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/**
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* Copyright (C) 2009 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.out;
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import java.sql.SQLException;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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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.mapping.out.DbExportIgnoreMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.DbFixedIntegerMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.DbFixedStringMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.IdIncMapper;
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import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper;
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import eu.etaxonomy.cdm.io.pesi.erms.ErmsLinkImport;
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import eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Extension;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.profiler.ProfilerController;
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/**
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* The export class for PESI ecology notes (marine, brackish, fresh, terrestrial) coming from ERMS tu table.<p>
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* @author a.mueller
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* @since 28.09.2019
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*/
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@Component
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public class PesiEcologyAndLinkExport extends PesiExportBase {
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private static final long serialVersionUID = -2567615286288369111L;
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private static final Logger logger = Logger.getLogger(PesiEcologyAndLinkExport.class);
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private static final Class<? extends CdmBase> standardMethodParameter = TaxonBase.class;
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private static int modCount = 1000;
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private static final String dbTableName = "Note";
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private static final String pluralString = "ecology or link notes";
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private static final String parentPluralString = "Taxa";
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public PesiEcologyAndLinkExport() {
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super();
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}
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int countNotes = 0;
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int countUrls = 0;
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String currentValue;
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@Override
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public Class<? extends CdmBase> getStandardMethodParameter() {
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return standardMethodParameter;
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}
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@Override
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protected void doInvoke(PesiExportState state) {
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try {
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logger.info("*** Started making " + pluralString + " ...");
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// Stores whether this invoke was successful or not.
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boolean success = true;
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// Get specific mappings: (CDM) TaxonBase.marker -> (PESI) Note (ecology)
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PesiExportMapping mapping = getEcologyMapping();
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mapping.initialize(state);
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PesiExportMapping urlMapping = getUrlMapping();
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urlMapping.initialize(state);
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//All
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success &= doPhase01(state, mapping, urlMapping);
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logger.info("*** Finished Making " + pluralString + " ..." + getSuccessString(success));
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if (!success){
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state.getResult().addError("An unknown problem occurred");
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}
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return;
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} catch (SQLException e) {
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e.printStackTrace();
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logger.error(e.getMessage());
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state.getResult().addException(e, e.getMessage());
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}
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}
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//PHASE 01: All
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private boolean doPhase01(PesiExportState state, PesiExportMapping mapping, PesiExportMapping urlMapping) throws SQLException {
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// logger.info("PHASE 1 (ecology...");
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int count = 0;
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int pastCount = 0;
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boolean success = true;
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int limit = state.getConfig().getLimitSave();
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List<TaxonBase> taxonList = null;
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TransactionStatus txStatus = startTransaction(true);
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if (logger.isDebugEnabled()){
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logger.info("Started new transaction. Fetching some " + parentPluralString + " (max: " + limit + ") ...");
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logger.debug("Start snapshot, before starting loop");
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ProfilerController.memorySnapshot();
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}
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List<String> propPath = Arrays.asList(new String[]{"markers.*","extensions.*"});
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int partitionCount = 0;
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while ((taxonList = getNextTaxonPartition(TaxonBase.class, limit, partitionCount++, propPath )) != null ) {
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if (logger.isDebugEnabled()) {
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logger.info("Fetched " + taxonList.size() + " " + parentPluralString + ". Exporting...");
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}
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for (TaxonBase<?> taxon : taxonList) {
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doCount(count++, modCount, pluralString);
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state.setCurrentTaxon(taxon);
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if (!taxon.getMarkers().isEmpty()){
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success &= handleSingleEcologyTaxon(taxon, mapping);
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}
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if (!taxon.getExtensions().isEmpty()){
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success &= handleSingleLinkTaxon(taxon, urlMapping);
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}
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}
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taxonList = null;
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state.setCurrentTaxon(null);
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// Commit transaction
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commitTransaction(txStatus);
