr = getValue(record, key);
 123         if (accStr == null){
 124             return null;
 125         }
 126         accStr = accStr.trim();
 127
 128         Taxon accTaxon = state.getHigherTaxon(accStr);
 129         if (accTaxon == null){
 130             String message = state.getCurrentLine()+  ": Higher taxon could not be found: " + accStr;
 131             logger.info(message); //not critical
 132             return null;
 133         }else{
 134             initAcceptedTaxonMap();
 135 //            accTaxon = (Taxon)getTaxonService().find(accTaxon.getUuid());
 136             accTaxon = acceptedTaxonMap.get(accTaxon.getUuid());
 137         }
 138         return accTaxon;
 139     }
 140
 141
 142     protected TaxonName makeFamilyName(SimpleExcelTaxonImportState<CONFIG> state,
 143             String famStr) {
 144         TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());
 145         famStr = famStr.substring(0,1).toUpperCase() + famStr.substring(1).toLowerCase();
 146         name.setGenusOrUninomial(famStr);
 147         name.addSource(makeOriginalSource(state));
 148         return name;
 149     }
 150
 151     protected TaxonName replaceNameAuthorsAndReferences(SimpleExcelTaxonImportState<CONFIG> state, TaxonName name) {
 152         TaxonName result = state.getDeduplicationHelper().getExistingName(name);
 153         state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(result);
 154         return result;
 155     }
 156
 157     @Override
 158     protected IdentifiableSource makeOriginalSource(SimpleExcelTaxonImportState<CONFIG> state) {
 159         return IdentifiableSource.NewDataImportInstance("line: " + state.getCurrentLine(), null, getSourceCitation(state));
 160     }
 161
 162 }