cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsVernacularImport.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.io.pesi.erms;
  11
  12 import java.sql.ResultSet;
  13 import java.sql.SQLException;
  14 import java.util.HashMap;
  15 import java.util.HashSet;
  16 import java.util.Map;
  17 import java.util.Set;
  18 import java.util.UUID;
  19
  20 import org.apache.log4j.Logger;
  21 import org.springframework.stereotype.Component;
  22
  23 import eu.etaxonomy.cdm.io.common.IOValidator;
  24 import eu.etaxonomy.cdm.io.common.mapping.DbImportAnnotationMapper;
  25 import eu.etaxonomy.cdm.io.common.mapping.DbImportCommonNameCreationMapper;
  26 import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;
  27 import eu.etaxonomy.cdm.io.common.mapping.DbImportObjectMapper;
  28 import eu.etaxonomy.cdm.io.common.mapping.DbImportStringMapper;
  29 import eu.etaxonomy.cdm.io.common.mapping.IInputTransformer;
  30 import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
  31 import eu.etaxonomy.cdm.io.common.mapping.out.DbLastActionMapper;
  32 import eu.etaxonomy.cdm.io.pesi.erms.validation.ErmsVernacularImportValidator;
  33 import eu.etaxonomy.cdm.model.common.AnnotationType;
  34 import eu.etaxonomy.cdm.model.common.CdmBase;
  35 import eu.etaxonomy.cdm.model.common.Language;
  36 import eu.etaxonomy.cdm.model.common.MarkerType;
  37 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  38 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  39
  40 /**
  41  * @author a.mueller
  42  * @since 20.02.2010
  43  */
  44 @Component
  45 public class ErmsVernacularImport  extends ErmsImportBase<CommonTaxonName> {
  46
  47     private static final long serialVersionUID = -5928250782824234181L;
  48
  49         private static final Logger logger = Logger.getLogger(ErmsVernacularImport.class);
  50
  51         private DbImportMapping<ErmsImportState, ErmsImportConfigurator> mapping;
  52 //      private ErmsImportState state;   //import instance is never used more than once for Erms ; dirty
  53
  54         private static final String pluralString = "vernaculars";
  55         private static final String dbTableName = "vernaculars";
  56         private static final Class<?> cdmTargetClass = CommonTaxonName.class;
  57
  58         public ErmsVernacularImport(){
  59                 super(pluralString, dbTableName, cdmTargetClass);
  60         }
  61
  62         @Override
  63         protected String getRecordQuery(ErmsImportConfigurator config) {
  64                 String strRecordQuery =
  65                         " SELECT v.*, tu.tu_acctaxon, tu.id, l.*, " +
  66                                " s.sessiondate lastActionDate, a.action_name lastAction, s.ExpertName " +
  67                         " FROM vernaculars v INNER JOIN tu ON v.tu_id = tu.id " +
  68                         "     LEFT OUTER JOIN languages l ON l.LanID = v.lan_id " +
  69             "     LEFT OUTER JOIN vernaculars_sessions MN ON MN.vernacular_id = v.id " +
  70             "     LEFT OUTER JOIN [sessions] s ON s.id = MN.session_id " +
  71             "     LEFT OUTER JOIN actions a ON a.id = MN.action_id " +
  72                         " WHERE ( v.id IN (" + ID_LIST_TOKEN + ") )" +
  73                         " ORDER BY v.id, s.sessiondate DESC, a.id DESC ";
  74                 return strRecordQuery;
  75         }
  76
  77         @Override
  78         protected DbImportMapping<ErmsImportState, ErmsImportConfigurator> getMapping() {
  79                 if (mapping == null){
  80                         mapping = new DbImportMapping<>();
  81
  82                         mapping.addMapper(DbImportCommonNameCreationMapper.NewInstance("id", VERNACULAR_NAMESPACE, "tu_id", ErmsImportBase.TAXON_NAMESPACE));
  83
  84                         mapping.addMapper(DbImportObjectMapper.NewInstance("lan_id", "language", LANGUAGE_NAMESPACE));
  85                         mapping.addMapper(DbImportStringMapper.NewInstance("vername", "name"));
  86                         mapping.addMapper(DbImportAnnotationMapper.NewInstance("note", AnnotationType.EDITORIAL(), Language.DEFAULT()));
  87                         //last action+expert
  88                 AnnotationType speciesExpertNameAnnType = getAnnotationType(ErmsTransformer.uuidAnnSpeciesExpertName, "species expert name", "species expert name", "species expert name");
  89                 mapping.addMapper(DbImportAnnotationMapper.NewInstance("ExpertName", speciesExpertNameAnnType)); //according to sql script ExpertName maps to SpeciesExpertName in ERMS
  90                         AnnotationType lastActionDateType = getAnnotationType(DbLastActionMapper.uuidAnnotationTypeLastActionDate, "Last action date", "Last action date", null);
  91             mapping.addMapper(DbImportAnnotationMapper.NewInstance("lastActionDate", lastActionDateType));
