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
  10 package eu.etaxonomy.cdm.app.wp6.diptera;
  11
  12 import java.util.HashMap;
  13 import java.util.HashSet;
  14 import java.util.List;
  15 import java.util.Map;
  16 import java.util.Set;
  17
  18 import org.apache.log4j.Logger;
  19 import org.springframework.transaction.TransactionStatus;
  20
  21 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  22 import eu.etaxonomy.cdm.api.service.INameService;
  23 import eu.etaxonomy.cdm.api.service.pager.Pager;
  24 import eu.etaxonomy.cdm.app.common.CdmDestinations;
  25 import eu.etaxonomy.cdm.database.DbSchemaValidation;
  26 import eu.etaxonomy.cdm.database.ICdmDataSource;
  27 import eu.etaxonomy.cdm.io.common.ImportResult;
  28 import eu.etaxonomy.cdm.model.common.Language;
  29 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  30 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  31 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  32 import eu.etaxonomy.cdm.model.description.Feature;
  33 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  34 import eu.etaxonomy.cdm.model.description.TextData;
  35 import eu.etaxonomy.cdm.model.name.TaxonName;
  36 import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
  37 import eu.etaxonomy.cdm.model.taxon.Taxon;
  38
  39 /**
  40  * @author a.mueller
  41  * @since 01.10.2009
  42  * @version 1.0
  43  */
  44 public class DipteraPostImportUpdater {
  45         private static final Logger logger = Logger.getLogger(DipteraPostImportUpdater.class);
  46
  47         static final ICdmDataSource cdmDestination = CdmDestinations.localH2Palmae();
  48
  49         /**
  50          * This method updateds the citation text by deleting <code>OriginalName</code> tags and
  51          * adding the original name to the source either as a link to an existing taxon name
  52          * or as a string. The later becomes true if there is not exactly one matching name
  53          * @param dataSource
  54          * @return
  55          */
  56         public ImportResult updateCitations(ICdmDataSource dataSource) {
  57
  58                         logger.warn("start updating citations");
  59                         ImportResult result = new ImportResult();
  60                         try{
  61                         CdmApplicationController cdmApp = CdmApplicationController.NewInstance(dataSource, DbSchemaValidation.VALIDATE);
  62                         Set<DescriptionElementBase> citationsToSave = new HashSet<DescriptionElementBase>();
  63                         TransactionStatus tx = cdmApp.startTransaction();
  64
  65                         logger.warn("start updating citations ... application context started");
  66                         int modCount = 100;
  67                         int page = 0;
  68                         List<Taxon> taxonList = cdmApp.getTaxonService().list(Taxon.class, 100000, page, null, null);
  69                         List<TaxonName> nameList = cdmApp.getNameService().list(null, 100000, page, null, null);
  70                         Map<String, TaxonName> nameMap = new HashMap<>();
  71                         Map<String, TaxonName> nameDuplicateMap = new HashMap<>();
  72                         fillNameMaps(nameList, nameMap, nameDuplicateMap);
  73
  74                         int i = 0;
  75
  76                         for (Taxon taxon : taxonList){
  77                                 if ((i++ % modCount) == 0){ logger.warn("taxa handled: " + (i-1));}
  78
  79                                 Set<TextData> citations = getCitations(taxon);
  80                                 for (TextData citation : citations){
  81                                         Language language = Language.DEFAULT();
  82                                         String text = citation.getText(language);
  83                                         String originalNameString = parseOriginalNameString(text);
  84                                         String newText = parseNewText(text);
  85                                         citation.removeText(language);
  86                                         citation.putText(language, newText);
  87                                         TaxonName scientificName = getScientificName(originalNameString, nameMap, nameDuplicateMap);
  88
  89                                         Set<DescriptionElementSource> sources = citation.getSources();
  90                                         if (sources.size() > 1){
  91                                                 logger.warn("There are more then 1 sources for a description");
  92                                         }else if (sources.size() == 0){
  93                                                 DescriptionElementSource source = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource);
  94                                                 citation.addSource(source);
  95                                                 sources = citation.getSources();
  96                                         }
  97                                         for (DescriptionElementSource source : sources){
  98                                                 if (scientificName != null){
  99                                                         source.setNameUsedInSource(scientificName);
 100                                                 }else{
 101                                                         source.setOriginalNameString(originalNameString);
