From 447c7c3599b3ef381fac05ac1460a0ed01a03764 Mon Sep 17 00:00:00 2001
From: javi <javicorvi@gmail.com>
Date: Mon, 21 Jun 2021 21:27:42 +0200
Subject: [PATCH 01/11] improves srdomaintemplate tab

---
 .../api/controllers/DocumentController.java   |  7 +++-
 .../rest/api/model/DocumentAnnotations.java   | 18 ++++++----
 .../ades/rest/api/model/SRDomainFinding.java  | 26 ++++++++++++++
 .../rest/api/services/DocumentService.java    |  4 ++-
 .../api/services/DocumentServiceImpl.java     | 34 ++++++++++++++-----
 5 files changed, 71 insertions(+), 18 deletions(-)

diff --git a/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java b/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
index f027c9e..37a4914 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
+++ b/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}")
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/model/DocumentAnnotations.java b/src/main/java/es/bsc/inb/ades/rest/api/model/DocumentAnnotations.java
index a79af0c..2bc5665 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/model/DocumentAnnotations.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/model/DocumentAnnotations.java
@@ -1,6 +1,7 @@
 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;
+	}
+
 	
 	
 }
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/model/SRDomainFinding.java b/src/main/java/es/bsc/inb/ades/rest/api/model/SRDomainFinding.java
index b601836..57fa5a5 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/model/SRDomainFinding.java
+++ b/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();
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java
index c95ff1b..cda7a3f 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java
+++ b/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);
 	
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
index 55966fe..aab25d0 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
+++ b/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"));
-- 
GitLab


From 24574a92c811cd602e91cf9df65c4093cdabb49f Mon Sep 17 00:00:00 2001
From: javi <javicorvi@gmail.com>
Date: Tue, 22 Jun 2021 16:34:16 +0200
Subject: [PATCH 02/11] export changes and curations features

---
 .../api/controllers/DocumentController.java   |  17 +-
 .../rest/api/services/DocumentService.java    |   6 +-
 .../api/services/DocumentServiceImpl.java     | 217 ++++++------------
 3 files changed, 83 insertions(+), 157 deletions(-)

diff --git a/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java b/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
index 37a4914..426b2e0 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
@@ -56,21 +56,14 @@ public class DocumentController {
 		return "";
 	}
 	
-	@RequestMapping("/documents/{id}/acceptFinding/{findingId}")
-	public String acceptFinding(@PathVariable(value="id") Long id, @PathVariable(value="findingId") Integer findingId) {
-		documentService.acceptFinding(id, findingId);
-		return "true";
-	}
-	
-	
-	@RequestMapping("/documents/{id}/rejectFinding/{findingId}")
-	public String rejectFinding(@PathVariable(value="id") Long id, @PathVariable(value="findingId") Integer findingId) {
-		documentService.rejectFinding(id, findingId);
+	@RequestMapping("/documents/{id}/exportFinding/{findingId}/{export_finding}")
+	public String setExportFinding(@PathVariable(value="id") Long id, @PathVariable(value="findingId") Integer findingId, @PathVariable(value="export_finding") String export_finding) {
+		documentService.setExportFinding(id, findingId, export_finding);
 		return "true";
 	}
 	
-	@RequestMapping("/documents/{id}/exportFinding/{findingId}/{export_finding}")
-	public String setExportFinding(@PathVariable(value="id") Long id, @PathVariable(value="findingId") Integer findingId, @PathVariable(value="export_finding") String export_finding) {
+	@RequestMapping("/documents/{id}/findingValidation/{findingId}/{status}")
+	public String setFindingValidation(@PathVariable(value="id") Long id, @PathVariable(value="findingId") Integer findingId, @PathVariable(value="export_finding") String export_finding) {
 		documentService.setExportFinding(id, findingId, export_finding);
 		return "true";
 	}
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java
index cda7a3f..192a195 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java
@@ -28,9 +28,7 @@ public interface DocumentService  {
 
