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