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logger.info("Exported " + (count - pastCount) + " " + parentPluralString + ". Total taxa: " + count + ". Ecology notes: " + countNotes + ". Link notes: " + countUrls);
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pastCount = count;
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if (logger.isDebugEnabled()) {
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ProfilerController.memorySnapshot();
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}
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// Start transaction
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txStatus = startTransaction(true);
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if(logger.isDebugEnabled()) {
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logger.info("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") for description import ...");
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}
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}
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// Commit transaction
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commitTransaction(txStatus);
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logger.debug("Committed transaction.");
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return success;
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}
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private boolean handleSingleEcologyTaxon(TaxonBase<?> taxon, PesiExportMapping mapping) {
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boolean success = true;
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String ecologyStr = getEcologyString(taxon);
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if (isNotBlank(ecologyStr)){
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success &= mapping.invoke(taxon);
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countNotes++;
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}
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return success;
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}
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private static String getEcologyString(TaxonBase<?> taxon) {
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String ecologyStr = null;
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ecologyStr = CdmUtils.concat(", ", ecologyStr, createEcologyStr(taxon, "marine", ErmsTransformer.uuidMarkerMarine));
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ecologyStr = CdmUtils.concat(", ", ecologyStr, createEcologyStr(taxon, "brackish", ErmsTransformer.uuidMarkerBrackish));
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ecologyStr = CdmUtils.concat(", ", ecologyStr, createEcologyStr(taxon, "fresh", ErmsTransformer.uuidMarkerFreshwater));
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ecologyStr = CdmUtils.concat(", ", ecologyStr, createEcologyStr(taxon, "terrestrial", ErmsTransformer.uuidMarkerTerrestrial));
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return ecologyStr;
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}
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private static String createEcologyStr(TaxonBase<?> taxon, String strEcology, UUID markerUuid) {
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Boolean value = taxon.markerValue(markerUuid);
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if (value == null){
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return null;
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}else if (value == true){
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return strEcology;
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}else{
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return "not " + strEcology;
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}
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}
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private boolean handleSingleLinkTaxon(TaxonBase<?> taxon, PesiExportMapping mapping) {
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boolean success = true;
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Set<Extension> urlExtensions = taxon.getFilteredExtensions(ErmsTransformer.uuidExtErmsLink);
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for (Extension extension : urlExtensions){
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mapping.invoke(extension);
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countUrls++;
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}
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return success;
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}
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protected boolean doDelete(PesiExportState state) {
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//Note table is already filled by Description import
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//=> we do not empty any table here
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return true;
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}
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@SuppressWarnings("unused") //used by mapper
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private static Integer getTaxonFk(TaxonBase<?> taxonBase, PesiExportState state) {
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return state.getDbId(taxonBase);
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}
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@SuppressWarnings("unused") //used by mapper
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private static Integer getCurrentTaxonFk(Extension extension, PesiExportState state) {
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return state.getDbId(state.getCurrentTaxon());
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}
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@SuppressWarnings("unused") //used by mapper
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private static String getNote_1(TaxonBase<?> taxon) {
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return getEcologyString(taxon);
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}
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@SuppressWarnings("unused") //used by mapper
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private static String getUrlNote_1(Extension extension) {
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String value = extension.getValue();
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if (value == null){
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return null;
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}else{
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//TODO use regex grouping
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String result = value.split(ErmsLinkImport.TOKEN_LINKTEXT)[0];
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result = result.replace(ErmsLinkImport.TOKEN_URL, "").trim();
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return result;
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}
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}
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// @SuppressWarnings("unused") //used by mapper
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private static String getUrlNote_2(Extension extension) {
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String value = extension.getValue();
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if (value == null){
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return null;
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}else{
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//TODO use regex grouping
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String[] split = value.split(ErmsLinkImport.TOKEN_LINKTEXT);
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if (split.length > 1){
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String result = split[1];
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result = result.trim();
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return CdmUtils.Ne(result);
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}else{
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return null;
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}
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}
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}
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// @SuppressWarnings("unused") //used by mapper
