56 lines
1.9 KiB
Java
56 lines
1.9 KiB
Java
package org.gcube.data.spd.wormsplugin.capabilities;
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import java.util.Collection;
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import org.gcube.data.spd.model.exceptions.ExternalRepositoryException;
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import org.gcube.data.spd.model.exceptions.StreamNonBlockingException;
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import org.gcube.data.spd.plugin.fwk.capabilities.ExpansionCapability;
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import org.gcube.data.spd.plugin.fwk.writers.ObjectWriter;
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import org.gcube.data.spd.wormsplugin.WormsPlugin;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import de.uni_jena.cs.fusion.client.worms.AphiaRecord;
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import de.uni_jena.cs.fusion.client.worms.WormsClientException;
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public class ExpansionCapabilityImpl implements ExpansionCapability {
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Logger logger = LoggerFactory.getLogger(ExpansionCapabilityImpl.class);
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@Override
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public void getSynonyms(ObjectWriter<String> writer, String scientifcName) throws ExternalRepositoryException {
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logger.debug("searching synonyms for "+scientifcName);
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int offset =1;
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int elements =20;
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Collection<AphiaRecord> records = null;
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do{
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try{
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records = WormsPlugin.wormsClient.aphiaRecordsByName(scientifcName, true, false, offset);
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if (records!=null){
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for (AphiaRecord record : records){
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try{
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Collection<AphiaRecord> synonyms = WormsPlugin.wormsClient.aphiaSynonymsByAphiaId(record.aphiaId);
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if (synonyms!=null){
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for (AphiaRecord synonym: synonyms){
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if (!writer.isAlive()) return;
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writer.write(synonym.scientificName);
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logger.debug("found synonym "+synonym.scientificName);
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}
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}
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}catch (Exception e) {
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writer.write(new StreamNonBlockingException("WoRMS",scientifcName));
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logger.error("error retrieving synonyms for aphia id "+record.aphiaId, e);
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}
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}
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}
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} catch (WormsClientException e) {
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throw new ExternalRepositoryException(e);
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}
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offset = elements+offset;
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}while(records!=null && records.size() == offset );
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}
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}
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