From b5d72ddd8223afa9b7a103015bf3621993270ab6 Mon Sep 17 00:00:00 2001
From: Fabio Sinibaldi <fabio.sinibaldi@isti.cnr.it>
Date: Thu, 2 Sep 2021 18:05:59 +0200
Subject: [PATCH] Refactored Serialization means

---
 pom.xml                                       | 17 +---
 .../geoportal/service/GeoPortalService.java   | 13 ++-
 .../engine/mongo/ConcessioniMongoManager.java |  8 +-
 .../service/rest/ConcessioniOverMongo.java    | 95 ++++++++-----------
 .../service/utils/Serialization.java          | 57 +----------
 .../service/ConcessioniOverMongoTest.java     | 30 +++---
 6 files changed, 75 insertions(+), 145 deletions(-)

diff --git a/pom.xml b/pom.xml
index 6e613f7..501f175 100644
--- a/pom.xml
+++ b/pom.xml
@@ -79,17 +79,15 @@
 			</exclusions>
 		</dependency>
 
+
+
 		<!-- INTERNAL LOGIC -->
 		<dependency>
 			<groupId>org.gcube.application</groupId>
 			<artifactId>geoportal-common</artifactId>
 			<version>[1.0.0,2.0.0)</version>
 		</dependency>
-<!--		<dependency>-->
-<!--			<groupId>org.gcube.application</groupId>-->
-<!--			<artifactId>geoportal-logic</artifactId>-->
-<!--			<version>[1.0.14,2.0.0)</version>-->
-<!--		</dependency>-->
+
 
 		<!-- SDI -->
 		<dependency>
@@ -137,18 +135,9 @@
 
 
 
-		<!-- Used to write centroids -->
-		<!-- <dependency> <groupId>net.postgis</groupId> <artifactId>postgis-jdbc</artifactId> 
-			<version>2.5.0</version> </dependency> -->
 
 
 
-		<!-- jackson java time -->
-		<!-- Serialization from library -->
-		<!-- <dependency> <groupId>com.fasterxml.jackson.datatype</groupId> <artifactId>jackson-datatype-jsr310</artifactId> 
-			<version>2.8.8</version> </dependency> -->
-
-
 		<!-- GPKG -->
 		<!-- Read Geopackage -->
 		<!-- <dependency> <groupId>mil.nga.geopackage</groupId> <artifactId>geopackage</artifactId> 
diff --git a/src/main/java/org/gcube/application/geoportal/service/GeoPortalService.java b/src/main/java/org/gcube/application/geoportal/service/GeoPortalService.java
index 3ea7ea9..7fb5902 100644
--- a/src/main/java/org/gcube/application/geoportal/service/GeoPortalService.java
+++ b/src/main/java/org/gcube/application/geoportal/service/GeoPortalService.java
@@ -1,10 +1,12 @@
 package org.gcube.application.geoportal.service;
 
+import com.fasterxml.jackson.jaxrs.json.JacksonJaxbJsonProvider;
 import org.gcube.application.geoportal.common.rest.InterfaceConstants;
 import org.gcube.application.geoportal.service.rest.ConcessioniOverMongo;
 import org.gcube.application.geoportal.service.rest.Profiles;
 import org.gcube.application.geoportal.service.rest.Projects;
 import org.gcube.application.geoportal.service.rest.Sections;
+import org.gcube.application.geoportal.service.utils.Serialization;
 import org.glassfish.jersey.server.ResourceConfig;
 
 import javax.ws.rs.ApplicationPath;
@@ -22,8 +24,15 @@ public class GeoPortalService extends ResourceConfig{
 		registerClasses(Projects.class);
 		registerClasses(Sections.class);
 		registerClasses(Profiles.class);
-		
-		
+
+
+
+
+
+		JacksonJaxbJsonProvider provider = new JacksonJaxbJsonProvider();
+		provider.setMapper(Serialization.mapper);
+		register(provider);
+
 	}
 	
 	
diff --git a/src/main/java/org/gcube/application/geoportal/service/engine/mongo/ConcessioniMongoManager.java b/src/main/java/org/gcube/application/geoportal/service/engine/mongo/ConcessioniMongoManager.java
index 010aa7b..2348d4e 100644
--- a/src/main/java/org/gcube/application/geoportal/service/engine/mongo/ConcessioniMongoManager.java
+++ b/src/main/java/org/gcube/application/geoportal/service/engine/mongo/ConcessioniMongoManager.java
@@ -98,21 +98,21 @@ public class ConcessioniMongoManager extends MongoManager{
 
