Merge branch 'develop' of

https://gitlab.bsc.es/inb/etransafe/pretox-rest-api.git into develop

Conflicts:
	src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
	src/main/resources/application.properties

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

@@ -15,6 +15,9 @@ import org.springframework.web.bind.annotation.RestController;
 
 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.Status;
+import es.bsc.inb.ades.rest.api.model.Tracking;
 import es.bsc.inb.ades.rest.api.security.basic.inmemory.AuthenticationBean;
 import es.bsc.inb.ades.rest.api.services.DocumentService;
 
@@ -36,6 +39,11 @@ public class DocumentController {
 		return documentService.findDocumentAnnotationsByDocumentId(id);
 	}
 	
+	@RequestMapping("/document_data/{id}")
+	public Document findDocument(@PathVariable(value="id") Long id) {
+		return documentService.findByDocumentId(id);
+	}
+	
 	@RequestMapping("/documents/{id}/srdomain")
 	public DocumentAnnotations findDocumentSRDomain(@PathVariable(value="id") Long id) {
 		return documentService.findDocumentSRDomainByDocumentId(id);
@@ -59,6 +67,12 @@ public class DocumentController {
 		return "";
 	}
 	
+	@RequestMapping("/documents/{id}/move/{status}")
+	public String moveDocument(@PathVariable(value="id") Long id, @PathVariable(value="status") Status status) {
+		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) {
 		documentService.setExportSRDomainFinding(id, srDomainId, export_srDomain);
@@ -101,5 +115,11 @@ public class DocumentController {
         head.setCacheControl("must-revalidate, post-check=0, pre-check=0");
         return new ResponseEntity<>(content, head,HttpStatus.OK);
     }
+
+    @RequestMapping("/documents/{id}/tracking")
+	public DocumentTracking findTrackings(@PathVariable(value="id") Long id) {
+		return documentService.findTrackings(id);
+	}
+    
 	
 }
\ No newline at end of file

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

+package es.bsc.inb.ades.rest.api.model;
+
+public enum Action {
+	 MOVE, REJECT, ACCEPT, EXPORT_SR_FINDING, NOT_EXPORT_SR_FINDING
+}
\ No newline at end of file

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

@@ -23,8 +23,8 @@ public class Document{
 	private String processDate;
 	
 	private String fileName;
-
-	private List<Finding> findings;
+	
+	private Status status;
 	
 	public Document() {
 		super();
@@ -63,22 +63,15 @@ public class Document{
 		this.name = name;
 	}
 
-
-
-	public List<Finding> getFindings() {
-		return findings;
+	public Status getStatus() {
+		if(status==null)return Status.DRAFT;
+		return status;
 	}
 
-
-
-	public void setFindings(List<Finding> findings) {
-		this.findings = findings;
+	public void setStatus(Status status) {
+		this.status = status;
 	}
 
-	
-
-
-
 	public String getProcessDate() {
 		return processDate;
 	}

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

@@ -5,7 +5,6 @@ import java.util.List;
 
 import org.bson.types.ObjectId;
 import org.springframework.data.annotation.Id;
-import org.springframework.data.annotation.Transient;
 import org.springframework.data.mongodb.core.mapping.Field;
 @org.springframework.data.mongodb.core.mapping.Document(collection="annotations")
 public class DocumentAnnotations {
@@ -25,7 +24,9 @@ public class DocumentAnnotations {
 	private ArrayList<Finding> findings;
 	
 	private List<SRDomainFinding> srdomainfindings;
-
+	
+	private Status status;
+	
 	public DocumentAnnotations() {}
 
 	public ObjectId get_id() {
@@ -77,6 +78,16 @@ public class DocumentAnnotations {
 		this.srdomainfindings = srdomainfindings;
 	}
 
+	public Status getStatus() {
+		if(status==null)return Status.DRAFT;
+		return status;
+	}
+
+	public void setStatus(Status status) {
+		this.status = status;
+	}
+
+	
 	