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private static Integer getNoteCategoryFk(Extension extension) {
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String linktext = getUrlNote_2(extension);
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int catFk = categoryByLinkText(linktext);
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return catFk;
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}
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private static int categoryByLinkText(String linktext) {
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if (linktext == null){
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return PesiTransformer.NoteCategory_undefined_link;
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}else if (linktext.matches("(?i)(to fishbase|marine life inf).*")){
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return PesiTransformer.NoteCategory_Link_to_general_information;
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}else if (linktext.matches("(?i).*(clemam|nemys|algaebase|fishbase).*")){
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return PesiTransformer.NoteCategory_Link_to_taxonomy;
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}else{
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return PesiTransformer.NoteCategory_undefined_link;
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}
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}
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@SuppressWarnings("unused") //used by mapper
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private static String getNoteCategoryCache(Extension extension) {
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int catFk = getNoteCategoryFk(extension);
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String result = categoryByLinkText(catFk);
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return result;
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}
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private static String categoryByLinkText(int catFk) {
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if(catFk == 22){
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return "";
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}else if (catFk == 23){
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return "";
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}else if (catFk == 24){
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return "";
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}else{
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logger.warn("Link category fk not yet supported: " + catFk);
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return null;
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}
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}
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//******************************* MAPPINGS ********************************************
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private IdIncMapper idIncMapperEcology = IdIncMapper.NewComputedInstance("NoteId");
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private PesiExportMapping getEcologyMapping() {
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PesiExportMapping mapping = new PesiExportMapping(dbTableName);
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mapping.addMapper(idIncMapperEcology);
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mapping.addMapper(MethodMapper.NewInstance("Note_1", this, standardMethodParameter));
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mapping.addMapper(DbFixedIntegerMapper.NewInstance(PesiTransformer.NoteCategory_ecology, "NoteCategoryFk"));
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mapping.addMapper(DbFixedStringMapper.NewInstance("ecology", "NoteCategoryCache"));
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mapping.addMapper(DbFixedIntegerMapper.NewInstance(12, "LanguageFk"));
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mapping.addMapper(DbFixedStringMapper.NewInstance("English", "LanguageCache"));
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mapping.addMapper(MethodMapper.NewInstance("TaxonFk", this, standardMethodParameter, PesiExportState.class));
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mapping.addMapper(DbExportIgnoreMapper.NewInstance("Note_2", "not used for ecology fact"));
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mapping.addMapper(DbExportIgnoreMapper.NewInstance("Region", "not used for ecology fact"));
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mapping.addMapper(DbExportIgnoreMapper.NewInstance("SpeciesExpertGUID", "not used for ecology fact"));
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mapping.addMapper(DbExportIgnoreMapper.NewInstance("SpeciesExpertName", "not used for ecology fact"));
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mapping.addMapper(DbExportIgnoreMapper.NewInstance("LastAction", "not used for ecology fact"));
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mapping.addMapper(DbExportIgnoreMapper.NewInstance("LastActionDate", "not used for ecology fact"));
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return mapping;
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}
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private PesiExportMapping getUrlMapping() {
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PesiExportMapping mapping = new PesiExportMapping(dbTableName);
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IdIncMapper idIncMapper = IdIncMapper.NewDependendInstance("NoteId", idIncMapperEcology);
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mapping.addMapper(idIncMapper);
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mapping.addMapper(MethodMapper.NewInstance("Note_1", this.getClass(), "getUrlNote_1", Extension.class));
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mapping.addMapper(MethodMapper.NewInstance("Note_2", this.getClass(), "getUrlNote_2", Extension.class));
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mapping.addMapper(MethodMapper.NewInstance("NoteCategoryFk", this.getClass(), Extension.class));
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mapping.addMapper(MethodMapper.NewInstance("NoteCategoryCache", this.getClass(), Extension.class));
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mapping.addMapper(MethodMapper.NewInstance("TaxonFk", this.getClass(), "getCurrentTaxonFk", Extension.class, PesiExportState.class));
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mapping.addMapper(DbExportIgnoreMapper.NewInstance("LanguageFk", "not used for link fact"));
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mapping.addMapper(DbExportIgnoreMapper.NewInstance("LanguageCache", "not used for link fact"));
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mapping.addMapper(DbExportIgnoreMapper.NewInstance("Region", "not used for link fact"));
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mapping.addMapper(DbExportIgnoreMapper.NewInstance("SpeciesExpertGUID", "not used for link fact"));
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mapping.addMapper(DbExportIgnoreMapper.NewInstance("SpeciesExpertName", "not used for link fact"));
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mapping.addMapper(DbExportIgnoreMapper.NewInstance("LastAction", "not used for link fact"));
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mapping.addMapper(DbExportIgnoreMapper.NewInstance("LastActionDate", "not used for link fact"));
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return mapping;
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}
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@Override
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protected boolean doCheck(PesiExportState state) {
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boolean result = true;
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return result;
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}
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@Override
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protected boolean isIgnore(PesiExportState state) {
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return ! state.getConfig().isDoEcologyAndLink();
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}
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}
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