 
 
-	public List<Concessione> list(){
-		ArrayList<Concessione> toReturn=new ArrayList<>();
+	public Iterable<Concessione> list(){
+		LinkedBlockingQueue queue=new LinkedBlockingQueue<Concessione>();
 		iterate(null, collectionName).forEach(
 				new Consumer<Document>() {
 					@Override
 					public void accept(Document d) {
 						try {
-							toReturn.add(asConcessione(d));
+							queue.put(asConcessione(d));
 						}catch(Throwable t) {
 							log.error("Unable to read Document as concessione ",t);
 							log.debug("Document was "+d.toJson());
 						}
 					}
 				});
-		return toReturn;
+		return queue;
 	}
 
 	public Iterable<Concessione> search(String filter){
diff --git a/src/main/java/org/gcube/application/geoportal/service/rest/ConcessioniOverMongo.java b/src/main/java/org/gcube/application/geoportal/service/rest/ConcessioniOverMongo.java
index 9056bd6..910dd77 100644
--- a/src/main/java/org/gcube/application/geoportal/service/rest/ConcessioniOverMongo.java
+++ b/src/main/java/org/gcube/application/geoportal/service/rest/ConcessioniOverMongo.java
@@ -9,9 +9,7 @@ import org.gcube.application.geoportal.common.rest.InterfaceConstants;
 import org.gcube.application.geoportal.service.engine.mongo.ConcessioniMongoManager;
 import org.gcube.application.geoportal.service.engine.postgis.PostgisIndex;
 import org.gcube.application.geoportal.service.model.internal.faults.DeletionException;
-import org.gcube.application.geoportal.service.utils.Serialization;
 import org.json.JSONArray;
-import org.json.JSONObject;
 
 import javax.ws.rs.*;
 import javax.ws.rs.core.MediaType;
@@ -25,15 +23,15 @@ public class ConcessioniOverMongo {
 	@GET
 	@Path(InterfaceConstants.Methods.CONFIGURATION_PATH)
 	@Produces(MediaType.APPLICATION_JSON)
-	public String getConfiguration(){
-		return new GuardedMethod<String>(){
+	public Configuration getConfiguration(){
+		return new GuardedMethod<Configuration>(){
 
 			@Override
-			protected String run() throws Exception, WebApplicationException {
+			protected Configuration run() throws Exception, WebApplicationException {
 				Configuration toReturn = new Configuration();
 				toReturn.setIndex(new PostgisIndex().getInfo());
 				log.info("Returning configuration {} ",toReturn);
-				return Serialization.write(toReturn);
+				return toReturn;
 			}
 		}.execute().getResult();
 	}
@@ -41,15 +39,16 @@ public class ConcessioniOverMongo {
 	@PUT
 	@Consumes(MediaType.APPLICATION_JSON)
 	@Produces(MediaType.APPLICATION_JSON)
-	public String replace(String jsonString) {
-		return new GuardedMethod<String> () {
+	public Concessione replace(Concessione c) {
+		return new GuardedMethod<Concessione> () {
 			@Override
-			protected String run() throws Exception, WebApplicationException {
-				Concessione c=Serialization.read(jsonString, Concessione.class);
+			protected Concessione run() throws Exception, WebApplicationException {
+				//Concessione c=Serialization.read(jsonString, Concessione.class);
 				ConcessioniMongoManager manager=new ConcessioniMongoManager();
 				manager.replace(c);
 				
-				return Serialization.write(manager.getById(c.getMongo_id()));
+//				return Serialization.write(manager.getById(c.getMongo_id()));
+				return manager.getById(c.getMongo_id());
 			}
 		}.execute().getResult();
 	}
@@ -57,13 +56,13 @@ public class ConcessioniOverMongo {
 	@POST
 	@Consumes(MediaType.APPLICATION_JSON)
 	@Produces(MediaType.APPLICATION_JSON)
-	public String createNew(String jsonString) {
-		return new GuardedMethod<String> () {
+	public Concessione createNew(Concessione c) {
+		return new GuardedMethod<Concessione>() {
 			@Override
-			protected String run() throws Exception, WebApplicationException {
-				Concessione c=Serialization.read(jsonString, Concessione.class);
+			protected Concessione run() throws Exception, WebApplicationException {
+
 				ConcessioniMongoManager manager=new ConcessioniMongoManager();
-				return Serialization.write(manager.registerNew(c));				
+				return manager.registerNew(c);
 			}
 		}.execute().getResult();
 	}
@@ -72,19 +71,12 @@ public class ConcessioniOverMongo {
 	
