cdmlib-eflora/src/main/java/eu/etaxonomy/cdm/io/eflora/centralAfrica/ferns/CentralAfricaFernsImportBase.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.eflora.centralAfrica.ferns;
  11
  12 import java.lang.reflect.Method;
  13 import java.sql.ResultSet;
  14 import java.sql.ResultSetMetaData;
  15 import java.sql.SQLException;
  16 import java.sql.Timestamp;
  17 import java.util.HashMap;
  18 import java.util.HashSet;
  19 import java.util.Map;
  20 import java.util.Set;
  21 import java.util.UUID;
  22
  23 import org.apache.commons.lang.StringUtils;
  24 import org.apache.log4j.Logger;
  25 import org.joda.time.DateTime;
  26
  27 import eu.etaxonomy.cdm.common.CdmUtils;
  28 import eu.etaxonomy.cdm.io.common.CdmImportBase;
  29 import eu.etaxonomy.cdm.io.common.ICdmIO;
  30 import eu.etaxonomy.cdm.io.common.IPartitionedIO;
  31 import eu.etaxonomy.cdm.io.common.ImportHelper;
  32 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  33 import eu.etaxonomy.cdm.io.common.Source;
  34 import eu.etaxonomy.cdm.io.common.IImportConfigurator.EDITOR;
  35 import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;
  36 import eu.etaxonomy.cdm.model.agent.Team;
  37 import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
  38 import eu.etaxonomy.cdm.model.common.Annotation;
  39 import eu.etaxonomy.cdm.model.common.AnnotationType;
  40 import eu.etaxonomy.cdm.model.common.CdmBase;
  41 import eu.etaxonomy.cdm.model.common.ExtensionType;
  42 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  43 import eu.etaxonomy.cdm.model.common.Language;
  44 import eu.etaxonomy.cdm.model.common.MarkerType;
  45 import eu.etaxonomy.cdm.model.common.User;
  46 import eu.etaxonomy.cdm.model.name.BotanicalName;
  47 import eu.etaxonomy.cdm.model.name.Rank;
  48 import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
  49
  50 /**
  51  * @author a.mueller
  52  * @created 20.03.2008
  53  * @version 1.0
  54  */
  55 public abstract class CentralAfricaFernsImportBase<CDM_BASE extends CdmBase> extends CdmImportBase<CentralAfricaFernsImportConfigurator, CentralAfricaFernsImportState> implements ICdmIO<CentralAfricaFernsImportState>, IPartitionedIO<CentralAfricaFernsImportState> {
  56         private static final Logger logger = Logger.getLogger(CentralAfricaFernsImportBase.class);
  57
  58         public static final UUID ID_IN_SOURCE_EXT_UUID = UUID.fromString("23dac094-e793-40a4-bad9-649fc4fcfd44");
  59
  60         protected static final String TAXON_NAMESPACE = "African_pteridophytes_Taxon";
  61         protected static final String NAME_NAMESPACE = "African_pteridophytes_Name";
  62         protected static final String HIGHER_TAXON_NAMESPACE = "African_pteridophytes_Higher_Taxon";
  63
  64         private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
  65
  66
  67         private String pluralString;
  68         private String dbTableName;
  69         //TODO needed?
