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package org.bgbm.biovel.drf.checklist;
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import java.rmi.RemoteException;
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import java.util.List;
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import javax.xml.rpc.ServiceException;
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import org.apache.http.HttpHost;
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import org.bgbm.biovel.drf.checklist.pesi.PESINameServiceLocator;
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import org.bgbm.biovel.drf.checklist.pesi.PESINameServicePortType;
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import org.bgbm.biovel.drf.checklist.pesi.PESIRecord;
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import org.bgbm.biovel.drf.tnr.msg.AcceptedName;
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import org.bgbm.biovel.drf.tnr.msg.NameType;
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import org.bgbm.biovel.drf.tnr.msg.ScrutinyType;
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import org.bgbm.biovel.drf.tnr.msg.SourceType;
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import org.bgbm.biovel.drf.tnr.msg.TaxonNameType;
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import org.bgbm.biovel.drf.tnr.msg.TnrMsg;
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import org.bgbm.biovel.drf.tnr.msg.TnrMsg.Query;
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import org.bgbm.biovel.drf.tnr.msg.TnrResponse;
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import org.bgbm.biovel.drf.tnr.msg.TnrResponse.Synonym;
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public class PESIClient extends BaseChecklistClient {
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public static final String ID = "pesi";
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public static final String LABEL = "PESI";
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public static final String URL = "http://www.eu-nomen.eu/portal/index.php";
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public static final String DATA_AGR_URL = "";
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public PESIClient() {
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super();
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}
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@Override
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public HttpHost getHost() {
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// TODO Auto-generated method stub
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return new HttpHost("http://www.eu-nomen.eu",80);
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}
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@Override
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public ServiceProviderInfo buildServiceProviderInfo() {
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ServiceProviderInfo checklistInfo = new ServiceProviderInfo(ID,LABEL,URL,DATA_AGR_URL);
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setChecklistInfo(checklistInfo);
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return checklistInfo;
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}
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@Override
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public void resolveNames(TnrMsg tnrMsg) throws DRFChecklistException {
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List<TnrMsg.Query> queryList = tnrMsg.getQuery();
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if(queryList.size() == 0) {
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throw new DRFChecklistException("PESI query list is empty");
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}
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if(queryList.size() > 1) {
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throw new DRFChecklistException("PESI query list has more than one query");
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}
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Query query = queryList.get(0);
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//http://www.catalogueoflife.org/col/webservice?response=full&name={sciName}
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String name = query.getTnrRequest().getTaxonName().getName().getNameComplete();
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PESINameServiceLocator pesins = new PESINameServiceLocator();
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PESINameServicePortType pesinspt;
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try {
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pesinspt = pesins.getPESINameServicePort();
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} catch (ServiceException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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throw new DRFChecklistException("Error in accessing PESINameService");
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}
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updateQueryWithResponse(query,pesinspt,name,getServiceProviderInfo());
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}
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@Override
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public int getMaxPageSize() {
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return 10;
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}
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private void updateQueryWithResponse(Query query ,
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PESINameServicePortType pesinspt,
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String name,
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ServiceProviderInfo ci) throws DRFChecklistException {
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try {
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String nameGUID = pesinspt.getGUID(name);
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System.out.println("nameGUID : " + nameGUID);
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PESIRecord record = pesinspt.getPESIRecordByGUID(nameGUID);
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if(record != null) {
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TnrResponse tnrResponse = new TnrResponse();
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tnrResponse.setChecklist(ci.getLabel());
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tnrResponse.setChecklistUrl(ci.getUrl());
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String accNameGUID = record.getValid_guid();
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// case when accepted name
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if(record.getGUID().equals(record.getValid_guid())) {
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AcceptedName accName = generateAccName(record);
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tnrResponse.setAcceptedName(accName);
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} else {
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// case when synonym
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PESIRecord accNameRecord = pesinspt.getPESIRecordByGUID(accNameGUID);
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AcceptedName accName = generateAccName(accNameRecord);
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tnrResponse.setAcceptedName(accName);
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}
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PESIRecord[] records = pesinspt.getPESISynonymsByGUID(accNameGUID);
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if(records != null && records.length > 0) {
