Fixed bug on taxon.getName()==null

git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/portlets/user/speciesdiscovery@117452 82a268e6-3cf1-43bd-a215-b396298e98cf

.settings/org.eclipse.wst.common.component

@@ -3,9 +3,6 @@
         <wb-resource deploy-path="/" source-path="/target/m2e-wtp/web-resources"/>
     <wb-resource deploy-path="/" source-path="/src/main/webapp" tag="defaultRootSource"/>
     <wb-resource deploy-path="/WEB-INF/classes" source-path="/src/main/java"/>
-        <dependent-module archiveName="gis-viewer-3.7.0-SNAPSHOT.jar" deploy-path="/WEB-INF/lib" handle="module:/resource/gis-viewer-TRUNK/gis-viewer-TRUNK">
-            <dependency-type>uses</dependency-type>
-        </dependent-module>
     <property name="java-output-path" value="/${module}/target/www/WEB-INF/classes"/>
         <property name="context-root" value="species-discovery"/>
   </wb-module>

src/main/java/org/gcube/portlets/user/speciesdiscovery/server/session/Fetcher.java

@@ -21,7 +21,7 @@ import org.gcube.portlets.user.speciesdiscovery.shared.FetchingElement;
 public class Fetcher<T extends FetchingElement> implements Runnable, Closeable {
 
 	protected Logger logger = Logger.getLogger(Fetcher.class);
-	protected final int MAX_CONSECUTIVE_ATTEMPTS_ON_NULL = 5;
+	protected final int MAX_CONSECUTIVE_ATTEMPTS_ON_NULL = 2;
 	protected FetchingBuffer<T> buffer;
 	protected CloseableIterator<T> source;
 	protected boolean complete = false;
@@ -75,6 +75,7 @@ public class Fetcher<T extends FetchingElement> implements Runnable, Closeable {
 					if(next!=null){
 						logger.info("item "+count++ +" fetch new row: "+next.getId());
 						buffer.add(next);
+						countNullItems = 0;
 					}
 					else{
 						countNullItems++;
@@ -120,6 +121,7 @@ public class Fetcher<T extends FetchingElement> implements Runnable, Closeable {
 	 */
 	public void close() throws IOException
 	{
+		logger.info("Fetcher closing iterator!!");
 		complete = true;
 		source.close();
 	}

src/main/java/org/gcube/portlets/user/speciesdiscovery/server/stream/AggregatorIterator.java

@@ -7,6 +7,8 @@ import java.io.IOException;
 import java.util.HashMap;
 import java.util.Map;
 
+import org.apache.log4j.Logger;
+
 /**
  * @author "Federico De Faveri defaveri@isti.cnr.it"
  *
@@ -15,6 +17,7 @@ public class AggregatorIterator<I> implements CloseableIterator<I> {
 	
 	protected CloseableIterator<I> source;
 	protected Map<String, Aggregator<I, ?>> aggregators;
+	protected Logger logger = Logger.getLogger(AggregatorIterator.class);
 	
 	/**
 	 * @param source
@@ -42,6 +45,12 @@ public class AggregatorIterator<I> implements CloseableIterator<I> {
 	@Override
 	public I next() {
 		I input = source.next();
+		//Another check
+		if(input==null){
+			logger.warn("Skipping conversion source.next() is Null!!");
+			return null;
+		}
+		
 		for (Aggregator<I, ?> aggregator:aggregators.values()) aggregator.aggregate(input);
 		return input;
 	}

src/main/java/org/gcube/portlets/user/speciesdiscovery/server/stream/ConversionIterator.java

@@ -41,6 +41,13 @@ public class ConversionIterator<I,O> implements CloseableIterator<O> {
 		assert hasNext();
 		try {
 			I input = source.next();
+			
+			////Another check
+			if(input==null){
+				logger.warn("Skipping conversion source.next() is Null!!");
+				return null;
+			}
+			
 			O output = converter.convert(input);
 			return output;
 		} catch (Exception e) {

src/main/java/org/gcube/portlets/user/speciesdiscovery/server/stream/aggregation/TaxonomyClassificationAggregator.java

@@ -48,19 +48,17 @@ public class TaxonomyClassificationAggregator<T extends TaxonomyProvider> implem
 
 	@Override
 	public void aggregate(TaxonomyProvider row) {
-
 //		System.out.println("TaxonomyProvider " + row);
-
 		List<? extends TaxonomyInterface> matchingTaxon = row.getParents();
 
 		if(matchingTaxon == null || matchingTaxon.size()==0) return;
 
 		EnumMap<MainTaxonomicRankEnum, TaxonomyInterface> groupedTaxon = groupTaxonByRank(matchingTaxon);
+//		System.out.println("GroupedTaxon Key Set: " + groupedTaxon.keySet());
 
 		for (MainTaxonomicRankEnum aggregationRank: MainTaxonomicRankEnum.values()){
 
 			TaxonomyInterface taxon = groupedTaxon.get(aggregationRank);
-
 			String taxonId;
 			
 			//IF RANK CLASS EXISTS INSERT INTO HASHMAP GROUP BY RANK
@@ -71,9 +69,10 @@ public class TaxonomyClassificationAggregator<T extends TaxonomyProvider> implem
 
 				String unknownRank = matchingTaxon.get(0).getRank()!=null?matchingTaxon.get(0).getRank():TAXONOMYUNKNOWN; // GET THE FIRST RANK CLASS
 
+				taxon = row.getParents().get(0);
 				//IF BASETAXONOMY CLASS IS NOT UNKNOWN -  INSERT INTO HASHMAP GROUP BY FIRST RANK
-				if(!row.getBaseTaxonValue().equalsIgnoreCase(TAXONOMYUNKNOWN)) {
+				if(!row.getBaseTaxonValue().equalsIgnoreCase(TAXONOMYUNKNOWN) && (taxon!=null)) {
-					taxonId = addTaxonToAggregation(aggregationRank, row.getParents().get(0), row.getBaseTaxonValue(), row.getBaseTaxonValue(), unknownRank);
+					taxonId = addTaxonToAggregation(aggregationRank, taxon, row.getBaseTaxonValue(), row.getBaseTaxonValue(), unknownRank);
 					setClassification(row, aggregationRank, taxonId);
 				} else {
 					//BASETAXONOMY UNKNOWN - INSERT INTO HASHMAP GROUP BY haskKey UNKNOWN RANK
@@ -119,7 +118,7 @@ public class TaxonomyClassificationAggregator<T extends TaxonomyProvider> implem
 
 	protected String addTaxonToAggregation(MainTaxonomicRankEnum aggregationRank, TaxonomyInterface taxon, String baseTaxonId, String baseTaxonValue, String classificationRank)
 	{
-		String taxonName = taxon.getName().toLowerCase();
+		String taxonName =taxon.getName()!=null?taxon.getName().toLowerCase():"No name";
 		return addTaxonToAggregation(aggregationRank, taxonName, taxonName, baseTaxonId, baseTaxonValue, classificationRank);
 	}