 	
 }

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

+package es.bsc.inb.ades.rest.api.model;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.bson.types.ObjectId;
+import org.springframework.data.annotation.Id;
+import org.springframework.data.mongodb.core.mapping.Field;
+@org.springframework.data.mongodb.core.mapping.Document(collection="tracking")
+public class DocumentTracking {
+
+	
+
+	@Field("_id")
+	@Id
+	private ObjectId _id;
+	
+	@Field("id")
+	private Long documentId;
+	
+	List<Tracking> trackings;
+
+	
+	
+	public DocumentTracking() {
+		super();
+	}
+
+
+
+	public DocumentTracking(Long documentId) {
+		this.documentId=documentId;
+		this.trackings = new ArrayList<Tracking>();
+	}
+
+
+
+	public void addTracking(Tracking tracking) {
+		if(trackings==null) {
+			trackings = new ArrayList<Tracking>();
+		}
+		
+		trackings.add(tracking);
+		
+	}
+
+
+
+	public Long getDocumentId() {
+		return documentId;
+	}
+
+
+
+	public void setDocumentId(Long documentId) {
+		this.documentId = documentId;
+	}
+
+
+
+	public List<Tracking> getTrackings() {
+		return trackings;
+	}
+
+
+
+	public void setTrackings(List<Tracking> trackings) {
+		this.trackings = trackings;
+	}
+	
+	
+	
+}	
\ No newline at end of file

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

@@ -432,6 +432,12 @@ public class Finding {
 	public void setSrDomainFindings(List<SRDomainFinding> srDomainFindings) {
 		this.srDomainFindings = srDomainFindings;
 	}
+
+
+	public String getTrackingSummary() {
+		
+		return findingId.toString();
+	}
 	
 	
 	

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

@@ -227,5 +227,9 @@ public class SRDomainFinding implements Cloneable{
 		}
 		return null;
 	}
+	public String getTrackingSummary() {
+		String summary = SRSEQ ;
+		return summary;
+	}
 	 
 }

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

+package es.bsc.inb.ades.rest.api.model;
+
+public enum Status {
+	 DRAFT, IN_PROGRESS, FINISHED, CLOSED  
+}

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

+package es.bsc.inb.ades.rest.api.model;
+
+import java.util.Date;
+
+public class Tracking {
+
+	private Date date;
+	
+	private String userName;
+	
+	private Action action;
+	
+	private String comment;
+
+	
+	public Tracking() {
+		super();
+	}
+
+	public Tracking(String userName, Action action, String comment) {
+		super();
+		this.date=new Date();
+		this.userName = userName;
+		this.action = action;
+		this.comment = comment;
+	}
+
+	public String getUserName() {
+		return userName;
+	}
+
+	public void setUserName(String userName) {
+		this.userName = userName;
+	}
+
+	public Action getAction() {
+		return action;
+	}
+
+	public void setAction(Action action) {
+		this.action = action;
+	}
+
+	public String getComment() {
+		return comment;
+	}
+
+	public void setComment(String comment) {
+		this.comment = comment;
+	}
+
+	public Date getDate() {
+		return date;
+	}
+
+	public void setDate(Date date) {
+		this.date = date;
+	}
+	
+	
+	
+}

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

 package es.bsc.inb.ades.rest.api.repository;
 
-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.Finding;
 

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

@@ -9,11 +9,9 @@ import org.springframework.data.mongodb.core.aggregation.Aggregation;
 import org.springframework.data.mongodb.core.aggregation.AggregationResults;
 import org.springframework.data.mongodb.core.aggregation.MatchOperation;
 import org.springframework.data.mongodb.core.aggregation.ProjectionOperation;
-import org.springframework.data.mongodb.core.query.BasicQuery;
 import org.springframework.data.mongodb.core.query.Criteria;
 import org.springframework.data.mongodb.core.query.Query;
 
-import es.bsc.inb.ades.rest.api.model.Annotation;
 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.Finding;
@@ -34,6 +32,7 @@ public class DocumentRepositoryImpl implements DocumentRepositoryCustom{
 		query.fields().include("fileName");
 		query.fields().include("name");
 		query.fields().include("processDate");
+		query.fields().include("status");
 		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/repository/DocumentTrackingRepository.java

+package es.bsc.inb.ades.rest.api.repository;
+
+import org.springframework.data.mongodb.repository.MongoRepository;
+import org.springframework.stereotype.Repository;
+
+import es.bsc.inb.ades.rest.api.model.DocumentTracking;
+
+@Repository
+public interface DocumentTrackingRepository extends DocumentTrackingRepositoryCustom, MongoRepository<DocumentTracking, String> {
+	
+	DocumentTracking findByDocumentId(Long documentId);
+
+		
+}

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

+package es.bsc.inb.ades.rest.api.repository;
+
+public interface DocumentTrackingRepositoryCustom {
+
+}

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

@@ -4,6 +4,9 @@ import java.util.List;
 
 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.Status;
+import es.bsc.inb.ades.rest.api.model.Tracking;
 
 
 public interface DocumentService  {
@@ -31,4 +34,8 @@ public interface DocumentService  {
 	Boolean setExportSRDomainFinding(Long id, Integer findingId, Boolean export_srdomain);
 	
