app-import/src/main/java/eu/etaxonomy/cdm/app/wp6/diptera/DipteraPostImportUpdater.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.wp6.diptera;
  10
  11 import java.util.HashMap;
  12 import java.util.HashSet;
  13 import java.util.List;
  14 import java.util.Map;
  15 import java.util.Set;
  16
  17 import org.apache.log4j.Logger;
  18 import org.springframework.transaction.TransactionStatus;
  19
  20 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  21 import eu.etaxonomy.cdm.api.service.INameService;
  22 import eu.etaxonomy.cdm.api.service.pager.Pager;
  23 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  24 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  25 import eu.etaxonomy.cdm.database.ICdmDataSource;
  26 import eu.etaxonomy.cdm.io.common.ImportResult;
  27 import eu.etaxonomy.cdm.model.common.Language;
  28 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  29 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  30 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  31 import eu.etaxonomy.cdm.model.description.Feature;
  32 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  33 import eu.etaxonomy.cdm.model.description.TextData;
  34 import eu.etaxonomy.cdm.model.name.TaxonName;
  35 import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
  36 import eu.etaxonomy.cdm.model.taxon.Taxon;
  37
  38 /**
  39  * @author a.mueller
  40  * @since 01.10.2009
  41  */
  42 public class DipteraPostImportUpdater {
  43         private static final Logger logger = Logger.getLogger(DipteraPostImportUpdater.class);
  44
  45         static final ICdmDataSource cdmDestination = CdmDestinations.localH2Palmae();
  46
  47         /**
  48          * This method updateds the citation text by deleting <code>OriginalName</code> tags and
  49          * adding the original name to the source either as a link to an existing taxon name
  50          * or as a string. The later becomes true if there is not exactly one matching name
  51          * @param dataSource
  52          * @return
  53          */
  54         public ImportResult updateCitations(ICdmDataSource dataSource) {
  55
  56                         logger.warn("start updating citations");
  57                         ImportResult result = new ImportResult();
  58                         try{
  59                         CdmApplicationController cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
  60                         Set<DescriptionElementBase> citationsToSave = new HashSet<>();
  61                         TransactionStatus tx = cdmApp.startTransaction();
  62
  63                         logger.warn("start updating citations ... application context started");
  64                         int modCount = 100;
  65                         int page = 0;
  66                         List<Taxon> taxonList = cdmApp.getTaxonService().list(Taxon.class, 100000, page, null, null);
  67                         List<TaxonName> nameList = cdmApp.getNameService().list(null, 100000, page, null, null);
  68                         Map<String, TaxonName> nameMap = new HashMap<>();
  69                         Map<String, TaxonName> nameDuplicateMap = new HashMap<>();
  70                         fillNameMaps(nameList, nameMap, nameDuplicateMap);
  71
  72                         int i = 0;
  73
  74                         for (Taxon taxon : taxonList){
  75                                 if ((i++ % modCount) == 0){ logger.warn("taxa handled: " + (i-1));}
  76
  77                                 Set<TextData> citations = getCitations(taxon);
  78                                 for (TextData citation : citations){
  79                                         Language language = Language.DEFAULT();
  80                                         String text = citation.getText(language);
  81                                         String originalNameString = parseOriginalNameString(text);
  82                                         String newText = parseNewText(text);
  83                                         citation.removeText(language);
  84                                         citation.putText(language, newText);
  85                                         TaxonName scientificName = getScientificName(originalNameString, nameMap, nameDuplicateMap);
  86
  87                                         Set<DescriptionElementSource> sources = citation.getSources();
  88                                         if (sources.size() > 1){
  89                                                 logger.warn("There are more then 1 sources for a description");
  90                                         }else if (sources.size() == 0){
  91                                                 DescriptionElementSource source = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource);
  92                                                 citation.addSource(source);
  93                                                 sources = citation.getSources();
  94                                         }
  95                                         for (DescriptionElementSource source : sources){
  96                                                 if (scientificName != null){
  97                                                         source.setNameUsedInSource(scientificName);
  98                                                 }else{
  99                                                         source.setOriginalNameString(originalNameString);