 	String findFindingsEvidenceByDocumentId(Long id);
 
-	Boolean acceptFinding(Long id, Integer findingId);
-	
-	Boolean rejectFinding(Long id, Integer findingId);
-
 	Boolean setExportFinding(Long id, Integer findingId, String export_finding);
+	
+	Boolean setFindingValidation(Long id, Integer findingId,String status);
 }
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
index aab25d0..1f4431a 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
@@ -123,30 +123,8 @@ public class DocumentServiceImpl implements DocumentService {
 		return "";
 	}
 	
-	
-	
 	@Override
-	public Boolean acceptFinding(Long id, Integer findingId) {
-		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
-		Finding findingSelected = null;
-		for (Annotation annotation : documentAnnotations.getRelevantSentences()) {
-			for (Finding finding : annotation.getFindings()) {
-				if(finding.getFindingId().equals(findingId)) {
-					findingSelected = finding;
-					break;
-				}
-			}
-		}
-		if(findingSelected!=null) {
-			findingSelected.setStatus("accepted");
-			documentAnnotationsRepository.save(documentAnnotations);
-			return true;
-		}
-		return false;
-	}
-
-	@Override
-	public Boolean rejectFinding(Long id, Integer findingId) {
+	public Boolean setFindingValidation(Long id, Integer findingId,String status) {
 		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
 		Finding findingSelected = null;
 		for (Annotation annotation : documentAnnotations.getRelevantSentences()) {
@@ -159,7 +137,7 @@ public class DocumentServiceImpl implements DocumentService {
 		}
 		if(findingSelected!=null) {
 			//https://stackoverflow.com/questions/47699646/updating-replacing-a-deeply-nested-object-in-mongodb-with-spring-data-mongodb
-			findingSelected.setStatus("rejected");
+			findingSelected.setStatus(status);
 			documentAnnotationsRepository.save(documentAnnotations);
 			return true;
 		}
@@ -288,127 +266,84 @@ public class DocumentServiceImpl implements DocumentService {
 		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"));
 		for (Finding finding : documentAnnotations.getFindings()) {
-			//STUDYID -- > Study Identifier  
-			retStr.append(id);
-			retStr.append("|");
-			//DOMAIN  -- > Domain Abbreviation, always SR 
-			retStr.append("SR");
-			retStr.append("|");
-			//SRSEQ  -- > Sequence number
-			retStr.append("");
-			retStr.append("|");
-			//SRRISK --> Effect Level Associated with a Group/Sex, NOEL, LOEL, NOAEL, LOAEL, HNSTD, STD, MTD 
-			retStr.append(finding.getRisk_level()==null?"":finding.getRisk_level().getValue());
-			retStr.append("|");
-			//SPGRPCD --> Sponsor-defined Group Code, group 1 , A 
-			retStr.append(finding.getGroup()==null?"":finding.getGroup().getValue());
-			retStr.append("|");
-			//GRPLBL --> Sponsor-defined Group Name, "low dose", "mid dose"
-			retStr.append(finding.getGroup()==null?"":finding.getGroup().getValue());
-			retStr.append("|");
-			//SRGRPDOS --> Group Dose Level, "20 mg/kg"
-			retStr.append(finding.getGroup()==null?"":finding.getGroup().getValue());
-			retStr.append("|");
-			//SRSEX -- > Sex
-			retStr.append(finding.getSex()==null?"":finding.getSex().getValue());
-			retStr.append("|");
-			//SRSTDY --> Study Day of Start of Finding
-			retStr.append("");
-			retStr.append("|");
-			//SRSTPHSE --> Study Phase of first Observation, “PRE-DOSING”, “DOSING”, “RECOVERY”
-			retStr.append("");
-			retStr.append("|");
-			//SROBSTDY --> Start Phase Day of Observation
-			retStr.append("");
-			retStr.append("|");
-			//SRENPHSE -->Study Phase of last Observation
-			retStr.append("");
-			retStr.append("|");
-			//SRDOMAIN --> Domain of Finding
-			retStr.append(finding.getStudy_domain()==null?"":finding.getStudy_domain().getValue());
-			retStr.append("|");
-			//SRSPEC --> Specimen of Finding
-			retStr.append(finding.getSpecimen()==null?"":finding.getSpecimen().getValue());
-			retStr.append("|");
-			//SRTSTCD --> Test Short Name
-			retStr.append(finding.getStudy_testcd()==null?"":finding.getStudy_testcd().getValue());
-			retStr.append("|");
-			//SRFNDG --> Finding
-			retStr.append(finding.getFinding()==null?"":finding.getFinding().getValue());
-			retStr.append("|");
-			//SRORES --> Observation (original result)
-			retStr.append(finding.getFinding()==null?"":finding.getFinding().getValue());
-			retStr.append("|");
-			//SROBSV --> Manifestation of Finding, “I” (Increase), “D” (Decrease), “P” (Present) or “A” (Absent)