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generateSynonyms(records,tnrResponse);
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}
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if(query != null) {
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query.getTnrResponse().add(tnrResponse);
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}
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}
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} catch (RemoteException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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throw new DRFChecklistException("Error in getGUID method in PESINameService");
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}
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}
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private AcceptedName generateAccName(PESIRecord taxon) {
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AcceptedName accName = new AcceptedName();
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TaxonNameType taxonName = new TaxonNameType();
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NameType name = new NameType();
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String resName = taxon.getScientificname();
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name.setNameComplete(resName + " " + taxon.getAuthority());
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name.setNameCanonical(resName);
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name.setNameStatus(taxon.getStatus());
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taxonName.setRank(taxon.getRank());
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taxonName.setAuthorship(taxon.getAuthority());
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taxonName.setName(name);
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accName.setTaxonName(taxonName);
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AcceptedName.Info info = new AcceptedName.Info();
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info.setUrl(taxon.getUrl());
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accName.setInfo(info);
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//FIXME : To fill in
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String sourceUrl = taxon.getUrl();
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String sourceDatasetID = "";
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String sourceDatasetName = "";
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String sourceName = "";
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SourceType source = new SourceType();
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source.setDatasetID(sourceDatasetID);
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source.setDatasetName(sourceDatasetName);
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source.setName(sourceName);
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source.setUrl(sourceUrl);
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accName.setSource(source);
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//FIXME : To fill in
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String accordingTo = taxon.getAuthority();
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String modified = "";
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ScrutinyType scrutiny = new ScrutinyType();
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scrutiny.setAccordingTo(accordingTo);
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scrutiny.setModified(modified);
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accName.setScrutiny(scrutiny);
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AcceptedName.Classification c = new AcceptedName.Classification();
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c.setKingdom(taxon.getKingdom());
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c.setPhylum(taxon.getPhylum());
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c.setClazz("");
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c.setOrder(taxon.getOrder());
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c.setFamily(taxon.getFamily());
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c.setGenus(taxon.getGenus());
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accName.setClassification(c);
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return accName;
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}
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private void generateSynonyms(PESIRecord[] synonyms, TnrResponse tnrResponse) {
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for(PESIRecord synRecord : synonyms) {
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TnrResponse.Synonym synonym = new Synonym();
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TaxonNameType taxonName = new TaxonNameType();
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NameType name = new NameType();
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String resName = synRecord.getScientificname();
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name.setNameComplete(resName + " " + synRecord.getAuthority());
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name.setNameCanonical(resName);
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name.setNameStatus(synRecord.getStatus());
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taxonName.setRank(synRecord.getRank());
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taxonName.setAuthorship(synRecord.getAuthority());
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taxonName.setName(name);
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synonym.setTaxonName(taxonName);
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Synonym.Info info = new Synonym.Info();
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info.setUrl(synRecord.getUrl());
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synonym.setInfo(info);
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//FIXME : To fill in
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String sourceUrl = synRecord.getUrl();
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String sourceDatasetID = "";
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String sourceDatasetName = "";
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String sourceName = "";
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SourceType source = new SourceType();
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source.setDatasetID(sourceDatasetID);
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source.setDatasetName(sourceDatasetName);
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source.setName(sourceName);
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source.setUrl(sourceUrl);
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synonym.setSource(source);
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//FIXME : To fill in
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String accordingTo = synRecord.getAuthority();
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String modified = "";
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ScrutinyType scrutiny = new ScrutinyType();
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scrutiny.setAccordingTo(accordingTo);
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scrutiny.setModified(modified);
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synonym.setScrutiny(scrutiny);
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tnrResponse.getSynonym().add(synonym);
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}
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}
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}
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