Merge branch 'remove-reports' into 'develop'

remove documents

See merge request !25

src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java

 package es.bsc.inb.ades.rest.api.controllers;
 
+import java.security.Principal;
 import java.util.List;
 
+import javax.servlet.http.HttpServletRequest;
+
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
+import org.springframework.security.oauth2.server.resource.authentication.JwtAuthenticationToken;
 import org.springframework.web.bind.annotation.CrossOrigin;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
@@ -23,6 +27,8 @@ import es.bsc.inb.ades.rest.api.services.DocumentService;
 @CrossOrigin(origins="*")
 public class DocumentController {
 	
+	
+	
 	@Autowired
 	public DocumentService documentService;
 	
@@ -69,6 +75,8 @@ public class DocumentController {
 		documentService.moveDocument(id, status);
 		return "true";
 	}
+
+	
 	
 	@RequestMapping("/documents/{id}/setExportSRDomain/{srDomainId}/{export_srDomain}")
 	public String setExportFinding(@PathVariable(value="id") Long id, @PathVariable(value="srDomainId") Integer srDomainId, @PathVariable(value="export_srDomain") Boolean export_srDomain) {
@@ -137,10 +145,26 @@ public class DocumentController {
         return new ResponseEntity<>(content, head,HttpStatus.OK);
     }
 
+    @RequestMapping(value = "/documents/remove/{id}")
+    public String removeDocument(@PathVariable("id") long documentId){
+		documentService.removeDocument(documentId);
+		return "true";
+    }
+    
+    @RequestMapping(value = "/documents/restore/{id}")
+    public String restoreDocument(@PathVariable("id") long documentId){
+		documentService.restoreDocument(documentId);
+		return "true";
+    }
+    
     @RequestMapping("/documents/{id}/tracking")
 	public DocumentTracking findTrackings(@PathVariable(value="id") Long id) {
-		return documentService.findTrackings(id);
+    	return documentService.findTrackings(id);
 	}
+
+	
+    
+    
     
 	
 }
\ No newline at end of file

src/main/java/es/bsc/inb/ades/rest/api/model/Document.java

@@ -26,6 +26,8 @@ public class Document{
 	
 	private Status status;
 	
+	private RecordState recordState;
+	
 	public Document() {
 		super();
 	}
@@ -90,5 +92,14 @@ public class Document{
 		this.fileName = fileName;
 	}
 
+	public RecordState getRecordState() {
+		return recordState;
+	}
+
+	public void setRecordState(RecordState recordState) {
+		this.recordState = recordState;
+	}
+
+	
 
 }

src/main/java/es/bsc/inb/ades/rest/api/model/RecordState.java

+package es.bsc.inb.ades.rest.api.model;
+
+public enum RecordState {
+
+	ACTIVE, DELETED; 
+	
+	
+}

src/main/java/es/bsc/inb/ades/rest/api/repository/DocumentRepositoryImpl.java

@@ -33,6 +33,8 @@ public class DocumentRepositoryImpl implements DocumentRepositoryCustom{
 		query.fields().include("name");
 		query.fields().include("processDate");
 		query.fields().include("status");
+		query.fields().include("recordState");
+		query.addCriteria(Criteria.where("recordState").ne("DELETED"));
 		//Sort sort = new Sort(Sort.Direction.ASC, "name");
 		//query.with(sort);
 		List<Document> documents = mongoTemplate.find(query,  Document.class);

src/main/java/es/bsc/inb/ades/rest/api/security/pkce/SecurityConfig.java

@@ -19,6 +19,7 @@ public class SecurityConfig extends WebSecurityConfigurerAdapter {
                 .authorizeRequests()
                 .antMatchers(HttpMethod.GET, "/liveness").permitAll()
 				.antMatchers(HttpMethod.GET, "/readiness").permitAll()
+				.antMatchers(HttpMethod.GET, "/documents/restore/*").permitAll()
 				.anyRequest().authenticated()
                 .and()
                 .sessionManagement()

src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java

@@ -46,5 +46,9 @@ public interface DocumentService  {
 	
 	Status moveDocument(Long id, Status status);
 	
-	DocumentTracking findTrackings(Long documentId); 
+	DocumentTracking findTrackings(Long documentId);
+
+	void removeDocument(long documentId); 
+	
+	void restoreDocument(long documentId); 
 }

src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java

 package es.bsc.inb.ades.rest.api.services;
 
 import java.nio.charset.Charset;
+import java.security.Principal;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
+import javax.servlet.http.HttpServletRequest;
+
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.security.core.Authentication;
+import org.springframework.security.core.context.SecurityContextHolder;
+import org.springframework.security.core.userdetails.UserDetails;
+import org.springframework.security.oauth2.server.resource.authentication.JwtAuthenticationToken;
 import org.springframework.stereotype.Service;
 
 import com.google.gson.Gson;
 import com.google.gson.GsonBuilder;
 import com.google.gson.JsonArray;
 import com.google.gson.JsonObject;
+import com.nimbusds.jwt.JWT;
 
 import es.bsc.inb.ades.rest.api.model.Action;
 import es.bsc.inb.ades.rest.api.model.Annotation;
@@ -21,6 +29,7 @@ import es.bsc.inb.ades.rest.api.model.Document;
 import es.bsc.inb.ades.rest.api.model.DocumentAnnotations;
 import es.bsc.inb.ades.rest.api.model.DocumentTracking;
 import es.bsc.inb.ades.rest.api.model.Finding;
+import es.bsc.inb.ades.rest.api.model.RecordState;
 import es.bsc.inb.ades.rest.api.model.SRDomainFinding;
 import es.bsc.inb.ades.rest.api.model.Status;
 import es.bsc.inb.ades.rest.api.model.Tracking;
@@ -33,7 +42,8 @@ import es.bsc.inb.ades.rest.api.util.Constants;
 @Service
 public class DocumentServiceImpl implements DocumentService {
 	
