fixed bug on ranking, after use case: check all/ unceck all

git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/portlets/user/speciesdiscovery@77520 82a268e6-3cf1-43bd-a215-b396298e98cf

pom.xml

@@ -19,7 +19,7 @@
 	<groupId>org.gcube.portlets.user</groupId>
 	<artifactId>species-discovery</artifactId>
 	<packaging>war</packaging>
-	<version>3.2.0-SNAPSHOT</version>
+	<version>3.3.0-SNAPSHOT</version>
 	<name>gCube Species Discovery</name>
 	<description>
 		gCube Species Discovery Portlet lets the users discovery species information from the Species Service.
@@ -52,12 +52,12 @@
 			<scope>provided</scope>
 		</dependency>
 
-<!-- 		<dependency> -->
+		<!-- <dependency> -->
-<!-- 			<groupId>org.gcube.core</groupId> -->
+		<!-- <groupId>org.gcube.core</groupId> -->
-<!-- 			<artifactId>common-fw-clients</artifactId> -->
+		<!-- <artifactId>common-fw-clients</artifactId> -->
-<!-- 			<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version> -->
+		<!-- <version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version> -->
-<!-- 			<scope>runtime</scope> -->
+		<!-- <scope>runtime</scope> -->
-<!-- 		</dependency> -->
+		<!-- </dependency> -->
 
 		<dependency>
 			<groupId>org.gcube.data.spd</groupId>
@@ -77,8 +77,8 @@
 			<groupId>org.gcube.data.spd</groupId>
 			<artifactId>spd-model</artifactId>
 			<version>1.0.0-SNAPSHOT</version>
-<!-- 			<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version> -->
+			<!-- <version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version> -->
-<!-- 			<scope>provided</scope> -->
+			<!-- <scope>provided</scope> -->
 		</dependency>
 
 		<dependency>
@@ -105,7 +105,7 @@
 		<dependency>
 			<groupId>org.gcube.contentmanagement</groupId>
 			<artifactId>storage-manager-wrapper</artifactId>
-<!-- 			<version>[1.0.1-SNAPSHOT, 1.1.0-SNAPSHOT)</version> -->
+			<!-- <version>[1.0.1-SNAPSHOT, 1.1.0-SNAPSHOT)</version> -->
 			<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
 			<scope>provided</scope>
 		</dependency>
@@ -113,11 +113,11 @@
 		<dependency>
 			<groupId>org.gcube.contentmanagement</groupId>
 			<artifactId>storage-manager-core</artifactId>
-<!-- 			<version>[1.0.1-SNAPSHOT, 1.11.0-SNAPSHOT)</version> -->
+			<!-- <version>[1.0.1-SNAPSHOT, 1.11.0-SNAPSHOT)</version> -->
 			<version>[2.0.0-SNAPSHOT,3.0.0-SNAPSHOT)</version>
 			<scope>provided</scope>
 		</dependency>
-		
+
 		<dependency>
 			<groupId>org.gcube.contentmanagement</groupId>
 			<artifactId>storage-resource-link-plugin</artifactId>
@@ -228,7 +228,7 @@
 			<version>[1.0.0-SNAPSHOT, 2.0.0-SNAPSHOT)</version>
 			<scope>provided</scope>
 		</dependency>
-		
+
 		<dependency>
 			<groupId>org.gcube.portlets.user</groupId>
 			<artifactId>home-library</artifactId>
@@ -259,6 +259,15 @@
 			<version>2.0</version>
 			<scope>provided</scope>
 		</dependency>
+
+
+		<!-- LOGGER -->
+
+		<dependency>
+			<groupId>log4j</groupId>
+			<artifactId>log4j</artifactId>
+			<version>1.2.16</version>
+		</dependency>
 		<dependency>
 			<groupId>org.slf4j</groupId>
 			<artifactId>slf4j-log4j12</artifactId>
@@ -271,6 +280,7 @@
 			<version>1.6.4</version>
 			<scope>runtime</scope>
 		</dependency>
+		
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>

src/main/java/org/gcube/portlets/user/speciesdiscovery/server/TaxonomySearchServiceImpl.java

@@ -355,7 +355,7 @@ public class TaxonomySearchServiceImpl extends RemoteServiceServlet implements T
 					resultRow.setProperties(null);
 				}
 
-//				System.out.println("resultRow "+resultRow);
+				System.out.println("################### ResultRow parents: "+resultRow.getParents());
 
 				chunk.add(resultRow);
 

src/main/java/org/gcube/portlets/user/speciesdiscovery/server/asl/SessionUtil.java

@@ -105,8 +105,8 @@ public class SessionUtil {
 //			user = "pasquale.pagano";
 //			user = "lucio.lelii";
 			
-//			String scope = "/gcube/devsec"; //Development
+			String scope = "/gcube/devsec"; //Development
-			String scope = "/d4science.research-infrastructures.eu/gCubeApps/BiodiversityResearchEnvironment"; //Production
+//			String scope = "/d4science.research-infrastructures.eu/gCubeApps/BiodiversityResearchEnvironment"; //Production
 			
 			httpSession.setAttribute(USERNAME_ATTRIBUTE, user);
 			ASLSession session = SessionManager.getInstance().getASLSession(sessionID, user);

src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/ResultItemConverter.java