 	@GET
 	@Produces(MediaType.APPLICATION_JSON)
-	public String list() {
-		return new GuardedMethod<String> () {
-			protected String run() throws Exception ,WebApplicationException {
+	public Iterable<Concessione> list() {
+		return new GuardedMethod<Iterable<Concessione>>() {
+			protected Iterable<Concessione> run() throws Exception ,WebApplicationException {
 				ConcessioniMongoManager manager=new ConcessioniMongoManager();
 				JSONArray toReturn=new JSONArray();
-				manager.list().forEach((Concessione c) -> {
-					try{
-					toReturn.put(new JSONObject(Serialization.write(c)));
-					}catch(Throwable t) {
-						log.error("Unable to serialize "+c);
-					}
-				});
-			return toReturn.toString();
+				return manager.list();
 			
 		};
 	}.execute().getResult();
@@ -97,12 +89,12 @@ public class ConcessioniOverMongo {
 	@GET
 	@Produces(MediaType.APPLICATION_JSON)
 	@Path("{"+InterfaceConstants.Parameters.PROJECT_ID+"}")
-	public String getById(@PathParam(InterfaceConstants.Parameters.PROJECT_ID) String id) {
-		return new GuardedMethod<String> () {
+	public Concessione getById(@PathParam(InterfaceConstants.Parameters.PROJECT_ID) String id) {
+		return new GuardedMethod<Concessione>() {
 			@Override
-			protected String run() throws Exception, WebApplicationException {
+			protected Concessione run() throws Exception, WebApplicationException {
 				ConcessioniMongoManager manager=new ConcessioniMongoManager();				
-				return Serialization.write(manager.getById(id));
+				return manager.getById(id);
 			}
 		}.execute().getResult();
 	}
@@ -132,18 +124,13 @@ public class ConcessioniOverMongo {
 	@Consumes(MediaType.APPLICATION_JSON)
 	@Produces(MediaType.APPLICATION_JSON)
 	@Path("{"+InterfaceConstants.Parameters.PROJECT_ID+"}")
-	public String update(@PathParam(InterfaceConstants.Parameters.PROJECT_ID) String id,String jsonString) {
-		return new GuardedMethod<String> () {
+	public Concessione update(@PathParam(InterfaceConstants.Parameters.PROJECT_ID) String id,Concessione c) {
+		return new GuardedMethod<Concessione>() {
 			@Override
-			protected String run() throws Exception, WebApplicationException {
+			protected Concessione run() throws Exception, WebApplicationException {
 				ConcessioniMongoManager manager=new ConcessioniMongoManager();
-
-				Concessione c=Serialization.read(jsonString, Concessione.class);
 				c.setMongo_id(id);
-
-				Concessione registered = manager.replace(c);
-				return Serialization.write(registered);
-
+				return manager.replace(c);
 			}
 		}.execute().getResult();
 	}
@@ -152,25 +139,25 @@ public class ConcessioniOverMongo {
 	@PUT
 	@Produces(MediaType.APPLICATION_JSON)
 	@Path("/{"+InterfaceConstants.Methods.PUBLISH_PATH+"}/{"+InterfaceConstants.Parameters.PROJECT_ID+"}")
-	public String publish(@PathParam(InterfaceConstants.Parameters.PROJECT_ID) String id) {
-		return new GuardedMethod<String> () {
+	public Concessione publish(@PathParam(InterfaceConstants.Parameters.PROJECT_ID) String id) {
+		return new GuardedMethod<Concessione>() {
 			@Override
-			protected String run() throws Exception, WebApplicationException {
+			protected Concessione run() throws Exception, WebApplicationException {
 				ConcessioniMongoManager manager=new ConcessioniMongoManager();				
-				return Serialization.write(manager.publish(id));				
+				return manager.publish(id);
 			}
 		}.execute().getResult();
 	}
 
