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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.globis;
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import java.lang.reflect.Method;
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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.sql.Timestamp;
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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 org.joda.time.DateTime;
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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.IImportConfigurator.EDITOR;
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import eu.etaxonomy.cdm.io.common.IPartitionedIO;
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import eu.etaxonomy.cdm.io.common.ImportHelper;
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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.DbImportMapping;
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import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
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import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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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.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.User;
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import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
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import eu.etaxonomy.cdm.model.name.ZoologicalName;
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import eu.etaxonomy.cdm.strategy.exceptions.StringNotParsableException;
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import eu.etaxonomy.cdm.strategy.parser.INonViralNameParser;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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/**
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* @author a.mueller
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* @created 20.03.2008
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* @version 1.0
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*/
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public abstract class GlobisImportBase<CDM_BASE extends CdmBase> extends CdmImportBase<GlobisImportConfigurator, GlobisImportState> implements ICdmIO<GlobisImportState>, IPartitionedIO<GlobisImportState> {
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private static final Logger logger = Logger.getLogger(GlobisImportBase.class);
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public static final UUID ID_IN_SOURCE_EXT_UUID = UUID.fromString("23dac094-e793-40a4-bad9-649fc4fcfd44");
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//NAMESPACES
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protected static final String REFERENCE_NAMESPACE = "Literatur";
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protected static final String TAXON_NAMESPACE = "current_species";
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private String pluralString;
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private String dbTableName;
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//TODO needed?
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private Class cdmTargetClass;
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private INonViralNameParser parser = NonViralNameParserImpl.NewInstance();
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/**
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* @param dbTableName
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* @param dbTableName2
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*/
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public GlobisImportBase(String pluralString, String dbTableName, Class cdmTargetClass) {
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this.pluralString = pluralString;
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this.dbTableName = dbTableName;
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this.cdmTargetClass = cdmTargetClass;
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}
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protected void doInvoke(GlobisImportState state){
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logger.info("start make " + getPluralString() + " ...");
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GlobisImportConfigurator 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 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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}
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logger.info("end make " + getPluralString() + " ... " + getSuccessString(true));
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return;
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}
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/**
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* @param authorAndYear
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* @param zooName
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*/
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protected void handleAuthorAndYear(String authorAndYear, ZoologicalName zooName) {
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if (isBlank(authorAndYear)){
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return;
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}
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try {
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String doubtfulAuthorAndYear = null;
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if(authorAndYear.matches(".+\\,\\s\\[\\d{4}\\].*")){
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doubtfulAuthorAndYear = authorAndYear;
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authorAndYear = authorAndYear.replace("[", "").replace("]", "");
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}
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if (authorAndYear.contains("?")){
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authorAndYear = authorAndYear.replace("H?bner", "H\u00fcbner");
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authorAndYear = authorAndYear.replace("Oberth?r", "Oberth\u00fcr");
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}
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parser.parseAuthors(zooName, authorAndYear);
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if (doubtfulAuthorAndYear != null){
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zooName.setAuthorshipCache(doubtfulAuthorAndYear, true);
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}
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} catch (StringNotParsableException e) {
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logger.warn("Author could not be parsed: " + authorAndYear);
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zooName.setAuthorshipCache(authorAndYear, true);
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}
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}
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/**
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* @param state
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* @param countryStr
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* @return
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*/
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protected WaterbodyOrCountry getCountry(GlobisImportState state, String countryStr) {
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WaterbodyOrCountry country = WaterbodyOrCountry.getWaterbodyOrCountryByLabel(countryStr);
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if (country == null){
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try {
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country = (WaterbodyOrCountry)state.getTransformer().getNamedAreaByKey(countryStr);
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} catch (UndefinedTransformerMethodException e) {
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e.printStackTrace();
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}
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}
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return country;
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}
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public boolean doPartition(ResultSetPartitioner partitioner, GlobisImportState state) {
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boolean success = true ;
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Set 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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/**
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* @return
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*/
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protected /*abstract*/ DbImportMapping<?, ?> getMapping(){
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return null;
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}
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/**
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* @return
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*/
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protected abstract String getRecordQuery(GlobisImportConfigurator config);
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/**
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* @return
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*/
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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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getPluralString()
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*/
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public String getPluralString(){
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return pluralString;
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}
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/**
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* @return
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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 doIdCreatedUpdatedNotes(GlobisImportState state, IdentifiableEntity identifiableEntity, ResultSet rs, long id, String namespace)
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throws SQLException{
