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 import java.util.UUID;
  19
  20 import org.apache.log4j.Logger;
  21 import org.springframework.transaction.TransactionStatus;
  22
  23 import eu.etaxonomy.cdm.common.CdmUtils;
  24 import eu.etaxonomy.cdm.io.common.CdmImportBase;
  25 import eu.etaxonomy.cdm.io.common.CdmIoBase;
  26 import eu.etaxonomy.cdm.io.common.ICdmIO;
  27 import eu.etaxonomy.cdm.io.common.ICdmImport;
  28 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  29 import eu.etaxonomy.cdm.io.common.ImportHelper;
  30 import eu.etaxonomy.cdm.io.common.MapWrapper;
  31 import eu.etaxonomy.cdm.io.common.Source;
  32 import eu.etaxonomy.cdm.model.common.Annotation;
  33 import eu.etaxonomy.cdm.model.common.CdmBase;
  34 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  35 import eu.etaxonomy.cdm.model.common.Language;
  36 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  37 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  38 import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;
  39
  40 /**
  41  * @author a.babadshanjan
  42  * @created 11.05.2009
  43  * @version 1.0
  44  */
  45 public abstract class FaunaEuropaeaImportBase extends CdmImportBase<FaunaEuropaeaImportConfigurator, FaunaEuropaeaImportState>
  46 implements ICdmImport<FaunaEuropaeaImportConfigurator,FaunaEuropaeaImportState> {
  47         private static final Logger logger = Logger.getLogger(FaunaEuropaeaImportBase.class);
  48
  49 //      /* Max number of taxa to retrieve (for test purposes) */
  50 //      protected static final int maxTaxa = 1000;
  51 //      /* Max number of taxa to be saved with one service call */
  52 //      protected int limit = 20000; // TODO: Make configurable
  53 //      /* Interval for progress info message when retrieving taxa */
  54 //      protected static final int modCount = 10000;
  55 //      /* Highest taxon index in the FauEu database */
  56 //      protected int highestTaxonIndex = 0;
  57
  58         protected boolean resultSetHasColumn(ResultSet rs, String columnName){
  59                 try {
  60                         ResultSetMetaData metaData = rs.getMetaData();
  61                         for (int i = 0; i < metaData.getColumnCount(); i++){
  62                                 if (metaData.getColumnName(i + 1).equalsIgnoreCase(columnName)){
  63                                         return true;
  64                                 }
  65                         }
  66                         return false;
  67                 } catch (SQLException e) {
  68             logger.warn("Exception in resultSetHasColumn");
  69             return false;
  70                 }
  71         }
  72
  73         protected boolean checkSqlServerColumnExists(Source source, String tableName, String columnName){
  74                 String strQuery = "SELECT  Count(t.id) as n " +
  75                                 " FROM sysobjects AS t " +
  76                                 " INNER JOIN syscolumns AS c ON t.id = c.id " +
  77                                 " WHERE (t.xtype = 'U') AND " +
  78                                 " (t.name = '" + tableName + "') AND " +
  79                                 " (c.name = '" + columnName + "')";
  80                 ResultSet rs = source.getResultSet(strQuery) ;
  81                 int n;
  82                 try {
  83                         rs.next();
  84                         n = rs.getInt("n");
  85                         return n>0;
  86                 } catch (SQLException e) {
  87                         e.printStackTrace();
  88                         return false;
  89                 }
  90
  91         }
  92
  93         /**
  94          * Returns a map that holds all values of a ResultSet. This is needed if a value needs to
  95          * be accessed twice
  96          * @param rs
  97          * @return
  98          * @throws SQLException
  99          */
 100         protected Map<String, Object> getValueMap(ResultSet rs) throws SQLException{
 101                 try{
 102                         Map<String, Object> valueMap = new HashMap<String, Object>();
 103                         int colCount = rs.getMetaData().getColumnCount();
 104                         for (int c = 0; c < colCount ; c++){
 105                                 Object value = rs.getObject(c+1);
 106                                 String label = rs.getMetaData().getColumnLabel(c+1).toLowerCase();
 107                                 if (value != null && ! CdmUtils.Nz(value.toString()).trim().equals("")){
 108                                         valueMap.put(label, value);
 109                                 }
 110                         }
 111                         return valueMap;
 112                 }catch(SQLException e){
 113                         throw e;
 114                 }
 115         }
 116
 117
 118         /**
 119          * @param state
 120          * @param sourceRef
 121          */
 122         protected TaxonomicTree getTaxonomicTreeFor(FaunaEuropaeaImportState state, ReferenceBase<?> sourceRef) {
 123
 124                 TaxonomicTree tree;
 125                 UUID treeUuid = state.getTreeUuid(sourceRef);
 126                 if (treeUuid == null){
 127                         if(logger.isInfoEnabled()) { logger.info(".. creating new taxonomic tree"); }
 128
 129                         TransactionStatus txStatus = startTransaction();
 130                         tree = makeTreeMemSave(state, sourceRef);
 131                         commitTransaction(txStatus);
 132
 133                 } else {
 134                         tree = getTaxonTreeService().getTaxonomicTreeByUuid(treeUuid);
 135                 }
 136                 return tree;
 137         }
 138
 139 }