 	@DELETE
 	@Path("/{"+InterfaceConstants.Methods.PUBLISH_PATH+"}/{"+InterfaceConstants.Parameters.PROJECT_ID+"}")
-	public String unpublish(@PathParam(InterfaceConstants.Parameters.PROJECT_ID) String id) {
+	public Concessione unpublish(@PathParam(InterfaceConstants.Parameters.PROJECT_ID) String id) {
 		log.info("Unpublishing {} ",id);
-		return new GuardedMethod<String> () {
+		return new GuardedMethod<Concessione>() {
 			@Override
-			protected String run() throws Exception, WebApplicationException {
+			protected Concessione run() throws Exception, WebApplicationException {
 				ConcessioniMongoManager manager=new ConcessioniMongoManager();
-				return Serialization.write(manager.unpublish(id));
+				return manager.unpublish(id);
 			}
 		}.execute().getResult();
 
@@ -182,19 +169,15 @@ public class ConcessioniOverMongo {
 	@Consumes(MediaType.APPLICATION_JSON)
 	@Produces(MediaType.APPLICATION_JSON)
 	@Path("/"+InterfaceConstants.Methods.REGISTER_FILES_PATH+"/{"+InterfaceConstants.Parameters.PROJECT_ID+"}")
-	public String registerFile(@PathParam(InterfaceConstants.Parameters.PROJECT_ID) String id,String jsonRequest) {
-		return new GuardedMethod<String> () {
+	public Concessione registerFile(@PathParam(InterfaceConstants.Parameters.PROJECT_ID) String id, AddSectionToConcessioneRequest request) {
+		return new GuardedMethod<Concessione>() {
 			@Override
-			protected String run() throws Exception, WebApplicationException {
-				AddSectionToConcessioneRequest request=Serialization.read(jsonRequest,AddSectionToConcessioneRequest.class);
+			protected Concessione run() throws Exception, WebApplicationException {
 				log.info("Registering {} file(s) for {} Concessione ID {}",
 						request.getStreams().size(),
 						request.getDestinationPath(),id);
 				ConcessioniMongoManager manager=new ConcessioniMongoManager();
-				Concessione toReturn= manager.persistContent(id, request.getDestinationPath(), request.getStreams());
-				
-				log.debug("Returning "+toReturn);
-				return Serialization.write(toReturn);				
+				return manager.persistContent(id, request.getDestinationPath(), request.getStreams());
 			}
 		}.execute().getResult();
 	}
diff --git a/src/main/java/org/gcube/application/geoportal/service/utils/Serialization.java b/src/main/java/org/gcube/application/geoportal/service/utils/Serialization.java
index 6a634dc..f44b1d0 100644
--- a/src/main/java/org/gcube/application/geoportal/service/utils/Serialization.java
+++ b/src/main/java/org/gcube/application/geoportal/service/utils/Serialization.java
@@ -3,6 +3,7 @@ package org.gcube.application.geoportal.service.utils;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.SerializationFeature;
 import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
 
 import java.io.IOException;
@@ -19,7 +20,9 @@ public class Serialization {
 		static {
 			mapper=new ObjectMapper();
 			mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES,false);
-			mapper.registerModule(new JavaTimeModule());			
+			mapper.configure(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS, false);
+			mapper.registerModule(new JavaTimeModule());
+
 		}
 		
 		public static <T> T read(String jsonString,Class<T> clazz) throws JsonProcessingException, IOException {
@@ -32,61 +35,11 @@ public class Serialization {
 
 
 		public static String write(Object toWrite) throws JsonProcessingException {
-//			if(toWrite instanceof Concessione)
-//				detach((Concessione) toWrite);
-
-
-
 			String toReturn= mapper.writeValueAsString(toWrite);
-
-//			if(toWrite instanceof Concessione)
-//				reattach((Concessione) toWrite);
 			return toReturn;
 		}
 
 
 