-			retStr.append(finding.getManifestation_finding()==null?"":finding.getManifestation_finding().getValue());
-			retStr.append("|");
-			//SROBSQ --> Observation Qualifier, “R” (Reversible), “T” (Transient) or ‘none’
-			retStr.append(finding.getObservation_qualification()==null?"":finding.getObservation_qualification().getValue());
-			retStr.append("|");
-			//SRSEV --> Severity of Finding
-			retStr.append("");
-			retStr.append("|");
-			//SRPCNT --> Scale of this Finding
-			retStr.append("");
-			retStr.append("|");
-			//SRSIGF --> Statistical Significance
-			retStr.append(finding.getStatistical_significance()==null?"":finding.getStatistical_significance().getValue());
-			retStr.append("|");
-			//SRTRTEF --> Treatment-Related
-			retStr.append(finding.getIs_treatment_related()==null?"":finding.getIs_treatment_related().getValue());
-			retStr.append("|");
-			//SRCOMNT --> Comment
-			retStr.append("\n");
+			for (SRDomainFinding srDomainFinding : finding.getSrDomainFindings()) {
+				//STUDYID -- > Study Identifier  
+				retStr.append(id);
+				retStr.append("|");
+				//DOMAIN  -- > Domain Abbreviation, always SR 
+				retStr.append("SR");
+				retStr.append("|");
+				//SRSEQ  -- > Sequence number
+				retStr.append("");
+				retStr.append("|");
+				//SRRISK --> Effect Level Associated with a Group/Sex, NOEL, LOEL, NOAEL, LOAEL, HNSTD, STD, MTD 
+				retStr.append(srDomainFinding.getSRRISK()==null?"":srDomainFinding.getSRRISK());
+				retStr.append("|");
+				//SPGRPCD --> Sponsor-defined Group Code, group 1 , A 
+				retStr.append(srDomainFinding.getSPGRPCD()==null?"":srDomainFinding.getSPGRPCD());
+				retStr.append("|");
+				//GRPLBL --> Sponsor-defined Group Name, "low dose", "mid dose"
+				retStr.append(srDomainFinding.getGRPLBL()==null?"":srDomainFinding.getGRPLBL());
+				retStr.append("|");
+				//SRGRPDOS --> Group Dose Level, "20 mg/kg"
+				retStr.append(srDomainFinding.getSRGRPDOS()==null?"":srDomainFinding.getSRGRPDOS());
+				retStr.append("|");
+				//SRSEX -- > Sex
+				retStr.append(srDomainFinding.getSRSEX()==null?"":srDomainFinding.getSRSEX());
+				retStr.append("|");
+				//SRSTDY --> Study Day of Start of Finding
+				retStr.append("");
+				retStr.append("|");
+				//SRSTPHSE --> Study Phase of first Observation, “PRE-DOSING”, “DOSING”, “RECOVERY”
+				retStr.append("");
+				retStr.append("|");
+				//SROBSTDY --> Start Phase Day of Observation
+				retStr.append("");
+				retStr.append("|");
+				//SRENPHSE -->Study Phase of last Observation
+				retStr.append("");
+				retStr.append("|");
+				//SRDOMAIN --> Domain of Finding
+				retStr.append(srDomainFinding.getSRDOMAIN()==null?"":srDomainFinding.getSRDOMAIN());
+				retStr.append("|");
+				//SRSPEC --> Specimen of Finding
+				retStr.append(srDomainFinding.getSRSPEC()==null?"":srDomainFinding.getSRSPEC());
+				retStr.append("|");
+				//SRTSTCD --> Test Short Name
+				retStr.append(srDomainFinding.getSRTSTCD()==null?"":srDomainFinding.getSRTSTCD());
+				retStr.append("|");
+				//SRFNDG --> Finding
+				retStr.append(srDomainFinding.getSRFNDG()==null?"":srDomainFinding.getSRFNDG());
+				retStr.append("|");
+				//SRORES --> Observation (original result)
+				retStr.append(srDomainFinding.getSRORES()==null?"":srDomainFinding.getSRORES());
+				retStr.append("|");
+				//SROBSV --> Manifestation of Finding, “I” (Increase), “D” (Decrease), “P” (Present) or “A” (Absent)
+				retStr.append(srDomainFinding.getSROBSV()==null?"":srDomainFinding.getSROBSV());
+				retStr.append("|");
+				//SROBSQ --> Observation Qualifier, “R” (Reversible), “T” (Transient) or ‘none’
+				retStr.append(srDomainFinding.getSROBSQ()==null?"":srDomainFinding.getSROBSQ());
+				retStr.append("|");
+				//SRSEV --> Severity of Finding
+				retStr.append("");
+				retStr.append("|");
+				//SRPCNT --> Scale of this Finding
+				retStr.append("");
+				retStr.append("|");
+				//SRSIGF --> Statistical Significance
+				retStr.append(srDomainFinding.getSRSIGF()==null?"":srDomainFinding.getSRSIGF());
+				retStr.append("|");
+				//SRTRTEF --> Treatment-Related
+				retStr.append(srDomainFinding.getSRTRTEF()==null?"":srDomainFinding.getSRTRTEF());
+				retStr.append("|");
+				//SRCOMNT --> Comment
+				retStr.append("\n");
+			}
+			
 		}
 		return retStr.toString().getBytes(Charset.forName("UTF-8"));
 	}
 	