-	
+	@Autowired
+	private HttpServletRequest request;
 	
 	@Autowired
 	public DocumentRepository documentRepository;
@@ -107,7 +117,7 @@ public class DocumentServiceImpl implements DocumentService {
 			//https://stackoverflow.com/questions/47699646/updating-replacing-a-deeply-nested-object-in-mongodb-with-spring-data-mongodb
 			findingSelected.setStatus(status);
 			documentAnnotationsRepository.save(documentAnnotations);
-			createTracking(id, "admin",  Action.ACCEPT, findingSelected.getTrackingSummary());
+			createTracking(id, Action.ACCEPT, findingSelected.getTrackingSummary());
 			return true;
 		}
 		return false;
@@ -132,7 +142,7 @@ public class DocumentServiceImpl implements DocumentService {
 			//https://stackoverflow.com/questions/47699646/updating-replacing-a-deeply-nested-object-in-mongodb-with-spring-data-mongodb
 			srDomainFindingelected.setStatus(status);
 			documentAnnotationsRepository.save(documentAnnotations);
-			createTracking(id, "admin",  Action.ACCEPT, srDomainFindingelected.getTrackingSummary());
+			createTracking(id,   Action.ACCEPT, srDomainFindingelected.getTrackingSummary());
 			return true;
 		}
 		return false;
@@ -158,7 +168,7 @@ public class DocumentServiceImpl implements DocumentService {
 			//https://stackoverflow.com/questions/47699646/updating-replacing-a-deeply-nested-object-in-mongodb-with-spring-data-mongodb
 			sRDomainFindingSelected.setExport(export_srdomainfinding);
 			documentAnnotationsRepository.save(documentAnnotations);
-			createTracking(id, "admin",  export_srdomainfinding?Action.EXPORT_SR_FINDING:Action.NOT_EXPORT_SR_FINDING, sRDomainFindingSelected.getTrackingSummary());
+			createTracking(id,   export_srdomainfinding?Action.EXPORT_SR_FINDING:Action.NOT_EXPORT_SR_FINDING, sRDomainFindingSelected.getTrackingSummary());
 			return true;
 		}
 		return false;
@@ -976,15 +986,16 @@ public class DocumentServiceImpl implements DocumentService {
 		documentAnnotation.setStatus(status);	
 		documentRepository.save(document);
 		documentAnnotationsRepository.save(documentAnnotation);
-		
-		createTracking(id, "admin",  Action.MOVE, status.toString());
-		
+		createTracking(id,   Action.MOVE, status.toString());
 		return status;
 	}
 
-	private void createTracking(Long id, String userName , Action action, String comment) {
+	private void createTracking(Long id, Action action, String comment) {
 		DocumentTracking documentTracking = this.findDocumentTrackingById(id);
-		Tracking tracking = new Tracking (userName, action, comment);
+//		Object principal = SecurityContextHolder.getContext().getAuthentication().getPrincipal();
+//		JwtAuthenticationToken token = (JwtAuthenticationToken)principal;
+//		Tracking tracking = new Tracking (token.getTokenAttributes().get("name").toString(), action, comment);
+		Tracking tracking = new Tracking (getUserName(), action, comment);
 		documentTracking.addTracking(tracking);
 		documentTrackingRepository.save(documentTracking);
 	}
@@ -1003,6 +1014,37 @@ public class DocumentServiceImpl implements DocumentService {
 		return documentTracking;
 	}
 
+	@Override
+	public void removeDocument(long documentId) {
+		Document document = this.findByDocumentId(documentId);
+		document.setRecordState(RecordState.DELETED);
+		documentRepository.save(document);
+	}
+
+	@Override
+	public void restoreDocument(long documentId) {
+		Document document = this.findByDocumentId(documentId);
+		document.setRecordState(RecordState.ACTIVE);
+		documentRepository.save(document);
+	}
 	
+	private String getUserName() {
+		Principal user = request.getUserPrincipal();
+		String userName = "";
+		if(user!=null && user instanceof JwtAuthenticationToken) {
+			JwtAuthenticationToken token = (JwtAuthenticationToken)user;
+			if(token.getTokenAttributes().get("name")!=null) {
+				userName = token.getTokenAttributes().get("name").toString();
+			};
+		}
+		return userName;
+	}
+	public HttpServletRequest getRequest() {
+		return request;
+	}
+
+	public void setRequest(HttpServletRequest request) {
+		this.request = request;
+	}
 	
 }

src/main/java/es/bsc/inb/ades/rest/api/services/FileServiceImp.java

@@ -18,6 +18,8 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import com.mongodb.client.MongoCollection;
 import com.mongodb.client.MongoDatabase;
 
+import es.bsc.inb.ades.rest.api.model.RecordState;
+
 import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.IOException;