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boolean success = true;
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//id
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success &= ImportHelper.setOriginalSource(identifiableEntity, state.getConfig().getSourceReference(), id, namespace);
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//createdUpdateNotes
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success &= doCreatedUpdatedNotes(state, identifiableEntity, rs, namespace);
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return success;
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}
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protected boolean doCreatedUpdatedNotes(GlobisImportState state, AnnotatableEntity annotatableEntity, ResultSet rs, String namespace)
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throws SQLException{
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GlobisImportConfigurator config = state.getConfig();
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Object createdWhen = rs.getObject("Created_When");
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String createdWho = rs.getString("Created_Who");
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Object updatedWhen = null;
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String updatedWho = null;
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try {
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updatedWhen = rs.getObject("Updated_When");
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updatedWho = rs.getString("Updated_who");
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} catch (SQLException e) {
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//Table "Name" has no updated when/who
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}
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String notes = rs.getString("notes");
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boolean success = true;
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//Created When, Who, Updated When Who
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if (config.getEditor() == null || config.getEditor().equals(EDITOR.NO_EDITORS)){
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//do nothing
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}else if (config.getEditor().equals(EDITOR.EDITOR_AS_ANNOTATION)){
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String createdAnnotationString = "Berlin Model record was created By: " + String.valueOf(createdWho) + " (" + String.valueOf(createdWhen) + ") ";
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if (updatedWhen != null && updatedWho != null){
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createdAnnotationString += " and updated By: " + String.valueOf(updatedWho) + " (" + String.valueOf(updatedWhen) + ")";
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}
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Annotation annotation = Annotation.NewInstance(createdAnnotationString, Language.DEFAULT());
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annotation.setCommentator(config.getCommentator());
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annotation.setAnnotationType(AnnotationType.TECHNICAL());
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annotatableEntity.addAnnotation(annotation);
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}else if (config.getEditor().equals(EDITOR.EDITOR_AS_EDITOR)){
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User creator = getUser(createdWho, state);
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User updator = getUser(updatedWho, state);
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DateTime created = getDateTime(createdWhen);
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DateTime updated = getDateTime(updatedWhen);
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annotatableEntity.setCreatedBy(creator);
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annotatableEntity.setUpdatedBy(updator);
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annotatableEntity.setCreated(created);
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annotatableEntity.setUpdated(updated);
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}else {
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logger.warn("Editor type not yet implemented: " + config.getEditor());
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}
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//notes
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if (StringUtils.isNotBlank(notes)){
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String notesString = String.valueOf(notes);
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if (notesString.length() > 65530 ){
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notesString = notesString.substring(0, 65530) + "...";
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logger.warn("Notes string is longer than 65530 and was truncated: " + annotatableEntity);
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}
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Annotation notesAnnotation = Annotation.NewInstance(notesString, null);
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//notesAnnotation.setAnnotationType(AnnotationType.EDITORIAL());
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//notes.setCommentator(bmiConfig.getCommentator());
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annotatableEntity.addAnnotation(notesAnnotation);
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}
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return success;
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}
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private User getUser(String userString, GlobisImportState state){
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if (StringUtils.isBlank(userString)){
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return null;
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}
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userString = userString.trim();
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User user = state.getUser(userString);
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if (user == null){
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user = getTransformedUser(userString,state);
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}
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if (user == null){
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user = makeNewUser(userString, state);
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}
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if (user == null){
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logger.warn("User is null");
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}
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return user;
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}
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private User getTransformedUser(String userString, GlobisImportState state){
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Method method = state.getConfig().getUserTransformationMethod();
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if (method == null){
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return null;
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}
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try {
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userString = (String)state.getConfig().getUserTransformationMethod().invoke(null, userString);
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} catch (Exception e) {
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logger.warn("Error when trying to transform userString " + userString + ". No transformation done.");
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}
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User user = state.getUser(userString);
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return user;
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}
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private User makeNewUser(String userString, GlobisImportState state){
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String pwd = getPassword();
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User user = User.NewInstance(userString, pwd);
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state.putUser(userString, user);
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getUserService().save(user);
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logger.info("Added new user: " + userString);
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return user;
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}
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private String getPassword(){
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String result = UUID.randomUUID().toString();
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return result;
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}
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private DateTime getDateTime(Object timeString){
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if (timeString == null){
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return null;
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}
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DateTime dateTime = null;
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if (timeString instanceof Timestamp){
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Timestamp timestamp = (Timestamp)timeString;
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dateTime = new DateTime(timestamp);
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}else{
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logger.warn("time ("+timeString+") is not a timestamp. Datetime set to current date. ");
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dateTime = new DateTime();
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}
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return dateTime;
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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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}
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