cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaImportBase.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.faunaEuropaea;
  11
  12 import java.sql.ResultSet;
  13 import java.sql.ResultSetMetaData;
  14 import java.sql.SQLException;
  15 import java.util.Collection;
  16 import java.util.HashMap;
  17 import java.util.Map;
  18
  19 import org.apache.log4j.Logger;
  20 import org.springframework.transaction.TransactionStatus;
  21
  22 import eu.etaxonomy.cdm.common.CdmUtils;
  23 import eu.etaxonomy.cdm.io.common.CdmImportBase;
  24 import eu.etaxonomy.cdm.io.common.CdmIoBase;
  25 import eu.etaxonomy.cdm.io.common.ICdmIO;
  26 import eu.etaxonomy.cdm.io.common.ICdmImport;
  27 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  28 import eu.etaxonomy.cdm.io.common.ImportHelper;
  29 import eu.etaxonomy.cdm.io.common.MapWrapper;
  30 import eu.etaxonomy.cdm.io.common.Source;
  31 import eu.etaxonomy.cdm.model.common.Annotation;
  32 import eu.etaxonomy.cdm.model.common.CdmBase;
  33 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  34 import eu.etaxonomy.cdm.model.common.Language;
  35 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  36
  37 /**
  38  * @author a.babadshanjan
  39  * @created 11.05.2009
  40  * @version 1.0
  41  */
  42 public abstract class FaunaEuropaeaImportBase extends CdmImportBase<FaunaEuropaeaImportConfigurator, FaunaEuropaeaImportState>
  43 implements ICdmImport<FaunaEuropaeaImportConfigurator,FaunaEuropaeaImportState> {
  44         private static final Logger logger = Logger.getLogger(FaunaEuropaeaImportBase.class);
  45
  46 //      /* Max number of taxa to retrieve (for test purposes) */
  47 //      protected static final int maxTaxa = 1000;
  48 //      /* Max number of taxa to be saved with one service call */
  49 //      protected int limit = 20000; // TODO: Make configurable
  50 //      /* Interval for progress info message when retrieving taxa */
  51 //      protected static final int modCount = 10000;
  52 //      /* Highest taxon index in the FauEu database */
  53 //      protected int highestTaxonIndex = 0;
  54
  55         protected boolean resultSetHasColumn(ResultSet rs, String columnName){
  56                 try {
  57                         ResultSetMetaData metaData = rs.getMetaData();
  58                         for (int i = 0; i < metaData.getColumnCount(); i++){
  59                                 if (metaData.getColumnName(i + 1).equalsIgnoreCase(columnName)){
  60                                         return true;
  61                                 }
  62                         }
  63                         return false;
  64                 } catch (SQLException e) {
  65             logger.warn("Exception in resultSetHasColumn");
  66             return false;
  67                 }
  68         }
  69
  70         protected boolean checkSqlServerColumnExists(Source source, String tableName, String columnName){
  71                 String strQuery = "SELECT  Count(t.id) as n " +
  72                                 " FROM sysobjects AS t " +
  73                                 " INNER JOIN syscolumns AS c ON t.id = c.id " +
  74                                 " WHERE (t.xtype = 'U') AND " +
  75                                 " (t.name = '" + tableName + "') AND " +
  76                                 " (c.name = '" + columnName + "')";
  77                 ResultSet rs = source.getResultSet(strQuery) ;
  78                 int n;
  79                 try {
  80                         rs.next();
  81                         n = rs.getInt("n");
  82                         return n>0;
  83                 } catch (SQLException e) {
  84                         e.printStackTrace();
  85                         return false;
  86                 }
  87
  88         }
  89
  90         /**
  91          * Returns a map that holds all values of a ResultSet. This is needed if a value needs to
  92          * be accessed twice
  93          * @param rs
  94          * @return
  95          * @throws SQLException
  96          */
  97         protected Map<String, Object> getValueMap(ResultSet rs) throws SQLException{
  98                 try{
  99                         Map<String, Object> valueMap = new HashMap<String, Object>();
 100                         int colCount = rs.getMetaData().getColumnCount();
 101                         for (int c = 0; c < colCount ; c++){
 102                                 Object value = rs.getObject(c+1);
 103                                 String label = rs.getMetaData().getColumnLabel(c+1).toLowerCase();
 104                                 if (value != null && ! CdmUtils.Nz(value.toString()).trim().equals("")){
 105                                         valueMap.put(label, value);
 106                                 }
 107                         }
 108                         return valueMap;
 109                 }catch(SQLException e){
 110                         throw e;
 111                 }
 112         }
 113
 114
 115         protected boolean saveTaxa(Map<String, MapWrapper<? extends CdmBase>> stores,
 116                         int highestTaxonIndex, int limit) {
 117
 118                 MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);
 119
 120                 int n = 0;
 121                 int nbrOfTaxa = highestTaxonIndex;
 122 //              int nbrOfTaxa = taxonStore.size();
 123                 boolean success = true;
 124
 125                 if(logger.isInfoEnabled()) { logger.info("Saving taxa ..."); }
 126
 127                 if (nbrOfTaxa < limit) {             // TODO: test with critical values
 128                         limit = nbrOfTaxa;
 129                 } else {
 130                         n = nbrOfTaxa / limit;
 131                 }
 132
 133                 if(logger.isInfoEnabled()) {
 134                         logger.info("number of taxa = " + taxonStore.size()
 135                                         + ", highest taxon index = " + highestTaxonIndex
 136                                         + ", limit = " + limit
 137                                         + ", n = " + n);
 138                 }
 139
 140                 // save taxa in blocks of <=limit
 141
 142                 for (int j = 1; j <= n + 1; j++)
 143                 {
 144                         int offset = j - 1;
 145                         int start = offset * limit;
 146
 147                         if(logger.isInfoEnabled()) {
 148                                 logger.info("Saving taxa: " + start + " - " + (start + limit - 1));
 149                         }
 150
 151                         if(logger.isInfoEnabled()) {
 152                                 logger.info("index = " + j
 153                                                 + ", offset = " + offset
 154                                                 + ", start = " + start);
 155                         }
 156
 157                         if (j == n + 1) {
 158                                 limit = nbrOfTaxa - n * limit;
 159                                 if(logger.isInfoEnabled()) {
 160                                         logger.info("n = " + n + ", limit = " + limit);
 161                                 }
 162                         }
 163
 164                 TransactionStatus txStatus = startTransaction();
 165
 166                         Collection<TaxonBase> taxonMapPart = taxonStore.objects(start, limit);
 167                         getTaxonService().saveTaxonAll(taxonMapPart);
 168                         taxonMapPart = null;
 169                         taxonStore.removeObjects(start, limit);
 170
 171                         commitTransaction(txStatus);
 172
 173                 }
 174
 175                 return success;
 176         }
 177 }