@@ -152,6 +152,10 @@ public class ResultItemConverter implements Converter<ResultItem, ResultRow> {
 			}
 		}
 
+		
+		//DEBUG
+//		System.out.println("Insert row id: "+row.getId());
+		
 		row.setMatchingTaxon(convertTaxon(input));
 		
 		row.setBaseTaxonValue(NormalizeString.lowerCaseUpFirstChar(getBaseTaxonValue(TaxonomySearchServiceImpl.BASETAXONOMY,input)));
@@ -186,6 +190,8 @@ public class ResultItemConverter implements Converter<ResultItem, ResultRow> {
 			Taxon tax = new Taxon(count++, taxon.getScientificName(), taxon.getCitation(), NormalizeString.lowerCaseUpFirstChar(taxon.getRank()));
 			listTaxon.add(tax);
 			taxon = taxon.getParent();
+			
+//			System.out.println("Insert tax parent id: "+tax.getId());
 		}
 		return listTaxon;	
 	}

src/main/java/org/gcube/portlets/user/speciesdiscovery/server/service/TaxonomyItemConverter.java

@@ -39,6 +39,9 @@ public class TaxonomyItemConverter implements Converter<TaxonomyItem, TaxonomyRo
 		TaxonomyRow taxonomy = createTaxonomyRow(input);
 		
 		//SET PARENTS
+		
+//		System.out.println("Convert Taxonomy parent for: "+taxonomy.getId());
+		
 		taxonomy.setParent(convertParentsTaxonomy(input));
 		
 		//SET BASE TAXON
@@ -180,9 +183,15 @@ public class TaxonomyItemConverter implements Converter<TaxonomyItem, TaxonomyRo
 		List<TaxonomyRow> listTaxonomy = new ArrayList<TaxonomyRow>();
 		TaxonomyItem parent = taxon.getParent();
 		
+		int i=0;
+		
 		while(parent!=null){
 			TaxonomyRow row = createTaxonomyRow(parent);
 			row.setParent(true);
+			row.setParentIndex(i++);
+			
+//			System.out.println("Insert Taxonomy parent id: "+row.getId() + ", row.getParentIndex: "+row.getParentIndex());
+			
 			listTaxonomy.add(row);
 			parent = parent.getParent();
 		}

src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/ResultRow.java

@@ -5,6 +5,7 @@ package org.gcube.portlets.user.speciesdiscovery.shared;
 
 import java.io.Serializable;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 
 import javax.persistence.CascadeType;
@@ -62,6 +63,7 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
 	public final static String PROPERTIES = "properties"; //USED
 	public static final String EXISTS_PROPERTIES = "existsProperties"; //USED
 
+
 	@Id
 	@GeneratedValue(strategy = GenerationType.IDENTITY)
 	protected int id;
@@ -528,6 +530,11 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
 
 
 	public List<Taxon> getParents() {
+	
+		Collections.sort(matchingTaxon);
+//		for (Taxon t : matchingTaxon) {
+//			System.out.println("+++ Parent :" +t.getId() + ", name: "+t.getName() +", rank: "+t.getRank());
+//		}
 		return matchingTaxon;
 	}
 
@@ -560,8 +567,7 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
 	public void setProperties(List<ItemParameter> properties) {
 		this.properties = properties;
 	}
-
+	
-
 	@Override
 	public String toString() {
 		StringBuilder builder = new StringBuilder();
@@ -638,5 +644,7 @@ public class ResultRow implements FetchingElement, SelectableElement, Serializab
 		builder.append("]");
 		return builder.toString();
 	}
-	
+
+
+
 }

src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/Taxon.java

@@ -13,7 +13,7 @@ import javax.persistence.Id;
  *
  */
 @Entity
-public class Taxon implements Serializable, FetchingElement, TaxonomyInterface {
+public class Taxon implements Serializable, FetchingElement, TaxonomyInterface, Comparable<Taxon>{
 
 	private static final long serialVersionUID = -3579358036639552802L;
 
@@ -25,6 +25,8 @@ public class Taxon implements Serializable, FetchingElement, TaxonomyInterface {
 
 	@Id
 	@GeneratedValue(strategy = GenerationType.IDENTITY)
+	protected int internalId;
+	
 	protected int id;
 	
 	protected String name;
@@ -106,10 +108,23 @@ public class Taxon implements Serializable, FetchingElement, TaxonomyInterface {
 		this.id = id;
 	}
 
