commit after pull

dmp-admin/src/app/datasets-viewer/datasets-viewer.component.html

@@ -102,11 +102,11 @@
 
 
 <!-- new profile editor -->
-
+<!--
 <div [ngClass]="{true:'visible', false:'invisible'}[viewingComponent==2]">
   <dataset-profile-gui-editor [profile]=profile (notifyClick)="goToMain()" ></dataset-profile-gui-editor>
 </div>
-
+-->
 <!-- end of new profile editor -->
 
 
@@ -118,7 +118,7 @@
 
 <!-- OLD Profile Editor -->
 
-<!--
+
 <div [ngClass]="{true:'visible', false:'invisible'}[viewingComponent==2]">
     <div class="panel panel-default margin10">
       <div class="panel-heading">
@@ -189,6 +189,6 @@
       </div>
     </div>
 </div>
--->
+
 <!-- End of OLD Profile Editor -->
 

dmp-backend/src/main/java/dao/entities/DMPDao.java

@@ -15,10 +15,6 @@ public interface DMPDao extends Dao<DMP, UUID> {
 
 	List<IDLabelPair> listAllIDsLabels();
 	
-	List<DMP> listUserDMPs(String userID);
-	
-	
-//	public boolean createFromForm();
 	
 	
 }

dmp-backend/src/main/java/dao/entities/DMPDaoImpl.java

@@ -41,29 +41,6 @@ public class DMPDaoImpl extends JpaDao<DMP, UUID> implements DMPDao {
 		.collect(Collectors.toList());
 	}
 
-	@Override
-	public List<DMP> listUserDMPs(String userID) {
-		
-//		String queryString = "select ui from UserInfo ui join UserAuth ui.authentication ua where ua.username=:username"; 
-		
-		String queryString = "select ui from UserInfo ui join Project ui.pro.authentication ua where ua.username=:username"; 
-		
-		
-//		TypedQuery<UserInfo> typedQuery = entityManager.createQuery(queryString, UserInfo.class);
-//		typedQuery.setParameter("username", username);
-		
-		return null;
-	}
 
-	
-	
-	
-	
-	
-//	@Override
-//	public boolean createFromForm(Map<String,String> keyVals) {
-//		String query = "insert into DMP () values"
-//		return false;
-//	}
 
 }

dmp-backend/src/main/java/dao/entities/DatasetDao.java

@@ -14,5 +14,6 @@ public interface DatasetDao extends Dao<Dataset, UUID> {
 
 	List<IDLabelPair> listAllIDsLabels();
 
+	List<Dataset> getDatasetsOfDmp(UUID dmpID);
 	
 }

dmp-backend/src/main/java/dao/entities/DatasetDaoImpl.java

@@ -1,6 +1,7 @@
 package dao.entities;
 
 import java.util.List;
+import java.util.Set;
 import java.util.UUID;
 import java.util.stream.Collectors;
 
@@ -38,5 +39,14 @@ public class DatasetDaoImpl extends JpaDao<Dataset, UUID> implements DatasetDao
 		.collect(Collectors.toList());
 	}
 
+	@Override
+	public List<Dataset> getDatasetsOfDmp(UUID dmpID) {
+		String queryString = "FROM Dataset dataset where dataset.dmp.id=:dmpID";
+		Query query = (Query) entityManager.createQuery(queryString);
+		query.setParameter("dmpID", dmpID);
+		List<Dataset> datasets = (List<Dataset>) query.getResultList();
+		return datasets;
+	}
+
 	
 }

dmp-backend/src/main/java/entities/DMP.java

@@ -191,7 +191,7 @@ public class DMP implements Serializable {
 	
 
 
-
+/*
 	public String toString() {
 		try {
 			return new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT).writeValueAsString(this);
@@ -200,4 +200,6 @@ public class DMP implements Serializable {
 		}
 	}
 	
+	*/
+	
 }

dmp-backend/src/main/java/entities/Dataset.java

@@ -28,14 +28,14 @@ import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.ObjectIdGenerators;
 import com.fasterxml.jackson.annotation.JsonInclude.Include;
 
-@Entity(name = "Dataset")
+@Entity
 @Table(name="\"Dataset\"")
 @JsonIdentityInfo(generator=ObjectIdGenerators.PropertyGenerator.class, property="id")
 public class Dataset implements Serializable {
 	
 	private static final long serialVersionUID = 3575723814399553259L;
 
