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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.pesi.indexFungorum;
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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.HashMap;
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import java.util.HashSet;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import com.ibm.lsid.MalformedLSIDException;
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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.ICdmIO;
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import eu.etaxonomy.cdm.io.common.IPartitionedIO;
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.io.common.mapping.out.DbLastActionMapper;
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import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.LSID;
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import eu.etaxonomy.cdm.model.common.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.name.INonViralName;
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import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.strategy.exceptions.StringNotParsableException;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
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/**
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* @author a.mueller
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* @since 27.02.2012
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*/
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public abstract class IndexFungorumImportBase extends CdmImportBase<IndexFungorumImportConfigurator, IndexFungorumImportState> implements ICdmIO<IndexFungorumImportState>, IPartitionedIO<IndexFungorumImportState> {
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private static final long serialVersionUID = -729872543287390949L;
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private static final Logger logger = Logger.getLogger(IndexFungorumImportBase.class);
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//NAMESPACES
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protected static final String NAMESPACE_REFERENCE = "reference";
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protected static final String NAMESPACE_TAXON = "Taxon";
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protected static final String NAMESPACE_SUPRAGENERIC_NAMES = "SupragenericNames";
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protected static final String NAMESPACE_GENERA = "Genera";
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protected static final String NAMESPACE_SPECIES = "Species";
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protected static final String INCERTAE_SEDIS = "Incertae sedis";
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protected static final String FOSSIL_FUNGI = "Fossil Fungi";
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protected static final String SOURCE_REFERENCE = "SOURCE_REFERENCE";
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private final String pluralString;
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private final String dbTableName;
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public IndexFungorumImportBase(String pluralString, String dbTableName, Class cdmTargetClass) {
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this.pluralString = pluralString;
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this.dbTableName = dbTableName;
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}
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@Override
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protected void doInvoke(IndexFungorumImportState state){
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System.out.println("start make " + getPluralString() + " ...");
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IndexFungorumImportConfigurator config = state.getConfig();
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Source source = config.getSource();
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String strIdQuery = getIdQuery();
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String strRecordQuery = getRecordQuery(config);
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int recordsPerTransaction = config.getRecordsPerTransaction();
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try{
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ResultSetPartitioner<IndexFungorumImportState> partitioner = ResultSetPartitioner.NewInstance(source, strIdQuery, strRecordQuery, recordsPerTransaction);
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while (partitioner.nextPartition()){
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partitioner.doPartition(this, state);
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}
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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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state.setUnsuccessfull();
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return;
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}
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logger.info("end make " + getPluralString() + " ... " + getSuccessString(true));
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return;
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}
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@Override
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public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, IndexFungorumImportState state) {
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boolean success = true ;
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Set<CdmBase> objectsToSave = new HashSet<>();
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// DbImportMapping<?, ?> mapping = getMapping();
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// mapping.initialize(state, cdmTargetClass);
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ResultSet rs = partitioner.getResultSet();
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try{
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while (rs.next()){
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// success &= mapping.invoke(rs,objectsToSave);
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}
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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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return false;
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}
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partitioner.startDoSave();
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getCommonService().save(objectsToSave);
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return success;
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}
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protected abstract String getRecordQuery(IndexFungorumImportConfigurator config);
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protected String getIdQuery(){
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String result = " SELECT id FROM " + getTableName();
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return result;
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}
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@Override
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public String getPluralString(){
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return pluralString;
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}
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protected String getTableName(){
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return this.dbTableName;
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}
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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<>();
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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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* Reads a foreign key field from the result set and adds its value to the idSet.
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* @param rs
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* @param teamIdSet
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* @throws SQLException
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*/
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protected void handleForeignKey(ResultSet rs, Set<String> idSet, String attributeName)
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throws SQLException {
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Object idObj = rs.getObject(attributeName);
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if (idObj != null){
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String id = String.valueOf(idObj);
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idSet.add(id);
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}
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}
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/**
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* Returns true if i is a multiple of recordsPerTransaction
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* @param i
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* @param recordsPerTransaction
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* @return
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*/
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protected boolean loopNeedsHandling(int i, int recordsPerLoop) {
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startTransaction();
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return (i % recordsPerLoop) == 0;
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}
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protected void doLogPerLoop(int count, int recordsPerLog, String pluralString){
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if ((count % recordsPerLog ) == 0 && count!= 0 ){ logger.info(pluralString + " handled: " + (count));}
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}
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protected void makeAuthorAndPublication(IndexFungorumImportState state, ResultSet rs, INonViralName name) throws SQLException {
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//authors
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NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
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String authorStr = rs.getString("AUTHORS");
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if (StringUtils.isNotBlank(authorStr)){
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try {
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parser.parseAuthors(name, authorStr);
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} catch (StringNotParsableException e){
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//logger.warn("Authorstring not parsable: " + authorStr);
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name.setAuthorshipCache(authorStr);
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}
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}
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//page
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String page = rs.getString("PAGE");
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if (StringUtils.isNotBlank(page)){
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name.setNomenclaturalMicroReference(page);
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}
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//Reference
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Reference ref = ReferenceFactory.newGeneric();
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boolean hasInReference = false;
