improves srdomaintemplate tab

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

@@ -30,7 +30,12 @@ public class DocumentController {
 	
 	@RequestMapping("/documents/{id}")
 	public DocumentAnnotations find(@PathVariable(value="id") Long id) {
-		return documentService.findByDocumentAnnotationsByDocumentId(id);
+		return documentService.findDocumentAnnotationsByDocumentId(id);
+	}
+	
+	@RequestMapping("/documents/{id}/srdomain")
+	public DocumentAnnotations findDocumentSRDomain(@PathVariable(value="id") Long id) {
+		return documentService.findDocumentSRDomainByDocumentId(id);
 	}
 	
 //	@RequestMapping("/documents/{id}")

src/main/java/es/bsc/inb/ades/rest/api/model/DocumentAnnotations.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;
@@ -22,6 +23,8 @@ public class DocumentAnnotations {
 	private ArrayList<Annotation> relevantSentences;
 	
 	private ArrayList<Finding> findings;
+	
+	private List<SRDomainFinding> srdomainfindings;
 
 	public DocumentAnnotations() {}
 
@@ -46,7 +49,6 @@ public class DocumentAnnotations {
 		return documentId;
 	}
 
-
 	public ArrayList<Annotation> getRelevantSentences() {
 		return relevantSentences;
 	}
@@ -59,20 +61,22 @@ public class DocumentAnnotations {
 		this.documentId = documentId;
 	}
 
-
-
-
 	public ArrayList<Finding> getFindings() {
 		return findings;
 	}
 
-
-
-
 	public void setFindings(ArrayList<Finding> findings) {
 		this.findings = findings;
 	}
 
+	public List<SRDomainFinding> getSrdomainfindings() {
+		return srdomainfindings;
+	}
+
+	public void setSrdomainfindings(List<SRDomainFinding> srdomainfindings) {
+		this.srdomainfindings = srdomainfindings;
+	}
+
 	
 	
 }

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

@@ -34,6 +34,11 @@ public class SRDomainFinding implements Cloneable{
 	private String SRSIGF="";
 	private String SRTRTEF="";
 	private String SRCOMNT="";
+	
+	private Boolean export;
+	private Integer findingId;
+	private Integer srDomainId;
+	
 	public String getSTUDYID() {
 		return STUDYID;
 	}
@@ -191,6 +196,27 @@ public class SRDomainFinding implements Cloneable{
 		SRCOMNT = sRCOMNT;
 	}
 	
+	
+	
+	
+	public Boolean getExport() {
+		return export;
+	}
+	public void setExport(Boolean export) {
+		this.export = export;
+	}
+	public Integer getSrDomainId() {
+		return srDomainId;
+	}
+	public void setSrDomainId(Integer srDomainId) {
+		this.srDomainId = srDomainId;
+	}
+	public Integer getFindingId() {
+		return findingId;
+	}
+	public void setFindingId(Integer findingId) {
+		this.findingId = findingId;
+	}
 	public SRDomainFinding clone() {
 		try {
 			return (SRDomainFinding)super.clone();

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

@@ -18,7 +18,9 @@ public interface DocumentService  {
 	
 	String findFindingEvidenceByDocumentIdAndFindingId(Long id, Integer findingId);
 	
-	DocumentAnnotations findByDocumentAnnotationsByDocumentId(Long id);
+	DocumentAnnotations findDocumentAnnotationsByDocumentId(Long id);
+	
+	DocumentAnnotations findDocumentSRDomainByDocumentId(Long id);
 
 	String findSentenceEvidenceByDocumentIdAndSentenceId(Long id, Integer sentenceId);
 	

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

@@ -28,6 +28,7 @@ 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;
+import es.bsc.inb.ades.rest.api.model.SRDomainFinding;
 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.util.Constants;
@@ -60,10 +61,25 @@ public class DocumentServiceImpl implements DocumentService {
 		return documentRepository.findDocumentTextSubstringByDocumentId(id, start, end);
 	}
 	
-	public DocumentAnnotations findByDocumentAnnotationsByDocumentId(Long id) {
+	public DocumentAnnotations findDocumentAnnotationsByDocumentId(Long id) {
 		return documentAnnotationsRepository.findByDocumentId(id);
 	}
 	