-		// Avoid infiniteLoop in JPA
-//		private static void detach(Concessione c) {
-//			if (c!=null) {
-//				detach(c.getRelazioneScavo());
-//				detach(c.getPosizionamentoScavo());
-//				if(c.getPianteFineScavo()!=null)
-//					c.getPianteFineScavo().forEach((LayerConcessione l)->{detach(l);});
-//				if(c.getImmaginiRappresentative()!=null)
-//					c.getImmaginiRappresentative().forEach(((UploadedImage u)->{detach(u);}));
-//				if(c.getGenericContent()!=null)
-//					c.getGenericContent().forEach(((OtherContent u)->{detach(u);}));
-//			}
-//		}
-//
-//		private static void detach(AssociatedContent a) {
-//			if(a!=null) {
-//				a.setRecord(null);
-//				if(a.getActualContent()!=null)
-//					a.getActualContent().forEach((PersistedContent p)->{p.setAssociated(null);});
-//			}
-//		}
-//
-//
-//		private static void reattach(Concessione c) {
-//			if(c!=null) {
-//				reattach(c.getRelazioneScavo(),c);
-//				reattach(c.getPosizionamentoScavo(),c);
-//				if(c.getPianteFineScavo()!=null)
-//					c.getPianteFineScavo().forEach((LayerConcessione l)->{reattach(l,c);});
-//				if(c.getImmaginiRappresentative()!=null)
-//					c.getImmaginiRappresentative().forEach(((UploadedImage u)->{reattach(u,c);}));
-//				if(c.getGenericContent()!=null)
-//					c.getGenericContent().forEach(((OtherContent u)->{reattach(u,c);}));
-//			}
-//		}
-//
-//		private static void reattach(AssociatedContent a,Record r) {
-//			if(a!=null) {
-//				a.setRecord(r);
-//				if(a.getActualContent()!=null)
-//					a.getActualContent().forEach((PersistedContent p)->{p.setAssociated(a);});
-//			}
-//		}
+
 }
diff --git a/src/test/java/org/gcube/application/geoportal/service/ConcessioniOverMongoTest.java b/src/test/java/org/gcube/application/geoportal/service/ConcessioniOverMongoTest.java
index 2089540..921f330 100644
--- a/src/test/java/org/gcube/application/geoportal/service/ConcessioniOverMongoTest.java
+++ b/src/test/java/org/gcube/application/geoportal/service/ConcessioniOverMongoTest.java
@@ -23,6 +23,7 @@ import java.nio.charset.Charset;
 import java.util.ArrayList;
 import java.util.Iterator;
 import java.util.List;
+import java.util.NoSuchElementException;
 import java.util.concurrent.atomic.AtomicLong;
 
 import static org.junit.Assert.*;
@@ -117,27 +118,22 @@ public class ConcessioniOverMongoTest extends BasicServiceTestUnit{
 	@Test
 	public void search() throws Exception {
 		WebTarget target=target(PATH);
-//		System.out.println("All :"+query(null,target).size());
-//		System.out.println("All (filter):"+queryFile("all.json",target).size());
 		AtomicLong validatedCount= new AtomicLong(0);
-		searchFile("validated.json",target).forEachRemaining(concessione -> {validatedCount.incrementAndGet();});
+		Iterator<Concessione> it=searchFile("validated.json",target);
+		it.forEachRemaining(concessione -> {validatedCount.incrementAndGet();});
 		System.out.println("Validated : "+ validatedCount.get());
-//		System.out.println("Legacy ID : "+ queryFile("legacyid.json",target).size());
-//		System.out.println("Non fabio : "+ queryFile("nonFabio.json",target).size());
-//		System.out.println("Missing Centroid : "+ queryFile("missingCentroid.json",target).size());
 	}
 
-// TODO check
-//	@Test
-//	public void query() throws Exception {
-//		WebTarget target=target(PATH);
-//		try {
-//			System.out.println("Last Registered : " + queryFile("lastRegistered.json", target).next().getCreationTime());
-//			System.out.println("First Registered : " + queryFile("firstRegistered.json", target).next().getCreationTime());
-//		}catch(NoSuchElementException e){
-//			System.out.println("NO element found, probably empty DB");
-//		}
-//	}
+ 	@Test
+	public void query() throws Exception {
+		WebTarget target=target(PATH);
+		try {
+			System.out.println("Last Registered : " + queryFile("lastRegistered.json", target).next().getCreationTime());
+			System.out.println("First Registered : " + queryFile("firstRegistered.json", target).next().getCreationTime());
+		}catch(NoSuchElementException e){
+			System.out.println("NO element found, probably empty DB");
+		}
+	}
 
 	@Test
 	public void getConfiguration() throws Exception {