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//publishing authors
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Team pubAuthor = null;
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String pubAuthorStr = rs.getString("PUBLISHING AUTHORS");
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if (StringUtils.isNotBlank(pubAuthorStr)){
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if (StringUtils.isNotBlank(authorStr)){
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if (! pubAuthorStr.equals(authorStr)){
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pubAuthor = Team.NewTitledInstance(pubAuthorStr, pubAuthorStr);
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}
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}else{
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logger.warn("'AUTHORS' is blank for not empty PUBLISHING_AUTHORS. This is not yet handled.");
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}
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}
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//inRef + inRefAuthor
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if (pubAuthor != null){
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Reference inRef = ReferenceFactory.newGeneric();
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inRef.setAuthorship(pubAuthor);
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ref.setInReference(inRef);
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hasInReference = true;
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}
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//refAuthor
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TeamOrPersonBase<?> refAuthor = CdmBase.deproxy(name.getCombinationAuthorship());
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if (refAuthor == null){
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refAuthor = Team.NewTitledInstance(authorStr, authorStr);
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}
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ref.setAuthorship(refAuthor);
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//location
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String location = rs.getString("pubIMIAbbrLoc");
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if (StringUtils.isNotBlank(location)){
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if (hasInReference){
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ref.getInReference().setPlacePublished(location);
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}else{
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ref.setPlacePublished(location);
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}
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}
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//title
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String titleMain = rs.getString("pubIMIAbbr");
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String supTitle = rs.getString("pubIMISupAbbr");
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String title = CdmUtils.concat(", ", titleMain, supTitle);
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//preliminary to comply with current Index Fungorum display
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if (StringUtils.isNotBlank(location)){
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title += " (" + location +")";
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}
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//end preliminary
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if (StringUtils.isNotBlank(title)){
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if (hasInReference){
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ref.getInReference().setTitle(title);
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}else{
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ref.setTitle(title);
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}
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}
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//Volume
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String volume = CdmUtils.Nz(rs.getString("VOLUME")).trim();
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String part = rs.getString("PART");
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if (StringUtils.isNotBlank(part)){
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volume = volume + "(" + part + ")";
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if (StringUtils.isBlank(volume)){
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logger.warn("'Part' is not blank for blank volume. This may be an inconsistency.");
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}
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}
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ref.setVolume(volume);
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//year //TODO why yearOfPubl 2x exact same value
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String yearOfPubl = rs.getString("YEAR OF PUBLICATION");
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String yearOnPubl = rs.getString("YEAR ON PUBLICATION");
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String year = null;
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if (StringUtils.isNotBlank(yearOfPubl)){
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year = yearOfPubl.trim();
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}
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if (StringUtils.isNotBlank(yearOnPubl)){
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year = CdmUtils.concat(" ", year, "[" + yearOnPubl + "]");
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}
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if (year != null){
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ref.setDatePublished(TimePeriodParser.parseStringVerbatim(year));
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}
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//preliminary, set protected titlecache as Generic Cache Generation with in references currently doesn't fully work yet
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String titleCache = CdmUtils.concat(", ", pubAuthorStr, title);
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if ( StringUtils.isNotBlank(pubAuthorStr)){
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titleCache = "in " + titleCache;
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}
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titleCache = CdmUtils.concat(" ", titleCache, volume);
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titleCache = CdmUtils.concat(": ", titleCache, page);
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titleCache = CdmUtils.concat(". ", titleCache, year);
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ref.setTitleCache(titleCache, true);
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//set nom ref
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if (StringUtils.isNotBlank(titleCache)){
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name.setNomenclaturalReference(ref);
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}
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}
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protected MarkerType getNoLastActionMarkerType(IndexFungorumImportState state) {
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return getMarkerType(state, DbLastActionMapper.uuidMarkerTypeHasNoLastAction,
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"has no last action", "No last action information available", "no last action");
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}
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protected void makeSource(IndexFungorumImportState state, Taxon taxon, Integer id, String namespace) {
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//source reference
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Reference sourceReference = state.getRelatedObject(NAMESPACE_REFERENCE, SOURCE_REFERENCE, Reference.class);
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//source
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String strId = (id == null ? null : String.valueOf(id));
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IdentifiableSource source = IdentifiableSource.NewInstance(OriginalSourceType.Import, strId, namespace, sourceReference, null);
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taxon.addSource(source);
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//no last action
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MarkerType hasNoLastAction = getNoLastActionMarkerType(state);
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taxon.addMarker(Marker.NewInstance(hasNoLastAction, true));
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//LSID
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makeLSID(taxon, strId, state);
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}
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private void makeLSID(Taxon taxon, String strId, IndexFungorumImportState state) {
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try {
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if (StringUtils.isNotBlank(strId) && strId != null){
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LSID lsid = new LSID(IndexFungorumTransformer.LSID_PREFIX + strId);
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taxon.setLsid(lsid);
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}else{
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logger.warn("No ID available for taxon " + taxon.getTitleCache() + ", " + taxon.getUuid());
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MarkerType missingGUID = getMissingGUIDMarkerType(state);
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taxon.addMarker(Marker.NewInstance(missingGUID, true));
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}
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} catch (MalformedLSIDException e) {
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logger.error(e.getMessage());
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}
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}
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protected MarkerType getMissingGUIDMarkerType(IndexFungorumImportState state) {
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MarkerType missingGUID = getMarkerType(state, PesiTransformer.uuidMarkerGuidIsMissing, "GUID is missing", "GUID is missing", null);
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return missingGUID;
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}
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protected Classification getClassification(IndexFungorumImportState state) {
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Classification result;
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UUID classificationUuid = state.getTreeUuid(state.getConfig().getSourceReference());
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if (classificationUuid == null){
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Reference sourceReference = state.getRelatedObject(NAMESPACE_REFERENCE, SOURCE_REFERENCE, Reference.class);
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result = makeTreeMemSave(state, sourceReference);
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} else {
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result = getClassificationService().find(classificationUuid);
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}
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return result;
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}
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}
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