 	Boolean setFindingValidation(Long id, Integer findingId,String status);
+	
+	Status moveDocument(Long id, Status status);
+	
+	DocumentTracking findTrackings(Long documentId); 
 }

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

 package es.bsc.inb.ades.rest.api.services;
 
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStreamWriter;
 import java.nio.charset.Charset;
-import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.Optional;
 
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.data.domain.Sort;
 import org.springframework.stereotype.Service;
 
 import com.google.gson.Gson;
@@ -24,13 +15,18 @@ import com.google.gson.GsonBuilder;
 import com.google.gson.JsonArray;
 import com.google.gson.JsonObject;
 
+import es.bsc.inb.ades.rest.api.model.Action;
 import es.bsc.inb.ades.rest.api.model.Annotation;
 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.SRDomainFinding;
+import es.bsc.inb.ades.rest.api.model.Status;
+import es.bsc.inb.ades.rest.api.model.Tracking;
 import es.bsc.inb.ades.rest.api.repository.DocumentAnnotationsRepository;
 import es.bsc.inb.ades.rest.api.repository.DocumentRepository;
+import es.bsc.inb.ades.rest.api.repository.DocumentTrackingRepository;
 import es.bsc.inb.ades.rest.api.util.Constants;
 
 
@@ -45,6 +41,9 @@ public class DocumentServiceImpl implements DocumentService {
 	@Autowired
 	public DocumentAnnotationsRepository documentAnnotationsRepository;
 	
+	@Autowired
+	public DocumentTrackingRepository documentTrackingRepository;
+	
 	static final Map<String, String> ANNOTATION_CLASS_STYLE = createMap();
 	
 	public List<Document> findAll() {
@@ -108,7 +107,7 @@ public class DocumentServiceImpl implements DocumentService {
 	}
 	
 	@Override
-	public Boolean setFindingValidation(Long id, Integer findingId,String status) {
+	public Boolean setFindingValidation(Long id, Integer findingId, String status) {
 		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
 		Finding findingSelected = null;
 		for (Annotation annotation : documentAnnotations.getRelevantSentences()) {
@@ -123,6 +122,7 @@ 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());
 			return true;
 		}
 		return false;
@@ -147,6 +147,7 @@ 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());
 			return true;
 		}
 		return false;
@@ -718,6 +719,41 @@ public class DocumentServiceImpl implements DocumentService {
         return Collections.unmodifiableMap(result);
     }
 
+	@Override
+	public Status moveDocument(Long id, Status status) {
+		Document document = this.findByDocumentId(id);
+		DocumentAnnotations documentAnnotation = this.findDocumentAnnotationsByDocumentId(id);
+		document.setStatus(status);
+		documentAnnotation.setStatus(status);	
+		documentRepository.save(document);
+		documentAnnotationsRepository.save(documentAnnotation);
+		
+		createTracking(id, "admin",  Action.MOVE, status.toString());
+		
+		return status;
+	}
+
+	private void createTracking(Long id, String userName , Action action, String comment) {
+		DocumentTracking documentTracking = this.findDocumentTrackingById(id);
+		Tracking tracking = new Tracking (userName, action, comment);
+		documentTracking.addTracking(tracking);
+		documentTrackingRepository.save(documentTracking);
+	}
+
+	private DocumentTracking findDocumentTrackingById(Long id) {
+		DocumentTracking documentTracking = documentTrackingRepository.findByDocumentId(id);
+		if(documentTracking==null) {
+			documentTracking = new DocumentTracking(id);
+			
+		}
+		return documentTracking;
+	}
+
+	public DocumentTracking findTrackings(Long documentId) {
+		DocumentTracking documentTracking = this.findDocumentTrackingById(documentId);
+		return documentTracking;
+	}
+
 	
 	
 }

src/main/resources/application.properties

@@ -5,7 +5,7 @@ server.servlet.context-path=/pretoxapi
 server.port = 8090
 #ADES Database
 #spring.data.mongodb.uri=mongodb://localhost:27017/etransafe
-spring.data.mongodb.uri=mongodb://etransafe_rw:etransafe_rw2019!@mdb-login.bsc.es:27017/etransafe
+spring.data.mongodb.uri=mongodb://REMOVED!REMOVED:REMOVED/REMOVED
 #development enviroment
 #docker run -d -p 27017-27019:27017-27019 -v /home/javi/eTRANSAFE_DATA/mongo-data-dev://data/db --name mongodb mongo:4.0.4