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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.faunaEuropaea;
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import java.sql.ResultSet;
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import java.sql.ResultSetMetaData;
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import java.sql.SQLException;
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import java.util.Collection;
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import java.util.HashMap;
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import java.util.Map;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.common.CdmImportBase;
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import eu.etaxonomy.cdm.io.common.CdmIoBase;
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import eu.etaxonomy.cdm.io.common.ICdmIO;
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import eu.etaxonomy.cdm.io.common.ICdmImport;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator;
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import eu.etaxonomy.cdm.io.common.ImportHelper;
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import eu.etaxonomy.cdm.io.common.MapWrapper;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;
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/**
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* @author a.babadshanjan
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* @created 11.05.2009
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* @version 1.0
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*/
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public abstract class FaunaEuropaeaImportBase extends CdmImportBase<FaunaEuropaeaImportConfigurator, FaunaEuropaeaImportState>
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implements ICdmImport<FaunaEuropaeaImportConfigurator,FaunaEuropaeaImportState> {
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private static final Logger logger = Logger.getLogger(FaunaEuropaeaImportBase.class);
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// /* Max number of taxa to retrieve (for test purposes) */
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// protected static final int maxTaxa = 1000;
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// /* Max number of taxa to be saved with one service call */
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// protected int limit = 20000; // TODO: Make configurable
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// /* Interval for progress info message when retrieving taxa */
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// protected static final int modCount = 10000;
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// /* Highest taxon index in the FauEu database */
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// protected int highestTaxonIndex = 0;
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protected boolean resultSetHasColumn(ResultSet rs, String columnName){
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try {
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ResultSetMetaData metaData = rs.getMetaData();
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for (int i = 0; i < metaData.getColumnCount(); i++){
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if (metaData.getColumnName(i + 1).equalsIgnoreCase(columnName)){
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return true;
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}
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}
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return false;
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} catch (SQLException e) {
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logger.warn("Exception in resultSetHasColumn");
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return false;
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}
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}
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protected boolean checkSqlServerColumnExists(Source source, String tableName, String columnName){
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String strQuery = "SELECT Count(t.id) as n " +
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" FROM sysobjects AS t " +
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" INNER JOIN syscolumns AS c ON t.id = c.id " +
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" WHERE (t.xtype = 'U') AND " +
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" (t.name = '" + tableName + "') AND " +
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" (c.name = '" + columnName + "')";
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ResultSet rs = source.getResultSet(strQuery) ;
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int n;
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try {
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rs.next();
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n = rs.getInt("n");
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return n>0;
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} catch (SQLException e) {
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e.printStackTrace();
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return false;
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}
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}
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/**
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* Returns a map that holds all values of a ResultSet. This is needed if a value needs to
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* be accessed twice
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* @param rs
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* @return
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* @throws SQLException
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*/
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protected Map<String, Object> getValueMap(ResultSet rs) throws SQLException{
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try{
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Map<String, Object> valueMap = new HashMap<String, Object>();
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int colCount = rs.getMetaData().getColumnCount();
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for (int c = 0; c < colCount ; c++){
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Object value = rs.getObject(c+1);
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String label = rs.getMetaData().getColumnLabel(c+1).toLowerCase();
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if (value != null && ! CdmUtils.Nz(value.toString()).trim().equals("")){
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valueMap.put(label, value);
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}
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}
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return valueMap;
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}catch(SQLException e){
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throw e;
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}
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}
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/**
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* @param state
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* @param sourceRef
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*/
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protected TaxonomicTree getTaxonomicTreeFor(FaunaEuropaeaImportState state, ReferenceBase<?> sourceRef) {
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TaxonomicTree tree;
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UUID treeUuid = state.getTreeUuid(sourceRef);
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if (treeUuid == null){
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if(logger.isInfoEnabled()) { logger.info(".. creating new taxonomic tree"); }
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TransactionStatus txStatus = startTransaction();
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tree = makeTreeMemSave(state, sourceRef);
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commitTransaction(txStatus);
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} else {
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tree = getTaxonTreeService().getTaxonomicTreeByUuid(treeUuid);
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}
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return tree;
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}
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}
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