+
+	/* 
+	 * 
+	 * Comparable on insertion order
+	 * @see java.lang.Comparable#compareTo(java.lang.Object)
+	 */
+	@Override
+	public int compareTo(Taxon o) {
+		return id-o.getId();
+	}
+
 	@Override
 	public String toString() {
 		StringBuilder builder = new StringBuilder();
-		builder.append("Taxon [id=");
+		builder.append("Taxon [internalId=");
+		builder.append(internalId);
+		builder.append(", id=");
 		builder.append(id);
 		builder.append(", name=");
 		builder.append(name);
@@ -120,6 +135,4 @@ public class Taxon implements Serializable, FetchingElement, TaxonomyInterface {
 		builder.append("]");
 		return builder.toString();
 	}
-	
-	
 }

src/main/java/org/gcube/portlets/user/speciesdiscovery/shared/TaxonomyRow.java

@@ -5,6 +5,7 @@ package org.gcube.portlets.user.speciesdiscovery.shared;
 
 import java.io.Serializable;
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 
 import javax.persistence.CascadeType;
@@ -22,7 +23,7 @@ import javax.persistence.OneToMany;
  */
 @Entity
 //@Customizer(org.gcube.portlets.user.speciesdiscovery.server.persistence.dao.TaxonomyCustomizer.class)
-public class TaxonomyRow implements FetchingElement, Serializable, TaxonomyInterface, TaxonomyProvider, SelectableElement {
+public class TaxonomyRow implements FetchingElement, Serializable, TaxonomyInterface, TaxonomyProvider, SelectableElement, Comparable<TaxonomyRow> {
 
 	private static final long serialVersionUID = 1028839024130840026L;
 
@@ -101,7 +102,9 @@ public class TaxonomyRow implements FetchingElement, Serializable, TaxonomyInter
 	@OneToMany(cascade=CascadeType.PERSIST, fetch=FetchType.EAGER)
 	protected List<TaxonomyRow> parents;
 	
+	//USED FOR PARENT
 	protected String parentID;
+	protected int parentIndex = -1;
 
 	protected TaxonomyRow() {
 		
@@ -246,6 +249,7 @@ public class TaxonomyRow implements FetchingElement, Serializable, TaxonomyInter
 
 	@Override
 	public List<TaxonomyRow> getParents() {
+		Collections.sort(parents);
 		return parents;
 	}
 
@@ -422,6 +426,14 @@ public class TaxonomyRow implements FetchingElement, Serializable, TaxonomyInter
 		this.isParent = isParent;
 	}
 
+	public int getParentIndex() {
+		return parentIndex;
+	}
+
+	public void setParentIndex(int parentIndex) {
+		this.parentIndex = parentIndex;
+	}
+
 	@Override
 	public String toString() {
 		StringBuilder builder = new StringBuilder();
@@ -487,8 +499,18 @@ public class TaxonomyRow implements FetchingElement, Serializable, TaxonomyInter
 		builder.append(parents);
 		builder.append(", parentID=");
 		builder.append(parentID);
+		builder.append(", parentIndex=");
+		builder.append(parentIndex);
 		builder.append("]");
 		return builder.toString();
 	}
 
+	/* (non-Javadoc)
+	 * Comparable on insertion order
+	 * @see java.lang.Comparable#compareTo(java.lang.Object)
+	 */
+	@Override
+	public int compareTo(TaxonomyRow o) {
+		return parentIndex - o.getParentIndex();
+	}
 }

src/test/java/org/gcube/portlets/user/speciesdiscovery/client/ServiceQuery.java

@@ -28,14 +28,30 @@ public class ServiceQuery {
 	 */
 	public static void main(String[] args) throws InvalidQueryException, UnsupportedPluginException {
 		String scope = "/gcube/devsec";
+//		String scope = "/d4science.research-infrastructures.eu/gCubeApps/BiodiversityResearchEnvironment"; //Production
 		ScopeProvider.instance.set(scope);
-		Manager call = manager().at(URI.create("http://node24.d.d4science.research-infrastructures.eu:9000")).withTimeout(3, TimeUnit.MINUTES).build();
+		
+		
+		Manager call  = manager().withTimeout(3, TimeUnit.MINUTES).build();
+		
+//		Manager call = manager().at(URI.create("http://node24.d.d4science.research-infrastructures.eu:9000")).withTimeout(3, TimeUnit.MINUTES).build();
 
 		//Stream<ResultElement> results = call.search("SEARCH BY CN 'shark' RESOLVE WITH OBIS EXPAND WITH ITIS RETURN Product");
-		Stream<ResultElement> results = call.search("SEARCH BY CN 'shark' RESOLVE WITH OBIS EXPAND WITH ITIS WHERE coordinate <= 15.12, 16.12 RETURN Product");
+//		Stream<ResultElement> results = call.search("SEARCH BY CN 'shark' RESOLVE WITH OBIS EXPAND WITH ITIS WHERE coordinate <= 15.12, 16.12 RETURN Product");
 		
-		if (results.hasNext()) results.next();
 		
+//		Stream<ResultElement> results = call.search("SEARCH BY SN 'sarda sarda' RESOLVE WITH OBIS EXPAND WITH ITIS WHERE coordinate <= 15.12, 16.12 RETURN Product");
+		
+		System.out.println("start query...");
+		
+		Stream<ResultElement> results = call.search("SEARCH BY SN 'sarda sarda' RETURN Product");
+		
+		int i=0;
+		if (results.hasNext()) {
+			ResultElement elem = results.next();
+			System.out.println(++i +") el: "+elem.getId());
+		
+		}
 		
 		results.close();
 		System.out.println("DONE");