 102                                                 }
 103                                         }
 104
 105                                         citationsToSave.add(citation);
 106                                 }
 107                         }
 108
 109                         cdmApp.getDescriptionService().saveDescriptionElement(citationsToSave);
 110                         //commit
 111                         cdmApp.commitTransaction(tx);
 112                         logger.warn("Citations updated!");
 113                         return result;
 114                 } catch (Exception e) {
 115                         e.printStackTrace();
 116                         result.addError("ERROR in citation update");
 117                         result.addException(e);
 118                         return result;
 119                 }
 120
 121         }
 122
 123         public ImportResult updateCollections(ICdmDataSource dataSource){
 124                 DipteraCollectionImport collectionImport = new DipteraCollectionImport();
 125                 return collectionImport.invoke(dataSource);
 126         }
 127
 128
 129         private void fillNameMaps(List<TaxonName> nameList, Map<String, TaxonName> nameMap, Map<String, TaxonName> duplicateMap) {
 130                 for (TaxonName name : nameList){
 131                         String nameCache = name.getNameCache();
 132                         if (nameMap.containsKey(nameCache)){
 133                                 duplicateMap.put(nameCache, name);
 134                         }else{
 135                                 nameMap.put(nameCache, name);
 136                         }
 137                 }
 138         }
 139
 140
 141         private TaxonName getScientificName(String originalNameString, Map<String, TaxonName> nameMap, Map<String, TaxonName> nameDuplicateMap) {
 142                 originalNameString = originalNameString.trim();
 143                 TaxonName result = nameMap.get(originalNameString);
 144                 if (nameDuplicateMap.containsKey(originalNameString)){
 145                         result = null;
 146                 }
 147                 return result;
 148         }
 149
 150         private TaxonName getScientificName(String originalNameString, INameService nameService) {
 151                 Pager<TaxonName> names = nameService.findByName(null, originalNameString, null, null, null, null, null, null);
 152                 if (names.getCount() != 1){
 153                         return null;
 154                 }else{
 155                         return names.getRecords().get(0);
 156                 }
 157         }
 158
 159         private String parseOriginalNameString(String text) {
 160                 String originalName = "<OriginalName>";
 161                 int start = text.indexOf(originalName);
 162                 int end = text.indexOf("</OriginalName>");
 163                 if (start >-1 ){
 164                         text = text.substring(start + originalName.length(), end);
 165                 }
 166                 text = text.trim();
 167                 return text;
 168         }
 169
 170         private String parseNewText(String text) {
 171                 int start = text.indexOf("</OriginalName>");
 172                 text = text.substring(start + "</OriginalName>".length());
 173                 text = text.trim();
 174                 if (text.startsWith(":")){
 175                         text = text.substring(1);
 176                 }
 177                 text = text.trim();
 178                 return text;
 179         }
 180
 181         private Set<TextData> getCitations(Taxon taxon) {
 182                 Set<TextData> result = new HashSet<TextData>();
 183                 Set<TaxonDescription> descriptions = taxon.getDescriptions();
 184                 for (DescriptionBase description : descriptions){
 185                         Set<DescriptionElementBase> elements = description.getElements();
 186                         for (DescriptionElementBase element : elements){
 187                                 Feature feature = element.getFeature();
 188                                 if (feature.equals(Feature.CITATION())){
 189                                         if (! element.isInstanceOf(TextData.class)){
 190                                                 logger.warn("Citation is not of class TextData but " + element.getClass().getSimpleName());
 191                                         }else{
 192                                                 TextData textData = element.deproxy(element, TextData.class);
 193                                                 result.add(textData);
 194                                         }
 195                                 }
 196                         }
 197                 }
 198                 return result;
 199         }
 200
 201
 202
 203
 204         /**
 205          * @param args
 206          */
 207         public static void main(String[] args) {
 208                 DipteraPostImportUpdater updater = new DipteraPostImportUpdater();
 209                 try {
 210                         updater.updateCitations(cdmDestination);
 211                 } catch (Exception e) {
 212                         e.printStackTrace();
 213                         logger.error("ERROR in feature tree update");
 214                 }
 215         }
 216
 217 }