-	
-	/**
-	 * Create a plain text file with the given string
-	 * @param path
-	 * @param plainText
-	 * @throws FileNotFoundException
-	 * @throws IOException
-	 */
-	private void createTxtFile(String path, String plainText) throws FileNotFoundException, IOException {
-		File fout = new File(path);
-		FileOutputStream fos = new FileOutputStream(fout);
-		BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(fos,StandardCharsets.UTF_8));
-		bw.write(plainText);
-		bw.flush();
-		bw.close();
-	}
-	
-//	/**
-//	 * 
-//	 * @param text
-//	 * @param findingSelected
-//	 * @return
-//	 */
-//	private String generateFindingSnippet(String text, Finding findingSelected) {
-//		System.out.println(text);
-//		Integer offsetSlicing = 0;
-//		
-//		List<Annotation> all = findingSelected.generateSortedAnnotations();
-//		Collections.sort(all);
-//		
-//		Annotation relevant_text = findingSelected.getRelevant_text();
-//		String init_ = "<span class='relevant_text'>";
-//		String end_ = "</span>"; 
-//		
-//		text = text.toString().substring(0, relevant_text.getStartOffset()) + init_ + relevant_text.getText() +  end_ + text.toString().substring(relevant_text.getEndOffset());
-//		offsetSlicing = init_.length();
-//		Object[] data = {text, offsetSlicing};
-//		for (Annotation annotation : all) {
-//			if(!annotationSuperposition(annotation, all)) {
-//				data = addColorToAnnotation(data, this.getAnnotationStyleClass(annotation), annotation);
-//			}
-//			System.out.println(data[0]);
-//		}
-//		return data[0].toString();
-//	}
-
 	/**
 	 * 
 	 * @param text
-- 
GitLab