-	//public Dataset () {}
+	public Dataset () {}
 	
 	
 	@Id
@@ -67,7 +67,9 @@ public class Dataset implements Serializable {
     @JoinColumn(name = "\"Profile\"", nullable = true)
 	private DatasetProfile profile;
 	
-	
+	@Type(type="typedefinition.XMLType")
+	@Column(name = "\"Reference\"", columnDefinition = "xml", nullable = true)
+	private String reference;
 	
 	@OneToMany(fetch = FetchType.LAZY)
     @JoinTable(name="\"DatasetDataRepository\"", 
@@ -182,5 +184,19 @@ public class Dataset implements Serializable {
 	public void setDataRepositories(Set<DataRepository> dataRepositories) {
 		this.dataRepositories = dataRepositories;
 	}
+
+
+	public String getReference() {
+		return reference;
+	}
+
+
+	public void setReference(String reference) {
+		this.reference = reference;
+	}
+	
+	
+	
+	
 	
 }

dmp-backend/src/main/java/helpers/SafeCleanAttribs.java

@@ -0,0 +1,18 @@
+package helpers;
+
+import entities.DMP;
+import entities.Dataset;
+
+public class SafeCleanAttribs {
+
+	
+	public static void clean(Dataset dataset) {
+		DMP dmp = dataset.getDmp();
+		if(dmp!=null) {
+			DMP newdmp = new DMP();
+			newdmp.setId(dmp.getId());
+			dataset.setDmp(newdmp);
+		}
+	}
+	
+}

dmp-backend/src/main/java/helpers/SerializerProvider.java

@@ -7,9 +7,11 @@ import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.StringUtils;
 
+import com.fasterxml.jackson.annotation.JsonInclude.Include;
 import com.fasterxml.jackson.core.JsonParseException;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.JavaType;
 import com.fasterxml.jackson.databind.JsonMappingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
@@ -30,11 +32,11 @@ public class SerializerProvider {
 	
 	public static void initialize() {
 		Hibernate5Module module = new Hibernate5Module();
-		module.enable(Feature.SERIALIZE_IDENTIFIER_FOR_LAZY_NOT_LOADED_OBJECTS);
+		//module.enable(Feature.SERIALIZE_IDENTIFIER_FOR_LAZY_NOT_LOADED_OBJECTS);
 		objectMapper = new ObjectMapper()
-//				.setSerializationInclusion(Include.NON_NULL)
-//				.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false)
-				.registerModule(new Hibernate5Module())
+				//.setSerializationInclusion(Include.NON_NULL)
+				//.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false)
+				.registerModule(module)
 				;
 	}
 	

dmp-backend/src/main/java/rest/entities/DMPs.java

@@ -147,6 +147,10 @@ public class DMPs  {
 	@Transactional
 	@RequestMapping(method = RequestMethod.POST, value = { "/dmp/update" }, consumes = "application/json", produces="application/json")
 	public @ResponseBody ResponseEntity<Object> updateDMP(@RequestBody DMP dmp) {
+		
+		DMP previousDmp = dMPDao.read(dmp.getId());
+		addForeignElems(previousDmp, dmp);
+		
 		try {
 			DMP updatedDMP = dMPDao.update(dmp);
 			return ResponseEntity.status(HttpStatus.CREATED).body(SerializerProvider.toJson(updatedDMP));
@@ -250,7 +254,7 @@ public class DMPs  {
 	@RequestMapping(method = RequestMethod.POST, value = { "/dmp/getdatasets" }, consumes = "application/json", produces="application/json")
 	public @ResponseBody ResponseEntity<Object> getDatasetsOfDMP(@RequestBody DMP dmp) {
 		try {
-			Set<Dataset> datasets = dMPDao.read(dmp.getId()).getDataset();
+			List<Dataset> datasets = datasetDao.getDatasetsOfDmp(dmp.getId());
 			return ResponseEntity.status(HttpStatus.OK).body(SerializerProvider.toJson(datasets));
 		} catch (Exception e) {
 			return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR).body("{\"msg\":\"Could not get datasets of DMP!\"");
@@ -306,7 +310,7 @@ public class DMPs  {
 		
 	}
 	
-	@RequestMapping(method = RequestMethod.POST, value = { "/dmp/createofuser" }, produces="text/plain")
+	@RequestMapping(method = RequestMethod.POST, value = { "/dmp/createofuser" }, produces="text/plain", consumes = "application/json")
 	public @ResponseBody ResponseEntity<Object> createDmpOfUser(@RequestBody DMP dmp){
 		
