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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.eflora.centralAfrica.ferns;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.HashSet;
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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 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.DbImportMapping;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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import eu.etaxonomy.cdm.model.name.Rank;
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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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* @since 20.03.2008
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* @version 1.0
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*/
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public abstract class CentralAfricaFernsImportBase<CDM_BASE extends CdmBase> extends CdmImportBase<CentralAfricaFernsImportConfigurator, CentralAfricaFernsImportState> implements ICdmIO<CentralAfricaFernsImportState>, IPartitionedIO<CentralAfricaFernsImportState> {
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private static final Logger logger = Logger.getLogger(CentralAfricaFernsImportBase.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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protected static final String TAXON_NAMESPACE = "African_pteridophytes_Taxon";
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protected static final String NAME_NAMESPACE = "African_pteridophytes_Name";
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protected static final String HIGHER_TAXON_NAMESPACE = "African_pteridophytes_Higher_Taxon";
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private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
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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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/**
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* @param dbTableName
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* @param dbTableName2
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*/
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public CentralAfricaFernsImportBase(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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@Override
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protected void doInvoke(CentralAfricaFernsImportState state){
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logger.info("start make " + getPluralString() + " ...");
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CentralAfricaFernsImportConfigurator 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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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(ResultSetPartitioner partitioner, CentralAfricaFernsImportState 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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/**
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* @return
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*/
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protected abstract String getRecordQuery(CentralAfricaFernsImportConfigurator 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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@Override
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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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/**
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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 setAuthor(IBotanicalName taxonName, ResultSet rs, String taxonNumber, boolean isHigherTaxon) throws SQLException {
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String authorsFull = null;
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String authorsAbbrev = null;
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if (! isHigherTaxon){
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authorsFull = rs.getString("Author/s - full");
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authorsAbbrev = rs.getString("Author/s - abbreviated");
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}
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Rank rank = taxonName.getRank();
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String authorString = null;
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if (rank != null){
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if (rank.equals(Rank.ORDER())){
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authorString = rs.getString("Order name author");
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}else if (rank.equals(Rank.SUBORDER())){
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authorString = rs.getString("Suborder name author");
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}else if (rank.equals(Rank.FAMILY())){
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authorString = rs.getString("Family name author");
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}else if (rank.equals(Rank.SUBFAMILY())){
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authorString = rs.getString("Subfamily name author");
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}else if (rank.equals(Rank.TRIBE())){
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authorString = rs.getString("Tribus author");
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}else if (rank.equals(Rank.SUBTRIBE())){
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authorString = rs.getString("Subtribus author");
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}else if (rank.equals(Rank.SECTION_BOTANY())){
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authorString = rs.getString("Section name author");
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}else if (rank.equals(Rank.SUBSECTION_BOTANY())){
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authorString = rs.getString("Subsection author");
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}else if (rank.equals(Rank.GENUS())){
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authorString = rs.getString("Genus name author");
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}else if (rank.equals(Rank.SUBGENUS())){
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authorString = rs.getString("Subgenus name author");
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}else if (rank.equals(Rank.SERIES())){
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authorString = rs.getString("Series name author");
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}else if (rank.equals(Rank.SPECIES())){
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authorString = rs.getString("Specific epithet author");
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}else if (rank.equals(Rank.SUBSPECIES())){
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authorString = rs.getString("Subspecies author");
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}else if (rank.equals(Rank.VARIETY())){
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authorString = rs.getString("Variety name author");
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}else if (rank.equals(Rank.SUBVARIETY())){
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authorString = rs.getString("Subvariety author");
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}else if (rank.equals(Rank.FORM())){
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authorString = rs.getString("Forma name author");
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}else if (rank.equals(Rank.SUBFORM())){
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authorString = rs.getString("Subforma author");
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}else{
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logger.warn("Author string could not be defined");
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if (! isHigherTaxon){
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authorString = authorsAbbrev;
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if (StringUtils.isBlank(authorString)){
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logger.warn("Authors abbrev string could not be defined");
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authorString = authorsFull;
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}
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}
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}
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}else{
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logger.warn(taxonNumber + ": Rank is null");
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authorString = authorsAbbrev;
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if (StringUtils.isBlank(authorString)){
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logger.warn(taxonNumber + ": Authors abbrev string could not be defined");
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authorString = authorsFull;
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}
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}
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if (StringUtils.isNotBlank(authorString)){
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parser.handleAuthors(taxonName, taxonName.getNameCache().trim() + " " + authorString, authorString);
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}
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if (! isHigherTaxon){
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String combinationAuthor = taxonName.getCombinationAuthorship()==null ? "" :taxonName.getCombinationAuthorship().getNomenclaturalTitle();
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if (StringUtils.isNotBlank(authorsAbbrev) && ! authorsAbbrev.equalsIgnoreCase(combinationAuthor)){
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//it is expected that the fullAuthor and the abbrevAuthor are the combination authors but very often it is not
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logger.warn(taxonNumber + ": Rank author and abbrev author are not equal: " + authorString + "\t<-> " + combinationAuthor + "\t<-> " + authorsAbbrev);
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}
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// if (StringUtils.isNotBlank(authorsFull) && ! authorsFull.equalsIgnoreCase(authorString)){
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// logger.warn("Rank author and full author are not equal Rankauthor: " + authorString + ", full author " + authorsFull);
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// }
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}
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}
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}
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