+	public DocumentAnnotations findDocumentSRDomainByDocumentId(Long id) {
+		DocumentAnnotations docAnno = documentAnnotationsRepository.findByDocumentId(id);
+		List<SRDomainFinding> srdomains = new ArrayList<SRDomainFinding>();
+		for (Annotation sentence : docAnno.getRelevantSentences()) {
+			for (Finding finding : sentence.getFindings()) {
+				for (SRDomainFinding sr : finding.getSrDomainFindings()) {
+					srdomains.add(sr);
+				}
+			}
+		}
+		docAnno.setSrdomainfindings(srdomains);
+		docAnno.setRelevantSentences(null);
+		docAnno.setFindings(null);
+		return docAnno;
+	}
 	
 	public Document findByDocumentId2(Long id) {
 		documentRepository.findByDocumentId(id);
@@ -91,7 +107,7 @@ public class DocumentServiceImpl implements DocumentService {
 	
 	@Override
 	public String findTextSnippetByDocumentIdAndFindingId2(Long id, Integer findingId) {
-		DocumentAnnotations documentAnnotations = this.findByDocumentAnnotationsByDocumentId(id);
+		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
 		Document document = this.findByDocumentId(id);
 		Finding findingSelected = null;
 		for (Finding finding : documentAnnotations.getFindings()) {
@@ -111,7 +127,7 @@ public class DocumentServiceImpl implements DocumentService {
 	
 	@Override
 	public Boolean acceptFinding(Long id, Integer findingId) {
-		DocumentAnnotations documentAnnotations = this.findByDocumentAnnotationsByDocumentId(id);
+		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
 		Finding findingSelected = null;
 		for (Annotation annotation : documentAnnotations.getRelevantSentences()) {
 			for (Finding finding : annotation.getFindings()) {
@@ -131,7 +147,7 @@ public class DocumentServiceImpl implements DocumentService {
 
 	@Override
 	public Boolean rejectFinding(Long id, Integer findingId) {
-		DocumentAnnotations documentAnnotations = this.findByDocumentAnnotationsByDocumentId(id);
+		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
 		Finding findingSelected = null;
 		for (Annotation annotation : documentAnnotations.getRelevantSentences()) {
 			for (Finding finding : annotation.getFindings()) {
@@ -152,7 +168,7 @@ public class DocumentServiceImpl implements DocumentService {
 	
 	@Override
 	public Boolean setExportFinding(Long id, Integer findingId,String export_finding) {
-		DocumentAnnotations documentAnnotations = this.findByDocumentAnnotationsByDocumentId(id);
+		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
 		Finding findingSelected = null;
 		for (Annotation annotation : documentAnnotations.getRelevantSentences()) {
 			for (Finding finding : annotation.getFindings()) {
@@ -174,7 +190,7 @@ public class DocumentServiceImpl implements DocumentService {
 	
 	@Override
 	public String findSentenceEvidenceByDocumentIdAndSentenceId(Long id, Integer sentenceId) {
-		DocumentAnnotations documentAnnotations = this.findByDocumentAnnotationsByDocumentId(id);
+		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
 		Annotation annotation = null;
 		for (Annotation sentence : documentAnnotations.getRelevantSentences()) {
 			if(sentence.getId().equals(sentenceId)) {
@@ -205,14 +221,14 @@ public class DocumentServiceImpl implements DocumentService {
 	}
 	
 	public String findFindingsEvidenceByDocumentId(Long id) {
-		DocumentAnnotations documentAnnotations = this.findByDocumentAnnotationsByDocumentId(id);
+		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
 		Document document = this.findByDocumentId(id);
 		return this.generateFindingsSnippet4(document.getText(), documentAnnotations.getFindings());
 	}
 	 
 	@Override
 	public String findFindingEvidenceByDocumentIdAndFindingId(Long id, Integer findingId) {
-		DocumentAnnotations documentAnnotations = this.findByDocumentAnnotationsByDocumentId(id);
+		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
 		Finding findingSelected = null;
 		for (Annotation annotation : documentAnnotations.getRelevantSentences()) {
 			for (Finding finding : annotation.getFindings()) {
@@ -267,7 +283,7 @@ public class DocumentServiceImpl implements DocumentService {
 	
 	
 	public byte[] exportDocumentAnnotation(Long id) {
-		DocumentAnnotations documentAnnotations = this.findByDocumentAnnotationsByDocumentId(id);
+		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
 		StringBuilder retStr = new StringBuilder("");
 		retStr.append("STUDYID|DOMAIN|SRSEQ|SRRISK|SPGRPCD|GRPLBL|SRGRPDOS|SRSEX|SRSTDY|SRSTPHSE|SROBSTDY|SRENDY|SRENPHSE|SROBENDY|SRDOMAIN|SRSPEC|SRTSTCD|SRFNDG|SRORES|SROBSV|SROBSQ|SRSEV|SRPCNT|SRSIGF|SRTRTEF|SRCOMNT");
 		retStr.append(System.getProperty("line.separator"));