app-import/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelWebMarkerImport.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.io.berlinModel.in;
  10
  11 import java.sql.ResultSet;
  12 import java.sql.SQLException;
  13 import java.util.HashMap;
  14 import java.util.HashSet;
  15 import java.util.Map;
  16 import java.util.Set;
  17
  18 import org.apache.log4j.Logger;
  19 import org.springframework.stereotype.Component;
  20
  21 import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelWebMarkerImportValidator;
  22 import eu.etaxonomy.cdm.io.common.ICdmIO;
  23 import eu.etaxonomy.cdm.io.common.IOValidator;
  24 import eu.etaxonomy.cdm.io.common.MapWrapper;
  25 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  26 import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
  27 import eu.etaxonomy.cdm.model.common.CdmBase;
  28 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  29 import eu.etaxonomy.cdm.model.common.Marker;
  30 import eu.etaxonomy.cdm.model.common.MarkerType;
  31 import eu.etaxonomy.cdm.model.taxon.Taxon;
  32 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  33
  34
  35 /**
  36  * @author a.mueller
  37  * @created 20.03.2008
  38  * @version 1.0
  39  */
  40 @Component
  41 public class BerlinModelWebMarkerImport extends BerlinModelImportBase {
  42         private static final Logger logger = Logger.getLogger(BerlinModelWebMarkerImport.class);
  43
  44         private static int modCount = 2000;
  45         private static final String dbTableName = "webMarker";
  46         private static final String pluralString = "markers";
  47
  48         public BerlinModelWebMarkerImport(){
  49                 super(dbTableName, pluralString);
  50         }
  51
  52
  53         /* (non-Javadoc)
  54          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery()
  55          */
  56         @Override
  57         protected String getIdQuery(BerlinModelImportState state) {
  58                 String result = " SELECT markerId FROM " + getTableName();
  59                 if (state.getConfig().getWebMarkerFilter() != null){
  60                         result += " WHERE " +  state.getConfig().getWebMarkerFilter();
  61                 }
  62                 return result;
  63         }
  64
  65         /* (non-Javadoc)
  66          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
  67          */
  68         @Override
  69         protected String getRecordQuery(BerlinModelImportConfigurator config) {
  70                 String strQuery =
  71                         " SELECT *  " +
  72             " FROM webMarker INNER JOIN webTableName ON webMarker.TableNameFk = webTableName.TableNameId " +
  73             " WHERE (markerId IN ("+ ID_LIST_TOKEN + ") )";
  74                 return strQuery;
  75
  76         }
  77
  78         /* (non-Javadoc)
  79          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
  80          */
  81         public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {
  82                 boolean success = true ;
  83
  84                 MapWrapper<Taxon> taxonMap = (MapWrapper<Taxon>)state.getStore(ICdmIO.TAXON_STORE);
  85                 Set<TaxonBase> taxaToBeSaved = new HashSet<TaxonBase>();
  86
  87                 Map<String, DefinedTermBase> definedTermMap = state.getDbCdmDefinedTermMap();
  88                 ResultSet rs = partitioner.getResultSet();
  89
  90                 int i = 0;
  91                 //for each reference
  92                 try{
  93                         while (rs.next()){
  94                                 try{
  95                                         if ((i++ % modCount ) == 0 && i!= 1 ){ logger.info(""+pluralString+" handled: " + (i-1));}
  96                                         //
  97                                         int markerId = rs.getInt("MarkerId");
  98                                         int markerCategoryFk = rs.getInt("MarkerCategoryFk");
  99                                         int rIdentifierFk = rs.getInt("RIdentifierFk");
 100                                         String tableName = rs.getString("TableName");
 101                                         Boolean activeFlag = rs.getBoolean("ActiveFlag");
 102
 103                                         AnnotatableEntity annotatableEntity;
 104                                         if ("PTaxon".equals(tableName)){
 105                                                 TaxonBase<?> taxon = taxonMap.get(String.valueOf(rIdentifierFk));
 106                                                 if (taxon != null){
 107                                                         annotatableEntity = taxon;
 108                                                         taxaToBeSaved.add(taxon);
 109                                                         addMarker(annotatableEntity, activeFlag, markerCategoryFk, definedTermMap);
 110                                                 }else{
 111                                                         logger.warn("TaxonBase (RIdentifier " + rIdentifierFk + ") could not be found for marker " + markerId);
 112                                                 }
 113                                         }else{
 114                                                 logger.warn("Marker for table " + tableName + " not yet implemented.");
 115                                                 success = false;
 116                                         }
 117
 118
 119                                 }catch(Exception ex){
 120                                         logger.error(ex.getMessage());
 121                                         ex.printStackTrace();
 122                                         success = false;
 123                                 }
 124                         } //while rs.hasNext()
 125                 } catch (SQLException e) {
 126                         logger.error("SQLException:" +  e);
 127                         return false;
 128                 }
 129
 130                 logger.info("save " + i + " "+pluralString + " ...");
 131                 getTaxonService().saveOrUpdate(taxaToBeSaved);
 132                 return success;
 133         }
 134
 135
 136         /* (non-Javadoc)
 137          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 138          */
 139         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 140                 String nameSpace;
 141                 Class cdmClass;
 142                 Set<String> idSet;
 143                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 144
 145                 try{
 146                         Set<String> taxonIdSet = new HashSet<String>();
 147                         while (rs.next()){
 148                                 int tableNameId = rs.getInt("TableNameFk");
 149                                 if (tableNameId != 500){
 150                                         //TODO
 151                                         logger.warn("A marker is not related to table PTaxon. This case is not handled yet!");
 152                                 }else{
 153                                         handleForeignKey(rs, taxonIdSet, "RIdentifierFk");
 154         }
 155                         }
 156
 157                         //taxon map
 158                         nameSpace = BerlinModelTaxonImport.NAMESPACE;
 159                         cdmClass = TaxonBase.class;
 160                         idSet = taxonIdSet;
 161                         Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 162                         result.put(nameSpace, taxonMap);
 163
 164                 } catch (SQLException e) {
 165                         throw new RuntimeException(e);
 166                 }
 167                 return result;
 168         }
 169
 170
 171         private boolean addMarker(AnnotatableEntity annotatableEntity, boolean activeFlag, int markerCategoryFk, Map<String, DefinedTermBase> map ){
 172                 MarkerType markerType = (MarkerType)map.get("webMarkerCategory_" + markerCategoryFk);
 173                 if (markerType == null){
 174                         logger.warn("MarkerType not found: " + markerCategoryFk);
 175                 }
 176                 Marker marker = Marker.NewInstance(markerType, activeFlag);
 177                 annotatableEntity.addMarker(marker);
 178                 return true;
 179
 180         }
 181
 182
 183         /* (non-Javadoc)
 184          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
 185          */
 186         @Override
 187         protected boolean doCheck(BerlinModelImportState state){
 188                 IOValidator<BerlinModelImportState> validator = new BerlinModelWebMarkerImportValidator();
 189                 return validator.validate(state);
 190         }
 191
 192
 193         /* (non-Javadoc)
 194          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 195          */
 196         protected boolean isIgnore(BerlinModelImportState state){
 197                 return ! state.getConfig().isDoMarker();
 198         }
 199
 200
 201 }