 		
@@ -382,5 +386,13 @@ public class DMPs  {
 	
 	
 	
+	private static void addForeignElems(DMP existing, DMP newone) {
+		newone.setDataset(existing.getDataset());
+		newone.setOrganisations(existing.getOrganisations());
+		newone.setResearchers(existing.getResearchers());
+		newone.setUsers(existing.getUsers());
+	}
+	
+	
 }
 

dmp-backend/src/main/java/rest/entities/DatasetProfiles.java

@@ -1,10 +1,6 @@
 package rest.entities;
 
-import java.io.IOException;
-import java.io.PrintStream;
-import java.util.HashSet;
 import java.util.List;
-import java.util.Set;
 import java.util.UUID;
 import java.util.stream.Collectors;
 

dmp-backend/src/main/java/rest/entities/Datasets.java

@@ -50,6 +50,7 @@ import entities.DatasetProfileRuleset;
 import entities.DatasetProfileViewstyle;
 import entities.Organisation;
 import entities.Project;
+import helpers.SafeCleanAttribs;
 import helpers.SerializerProvider;
 import helpers.Transformers;
 import responses.RestResponse;
@@ -92,6 +93,7 @@ public class Datasets  {
 	public @ResponseBody ResponseEntity<Object> getDataset(@PathVariable("id") String id) {
 		try {
 			Dataset ds = datasetDao.read(UUID.fromString(id));
+			ds.setDmp(ds.getDmp());
 			return ResponseEntity.status(HttpStatus.OK).body(SerializerProvider.toJson(ds));
 		}
 		catch(Exception ex) {
@@ -118,7 +120,7 @@ public class Datasets  {
 	}
 	
 	
-	@RequestMapping(method = RequestMethod.POST, value = { "/dataset/create" }, consumes = "application/json")
+	@RequestMapping(method = RequestMethod.POST, value = { "/dataset/create" }, consumes = "application/json", produces="application/json")
 	public @ResponseBody ResponseEntity<Object> createDataset(@RequestBody Dataset dataset) {
 		
 		dataset.setId(null);
@@ -133,13 +135,21 @@ public class Datasets  {
 	}
 	
 	
-	@RequestMapping(method = RequestMethod.POST, value = { "/dataset/update" }, consumes = "application/json")
-	public @ResponseBody ResponseEntity<Object> updateDataset(@RequestBody Dataset dataset) {
+	@RequestMapping(method = RequestMethod.POST, value = { "/dataset/update" }, consumes = "application/json", produces="application/json")
+	public @ResponseBody ResponseEntity<Object> updateDataset(@RequestBody String datasetJson) {
+		
+		Dataset dataset;
+		try {
+			dataset = SerializerProvider.fromJson(datasetJson, Dataset.class);
+		} catch (Exception e) {
+			return ResponseEntity.status(HttpStatus.INTERNAL_SERVER_ERROR).body("Could not create or update Dataset! Reason: " + e.getMessage());
+		}
+		
+		SafeCleanAttribs.clean(dataset);
 		
 		try {
 			dataset = datasetDao.update(dataset);
-			RestResponse rr = new RestResponse("Updated dataset with id: "+dataset.toString(), dataset.getId().toString());
-			return ResponseEntity.status(HttpStatus.CREATED).body(rr.toString());
+			return ResponseEntity.status(HttpStatus.CREATED).body(SerializerProvider.toJson(dataset));
 		}
 		catch(Exception ex) {
 			ex.printStackTrace();
@@ -149,8 +159,6 @@ public class Datasets  {
 	}
 	
 	
-	
-	
 	@RequestMapping(method = RequestMethod.POST, value = { "/dataset/delete" }, consumes = "application/json")
 	public @ResponseBody ResponseEntity<Object> deleteDataset(@RequestBody Dataset dataset) {
 		
@@ -208,5 +216,8 @@ public class Datasets  {
 	
 	
 	
+
+	
+	
 }
 

dmp-backend/src/main/java/rest/entities/Projects.java

@@ -210,7 +210,7 @@ public class Projects  {
 	}
 	
 	@Transactional
-	@RequestMapping(method = RequestMethod.POST, value = { "/project/createofuser" }, produces="text/plain")
+	@RequestMapping(method = RequestMethod.POST, value = { "/project/createofuser" }, produces="text/plain", consumes = "application/json")
 	public @ResponseBody ResponseEntity<Object> createProjectOfUser(@RequestBody Project project){
 		