  70         private Class cdmTargetClass;
  71
  72
  73
  74
  75         /**
  76          * @param dbTableName
  77          * @param dbTableName2
  78          */
  79         public CentralAfricaFernsImportBase(String pluralString, String dbTableName, Class cdmTargetClass) {
  80                 this.pluralString = pluralString;
  81                 this.dbTableName = dbTableName;
  82                 this.cdmTargetClass = cdmTargetClass;
  83         }
  84
  85         protected void doInvoke(CentralAfricaFernsImportState state){
  86                 logger.info("start make " + getPluralString() + " ...");
  87                 CentralAfricaFernsImportConfigurator config = state.getConfig();
  88                 Source source = config.getSource();
  89
  90                 String strIdQuery = getIdQuery();
  91                 String strRecordQuery = getRecordQuery(config);
  92
  93                 int recordsPerTransaction = config.getRecordsPerTransaction();
  94                 try{
  95                         ResultSetPartitioner partitioner = ResultSetPartitioner.NewInstance(source, strIdQuery, strRecordQuery, recordsPerTransaction);
  96                         while (partitioner.nextPartition()){
  97                                 partitioner.doPartition(this, state);
  98                         }
  99                 } catch (SQLException e) {
 100                         logger.error("SQLException:" +  e);
 101                         state.setUnsuccessfull();
 102                         return;
 103                 }
 104
 105                 logger.info("end make " + getPluralString() + " ... " + getSuccessString(true));
 106                 return;
 107         }
 108
 109         public boolean doPartition(ResultSetPartitioner partitioner, CentralAfricaFernsImportState state) {
 110                 boolean success = true ;
 111                 Set objectsToSave = new HashSet();
 112
 113                 DbImportMapping<?, ?> mapping = getMapping();
 114                 mapping.initialize(state, cdmTargetClass);
 115
 116                 ResultSet rs = partitioner.getResultSet();
 117                 try{
 118                         while (rs.next()){
 119                                 success &= mapping.invoke(rs,objectsToSave);
 120                         }
 121                 } catch (SQLException e) {
 122                         logger.error("SQLException:" +  e);
 123                         return false;
 124                 }
 125
 126                 partitioner.startDoSave();
 127                 getCommonService().save(objectsToSave);
 128                 return success;
 129         }
 130
 131
 132
 133         /**
 134          * @return
 135          */
 136         protected abstract DbImportMapping<?, ?> getMapping();
 137
 138         /**
 139          * @return
 140          */
 141         protected abstract String getRecordQuery(CentralAfricaFernsImportConfigurator config);
 142
 143         /**
 144          * @return
 145          */
 146         protected String getIdQuery(){
 147                 String result = " SELECT id FROM " + getTableName();
 148                 return result;
 149         }
 150
 151         /* (non-Javadoc)
 152          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getPluralString()
 153          */
 154         public String getPluralString(){
 155                 return pluralString;
 156         }
 157
 158         /**
 159          * @return
 160          */
 161         protected String getTableName(){
 162                 return this.dbTableName;
 163         }
 164
 165
 166         /**
 167          * Reads a foreign key field from the result set and adds its value to the idSet.
 168          * @param rs
 169          * @param teamIdSet
 170          * @throws SQLException
 171          */
 172         protected void handleForeignKey(ResultSet rs, Set<String> idSet, String attributeName)
 173                         throws SQLException {
 174                 Object idObj = rs.getObject(attributeName);
 175                 if (idObj != null){
 176                         String id  = String.valueOf(idObj);
 177                         idSet.add(id);
 178                 }
 179         }
 180
 181         /**
 182          * Returns true if i is a multiple of recordsPerTransaction
 183          * @param i
 184          * @param recordsPerTransaction
 185          * @return
 186          */
 187         protected boolean loopNeedsHandling(int i, int recordsPerLoop) {
 188                 startTransaction();
 189                 return (i % recordsPerLoop) == 0;
 190         }
 191
 192         protected void doLogPerLoop(int count, int recordsPerLog, String pluralString){
 193                 if ((count % recordsPerLog ) == 0 && count!= 0 ){ logger.info(pluralString + " handled: " + (count));}
 194         }
 195
 196
 197
 198         protected void setAuthor(BotanicalName taxonName, ResultSet rs, String taxonNumber, boolean isHigherTaxon) throws SQLException {
 199
 200                 String authorsFull = null;
 201                 String authorsAbbrev = null;
 202                 if (! isHigherTaxon){
 203                         authorsFull = rs.getString("Author/s - full");