  92             AnnotationType lastActionType = getAnnotationType(DbLastActionMapper.uuidAnnotationTypeLastAction, "Last action", "Last action", null);
  93             MarkerType hasNoLastActionMarkerType = getMarkerType(DbLastActionMapper.uuidMarkerTypeHasNoLastAction, "has no last action", "No last action information available", "no last action");
  94             mapping.addMapper(DbImportAnnotationMapper.NewInstance("lastAction", lastActionType, hasNoLastActionMarkerType));
  95                 }
  96                 return mapping;
  97         }
  98
  99     Integer lastVernacularId = null;
 100     @Override
 101     protected boolean ignoreRecord(ResultSet rs) throws SQLException {
 102         Integer id = rs.getInt("id");
 103         boolean result = id.equals(lastVernacularId);
 104         lastVernacularId = id;
 105         return result;
 106     }
 107
 108         @Override
 109         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, ErmsImportState state) {
 110
 111             String nameSpace;
 112                 Set<String> idSet;
 113                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
 114
 115                 Map<String, Language> languageMap = new HashMap<>();
 116                 try{
 117                         Set<String> taxonIdSet = new HashSet<>();
 118                         while (rs.next()){
 119                                 handleForeignKey(rs, taxonIdSet, "tu_id");
 120                                 addLanguage(rs, languageMap, state);
 121                         }
 122
 123                         //taxon map
 124                         nameSpace = ErmsImportBase.TAXON_NAMESPACE;
 125                         idSet = taxonIdSet;
 126                         @SuppressWarnings("rawtypes")
 127             Map<String, TaxonBase> taxonMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonBase.class, idSet, nameSpace);
 128                         result.put(nameSpace, taxonMap);
 129
 130                         //language map
 131                         nameSpace = LANGUAGE_NAMESPACE;
 132                         result.put(nameSpace, languageMap);
 133
 134                 } catch (SQLException e) {
 135                         throw new RuntimeException(e);
 136                 }
 137                 return result;
 138         }
 139
 140     private void addLanguage(ResultSet rs, Map<String, Language> languageMap, ErmsImportState state) throws SQLException {
 141         IInputTransformer transformer = state.getTransformer();
 142         String id639_1 = rs.getString("639_1");
 143         String id639_2 = rs.getString("639_2");
 144         String lanId = rs.getString("LanID");
 145
 146         if (isNotBlank(id639_1) && Language.getLanguageByIsoCode(id639_1)!= null){
 147             languageMap.put(lanId, Language.getLanguageByIsoCode(id639_1));
 148         }else if (isNotBlank(id639_2) && Language.getLanguageByIsoCode(id639_2)!= null){
 149             languageMap.put(lanId, Language.getLanguageByIsoCode(id639_2));
 150         }else{
 151             try {
 152                 Language language = transformer.getLanguageByKey(lanId);
 153                 persistLanguage(language);
 154                 if (language == null || language.equals(Language.UNDETERMINED())){
 155                     UUID uuidLang = transformer.getLanguageUuid(lanId);
 156                     if (uuidLang != null){
 157                         language = getLanguage(state, uuidLang, rs.getString("LanName"), "LanName", "639_3");
 158                     }
 159                     if (language == null || language.equals(Language.UNDETERMINED() )){
 160                         logger.warn("Language undefined: " + lanId);
 161                     }
 162                 }if (language != null){
 163                     languageMap.put(lanId, language);
 164                 }
 165             } catch (IllegalArgumentException | UndefinedTransformerMethodException e) {
 166                 e.printStackTrace();
 167                 logger.error("Error when retrieving language", e);
 168             }
 169         }
 170     }
 171
 172     private void persistLanguage(Language language) {
 173         if(!language.isPersited()){
 174             getTermService().saveOrUpdate(language);
 175         }
 176         if (!language.getVocabulary().isPersited()){
 177             getVocabularyService().saveOrUpdate(language.getVocabulary());
 178         }
 179     }
 180
 181     @Override
 182         protected boolean doCheck(ErmsImportState state){
 183                 IOValidator<ErmsImportState> validator = new ErmsVernacularImportValidator();
 184                 return validator.validate(state);
 185         }
 186
 187         @Override
 188         protected boolean isIgnore(ErmsImportState state){
 189                 return ! state.getConfig().isDoVernaculars();
 190         }
 191 }