 

dmp-backend/src/test/java/TestRest.java

@@ -36,6 +36,7 @@ import dao.entities.RegistryDao;
 import dao.entities.ResearcherDao;
 import dao.entities.ServiceDao;
 import dao.entities.UserInfoDao;
+import entities.DMP;
 import entities.DatasetProfile;
 import entities.DatasetProfileRuleset;
 import entities.DatasetProfileViewstyle;
@@ -160,7 +161,7 @@ public class TestRest {
 	
 	
 	
-	@Test
+	//@Test
     public void testUserProject() {
 		
 //		System.out.println(projectsService.listProjects().getBody());
@@ -186,15 +187,33 @@ public class TestRest {
 
     }
 	
-//	@Test
+	//@Test
     public void testDmpUser() {
 		
-		System.out.println(dmpsService.getDmpsOfUser().getBody());
+//		System.out.println(dmpsService.getDmpsOfUser());
+		
+		DMP dmp = new DMP();
+		dmp.setId(UUID.fromString("52239f0e-4460-4459-a393-bffcb833f39d"));
+		
+		System.out.println(dmpsService.getDatasetsOfDMP(dmp).getBody());
 		
         assertEquals("aaa", "aaa");
 		
 
     }
 	
+    
+    @Test
+    public void testDataset() {
+		
+		System.out.println(datasetsService.getAllDatasets().getBody());
+		
+//		System.out.println(dmpsService.getDatasetsOfDMP(dmp).getBody());
+		
+        assertEquals("aaa", "aaa");
+		
+
+    }
+    
 	
 }

dmp-frontend/src/app/app.component.html

@@ -38,19 +38,18 @@
             </div><!-- /.navbar-collapse -->
           </div><!-- /.container-fluid -->
         </nav>
-        <!--
-        -->
-        <router-outlet ></router-outlet> 
+
+        <router-outlet [ngClass]="{true:'visible'}[tokenService.isLoggedIn() == true]" ></router-outlet> 
+
         <!--
         <main-window [ngClass]="{false:'invisible'}[tokenService.isLoggedIn() == true]"></main-window>
         -->
-        <!--
-        <app-main-sign-in [ngClass]="{true:'invisible'}[tokenService.isLoggedIn() == true]"></app-main-sign-in>
-        -->
+
+        
+        <!--this should be invisible -->
+        <app-main-sign-in [ngClass]="'invisible'"></app-main-sign-in>
         
 
-        <!--  
-      <router-outlet></router-outlet>
-      -->
+
 
     </div>

dmp-frontend/src/app/app.component.ts

@@ -1,4 +1,4 @@
-import { Component } from '@angular/core';
+import { Component, OnInit} from '@angular/core';
 import { ServerService } from './services/server.service';
 import { FieldBase } from '../app/form/fields/field-base';
 import { JsonObjest } from '../app/entities/JsonObject.class';
@@ -12,7 +12,7 @@ import { MainSignInComponent } from './login/main-sign-in/main-sign-in.component
   styleUrls: ['./app.component.css'],
   providers:  []
 })
-export class AppComponent {
+export class AppComponent implements OnInit {
   
   fields: any[];
 
@@ -21,6 +21,12 @@ export class AppComponent {
 
   }
 
+  ngOnInit() {
+    
+    
+      
+  }
+  
 
   //loggedInAs : string = null; 
 

dmp-frontend/src/app/datasets/dataset.component.ts

@@ -92,10 +92,10 @@ export class DatasetsComponent implements OnInit {
 
   }
 
-  ngOnInit() {   debugger; 
+  ngOnInit() {    
     //this.projects = this.serverService.getDummyProjects();
     this.datasets = [];
-    console.log(this.dmpIdforDatasets);debugger;
+    console.log(this.dmpIdforDatasets);
     this.serverService.getDatasetForDmp({ "id": this.dmpIdforDatasets }).subscribe(
       response => {
         this.tableData = response;

dmp-frontend/src/app/dmps/dmp.component.ts

@@ -93,19 +93,12 @@ export class DmpComponent implements OnInit{
 
   ngOnInit() {
     //this.projects = this.serverService.getDummyProjects();
-    gapi.load('auth2', function() {
-      gapi.auth2.init({});
-    });
     this.serverService.getDmpOfUser().subscribe( 
       response => { 
         this.tableData = response;
       },
       (err: HttpErrorResponse) => {
-        if (err.error instanceof Error) {
-          console.log("An error occurred:", err.error.message);
-        } else {
-          console.log("Backend returned code ${err.status}, body was: ${err.error}");
-        }
+        
       }      
     ); 
 