 204                         authorsAbbrev = rs.getString("Author/s - abbreviated");
 205                 }
 206
 207                 Rank rank = taxonName.getRank();
 208                 String authorString = null;
 209                 if (rank != null){
 210                         if (rank.equals(Rank.ORDER())){
 211                                 authorString =  rs.getString("Order name author");
 212                         }else if (rank.equals(Rank.SUBORDER())){
 213                                 authorString = rs.getString("Suborder name author");
 214                         }else if (rank.equals(Rank.FAMILY())){
 215                                 authorString = rs.getString("Family name author");
 216                         }else if (rank.equals(Rank.SUBFAMILY())){
 217                                 authorString = rs.getString("Subfamily name author");
 218                         }else if (rank.equals(Rank.TRIBE())){
 219                                 authorString = rs.getString("Tribus author");
 220                         }else if (rank.equals(Rank.SUBTRIBE())){
 221                                 authorString = rs.getString("Subtribus author");
 222                         }else if (rank.equals(Rank.SECTION_BOTANY())){
 223                                 authorString = rs.getString("Section name author");
 224                         }else if (rank.equals(Rank.SUBSECTION_BOTANY())){
 225                                 authorString = rs.getString("Subsection author");
 226                         }else if (rank.equals(Rank.GENUS())){
 227                                 authorString = rs.getString("Genus name author");
 228                         }else if (rank.equals(Rank.SUBGENUS())){
 229                                 authorString = rs.getString("Subgenus name author");
 230                         }else if (rank.equals(Rank.SERIES())){
 231                                 authorString = rs.getString("Series name author");
 232                         }else if (rank.equals(Rank.SPECIES())){
 233                                 authorString =  rs.getString("Specific epithet author");
 234                         }else if (rank.equals(Rank.SUBSPECIES())){
 235                                 authorString = rs.getString("Subspecies author");
 236                         }else if (rank.equals(Rank.VARIETY())){
 237                                 authorString =  rs.getString("Variety name author");
 238                         }else if (rank.equals(Rank.SUBVARIETY())){
 239                                 authorString = rs.getString("Subvariety author");
 240                         }else if (rank.equals(Rank.FORM())){
 241                                 authorString = rs.getString("Forma name author");
 242                         }else if (rank.equals(Rank.SUBFORM())){
 243                                 authorString = rs.getString("Subforma author");
 244                         }else{
 245                                 logger.warn("Author string could not be defined");
 246                                 if (! isHigherTaxon){
 247                                         authorString = authorsAbbrev;
 248                                         if (StringUtils.isBlank(authorString)){
 249                                                 logger.warn("Authors abbrev string could not be defined");
 250                                                 authorString = authorsFull;
 251                                         }
 252                                 }
 253                         }
 254                 }else{
 255                         logger.warn(taxonNumber + ": Rank is null");
 256                         authorString = authorsAbbrev;
 257                         if (StringUtils.isBlank(authorString)){
 258                                 logger.warn(taxonNumber + ": Authors abbrev string could not be defined");
 259                                 authorString = authorsFull;
 260                         }
 261                 }
 262
 263                 if (StringUtils.isNotBlank(authorString)){
 264                         parser.handleAuthors(taxonName, taxonName.getNameCache().trim() + " " + authorString, authorString);
 265                 }
 266                 if (! isHigherTaxon){
 267                         String combinationAuthor = taxonName.getCombinationAuthorTeam()==null ? "" :taxonName.getCombinationAuthorTeam().getNomenclaturalTitle();
 268                         if (StringUtils.isNotBlank(authorsAbbrev) && ! authorsAbbrev.equalsIgnoreCase(combinationAuthor)){
 269                                 //it is expected that the fullAuthor and the abbrevAuthor are the combination authors but very often it is not
 270                                 logger.warn(taxonNumber + ": Rank author and abbrev author are not equal: " + authorString + "\t<-> " + combinationAuthor + "\t<-> " + authorsAbbrev);
 271                         }
 272         //              if (StringUtils.isNotBlank(authorsFull) && ! authorsFull.equalsIgnoreCase(authorString)){
 273         //                      logger.warn("Rank author and full author are not equal Rankauthor: " + authorString + ", full author " + authorsFull);
 274         //              }
 275                 }
 276         }
 277
 278
 279
 280
 281
 282 }