 100                                                 }
 101                                         }
 102
 103                                         citationsToSave.add(citation);
 104                                 }
 105                         }
 106
 107                         cdmApp.getDescriptionElementService().save(citationsToSave);
 108                         //commit
 109                         cdmApp.commitTransaction(tx);
 110                         logger.warn("Citations updated!");
 111                         return result;
 112                 } catch (Exception e) {
 113                         e.printStackTrace();
 114                         result.addError("ERROR in citation update");
 115                         result.addException(e);
 116                         return result;
 117                 }
 118
 119         }
 120
 121         public ImportResult updateCollections(ICdmDataSource dataSource){
 122                 DipteraCollectionImport collectionImport = new DipteraCollectionImport();
 123                 return collectionImport.invoke(dataSource);
 124         }
 125
 126
 127         private void fillNameMaps(List<TaxonName> nameList, Map<String, TaxonName> nameMap, Map<String, TaxonName> duplicateMap) {
 128                 for (TaxonName name : nameList){
 129                         String nameCache = name.getNameCache();
 130                         if (nameMap.containsKey(nameCache)){
 131                                 duplicateMap.put(nameCache, name);
 132                         }else{
 133                                 nameMap.put(nameCache, name);
 134                         }
 135                 }
 136         }
 137
 138
 139         private TaxonName getScientificName(String originalNameString, Map<String, TaxonName> nameMap, Map<String, TaxonName> nameDuplicateMap) {
 140                 originalNameString = originalNameString.trim();
 141                 TaxonName result = nameMap.get(originalNameString);
 142                 if (nameDuplicateMap.containsKey(originalNameString)){
 143                         result = null;
 144                 }
 145                 return result;
 146         }
 147
 148         private TaxonName getScientificName(String originalNameString, INameService nameService) {
 149                 Pager<TaxonName> names = nameService.findByName(null, originalNameString, null, null, null, null, null, null);
 150                 if (names.getCount() != 1){
 151                         return null;
 152                 }else{
 153                         return names.getRecords().get(0);
 154                 }
 155         }
 156
 157         private String parseOriginalNameString(String text) {
 158                 String originalName = "<OriginalName>";
 159                 int start = text.indexOf(originalName);
 160                 int end = text.indexOf("</OriginalName>");
 161                 if (start >-1 ){
 162                         text = text.substring(start + originalName.length(), end);
 163                 }
 164                 text = text.trim();
 165                 return text;
 166         }
 167
 168         private String parseNewText(String text) {
 169                 int start = text.indexOf("</OriginalName>");
 170                 text = text.substring(start + "</OriginalName>".length());
 171                 text = text.trim();
 172                 if (text.startsWith(":")){
 173                         text = text.substring(1);
 174                 }
 175                 text = text.trim();
 176                 return text;
 177         }
 178
 179         private Set<TextData> getCitations(Taxon taxon) {
 180                 Set<TextData> result = new HashSet<TextData>();
 181                 Set<TaxonDescription> descriptions = taxon.getDescriptions();
 182                 for (DescriptionBase description : descriptions){
 183                         Set<DescriptionElementBase> elements = description.getElements();
 184                         for (DescriptionElementBase element : elements){
 185                                 Feature feature = element.getFeature();
 186                                 if (feature.equals(Feature.CITATION())){
 187                                         if (! element.isInstanceOf(TextData.class)){
 188                                                 logger.warn("Citation is not of class TextData but " + element.getClass().getSimpleName());
 189                                         }else{
 190                                                 TextData textData = element.deproxy(element, TextData.class);
 191                                                 result.add(textData);
 192                                         }
 193                                 }
 194                         }
 195                 }
 196                 return result;
 197         }
 198
 199
 200
 201
 202         /**
 203          * @param args
 204          */
 205         public static void main(String[] args) {
 206                 DipteraPostImportUpdater updater = new DipteraPostImportUpdater();
 207                 try {
 208                         updater.updateCitations(cdmDestination);
 209                 } catch (Exception e) {
 210                         e.printStackTrace();
 211                         logger.error("ERROR in feature tree update");
 212                 }
 213         }
 214
 215 }