@@ -135,11 +128,7 @@ getDmps(){
       this.tableData = response;
     },
     (err: HttpErrorResponse) => {
-      if (err.error instanceof Error) {
-        console.log("An error occurred:", err.error.message);
-      } else {
-        console.log("Backend returned code ${err.status}, body was: ${err.error}");
-      }
+      
     }      
   ); 
 }
@@ -169,8 +158,7 @@ updateDMP(){
   this.serverService.updateDmp(this.dmp)
   .subscribe(
     response =>{
-      console.log("response");
-      console.log(response);
+      this.getDmps();
     }
   );
   $("#newDmpModal").modal("hide");

dmp-frontend/src/app/dmps/dmps.html

@@ -195,6 +195,3 @@
 
 <!--DATASET TABLE-->
 <datasets-table *ngIf="dataSetVisibe" [dmpIdforDatasets]="dmpIdforDatasets" [dmpLabelforDatasets]="dmpLabelforDatasets" [(dataSetVisibe)]="dataSetVisibe"></datasets-table>
-
-<a href="#" (click)="signOut();" #isignOutBtn>Sign out</a>
-<router-outlet></router-outlet>

dmp-frontend/src/app/login/googgle-sign-in/googgle-sign-in.component.ts

@@ -60,7 +60,7 @@ export class GooggleSignInComponent implements OnInit, AfterViewInit {
         this.router.navigate(['/dmps'], { queryParams: { /*returnUrl: this.state.url*/ }});
       }, 
       function (error) {
-        simple_notifier("danger",null,"Failed to login");
+        //simple_notifier("danger",null,"Failed to login");
         console.log(JSON.stringify(error, undefined, 2));
       });
 

dmp-frontend/src/app/projects/project.html

@@ -125,6 +125,3 @@
 
 <!--DATASET TABLE-->
 <datasets-table *ngIf="dataSetVisibe"  [(dataSetVisibe)]="dataSetVisibe"></datasets-table> <!--*ngIf="dataSetVisibe == true"-->
-
-<a href="#" (click)="signOut();" #isignOutBtn >Sign out</a>
-<router-outlet></router-outlet>

dmp-frontend/src/app/projects/projects.component.ts

@@ -83,17 +83,13 @@ export class ProjectsComponent implements OnInit{
 
   ngOnInit() {
 
-    gapi.load('auth2', function() {
-      gapi.auth2.init({});
-    });
-    this.getProjects();
-    //this.projects = this.serverService.getDummyProjects();
     this.projects = [];
+    this.getProjects();
      
   }
 
 getProjects(){
-  this.serverService.getProjectOfUer().subscribe(  //getProjects()
+  this.serverService.getProjectOfUer().subscribe(  
   response => {
     this.tableData = response;
     
@@ -191,10 +187,6 @@ editRow(item, event){
     
   }
 
-signOut() {
-      this.serverService.logOut();
-}
-     
 
 
 }

dmp-frontend/src/app/services/interceptor.ts

@@ -20,6 +20,7 @@ export class GlobalInterceptor implements HttpInterceptor {
       }, (err: any) => {
         if (err instanceof HttpErrorResponse) {
           if (err.status === 401) {
+            console.log("Received an unauthorized... redirecting to login page");
             this.tokenService.logout();
             this.router.navigate(['/login'], { queryParams: { /*returnUrl: this.state.url*/ }});
           }

dmp-frontend/src/app/services/rest-base.ts

@@ -17,6 +17,7 @@ export class RestBase {
     
     
 
+    
 
     protocol: string = "http";
     hostname: string ="dl010.madgik.di.uoa.gr" ;//"localhost";//"dl010.madgik.di.uoa.gr";//
@@ -25,10 +26,12 @@ export class RestBase {
 
     
 
-    /*protocol: string = "http";
+    
+   /* protocol: string = "http";
     hostname: string = "dionysus.di.uoa.gr" ;
     port: number = 7070;
     webappname: string = "dmp-backend";*/
+    
 
 
     proxyPath : string = this.protocol+"://"+this.hostname+":"+this.port+"/"+this.webappname+"/proxy/";