From 310ae6dbfa003672e7f0b2288fa98f71594bcf79 Mon Sep 17 00:00:00 2001
From: javi <javicorvi@gmail.com>
Date: Tue, 22 Jun 2021 16:52:28 +0200
Subject: [PATCH 03/11] export srdomain finding

---
 .../api/controllers/DocumentController.java     |  8 ++++----
 .../ades/rest/api/services/DocumentService.java |  2 +-
 .../rest/api/services/DocumentServiceImpl.java  | 17 ++++++++++-------
 3 files changed, 15 insertions(+), 12 deletions(-)

diff --git a/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java b/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
index 426b2e0..ff77bbe 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
@@ -56,15 +56,15 @@ public class DocumentController {
 		return "";
 	}
 	
-	@RequestMapping("/documents/{id}/exportFinding/{findingId}/{export_finding}")
-	public String setExportFinding(@PathVariable(value="id") Long id, @PathVariable(value="findingId") Integer findingId, @PathVariable(value="export_finding") String export_finding) {
-		documentService.setExportFinding(id, findingId, export_finding);
+	@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);
 		return "true";
 	}
 	
 	@RequestMapping("/documents/{id}/findingValidation/{findingId}/{status}")
 	public String setFindingValidation(@PathVariable(value="id") Long id, @PathVariable(value="findingId") Integer findingId, @PathVariable(value="export_finding") String export_finding) {
-		documentService.setExportFinding(id, findingId, export_finding);
+		documentService.setFindingValidation(id, findingId, export_finding);
 		return "true";
 	}
 	
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java
index 192a195..dd2f6bf 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java
@@ -28,7 +28,7 @@ public interface DocumentService  {
 
 	String findFindingsEvidenceByDocumentId(Long id);
 
-	Boolean setExportFinding(Long id, Integer findingId, String export_finding);
+	Boolean setExportSRDomainFinding(Long id, Integer findingId, Boolean export_srdomain);
 	
 	Boolean setFindingValidation(Long id, Integer findingId,String status);
 }
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
index 1f4431a..2661813 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
@@ -145,20 +145,23 @@ public class DocumentServiceImpl implements DocumentService {
 	}
 	
 	@Override
-	public Boolean setExportFinding(Long id, Integer findingId,String export_finding) {
+	public Boolean setExportSRDomainFinding(Long id, Integer srDomainId,Boolean export_srdomainfinding) {
 		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
-		Finding findingSelected = null;
+		SRDomainFinding sRDomainFindingSelected = null;
 		for (Annotation annotation : documentAnnotations.getRelevantSentences()) {
 			for (Finding finding : annotation.getFindings()) {
-				if(finding.getFindingId().equals(findingId)) {
-					findingSelected = finding;
-					break;
+				for (SRDomainFinding srDomainFinding : finding.getSrDomainFindings()) {
+					if(srDomainFinding.getSrDomainId().equals(srDomainId)) {
+						sRDomainFindingSelected = srDomainFinding;
+						break;
+					}
 				}
+				
 			}
 		}
-		if(findingSelected!=null) {
+		if(sRDomainFindingSelected!=null) {
 			//https://stackoverflow.com/questions/47699646/updating-replacing-a-deeply-nested-object-in-mongodb-with-spring-data-mongodb
-			findingSelected.setExport(export_finding);
+			sRDomainFindingSelected.setExport(export_srdomainfinding);
 			documentAnnotationsRepository.save(documentAnnotations);
 			return true;
 		}
-- 
GitLab


From 5548b059293bbaf214de193f39a6ccb09bcb20a2 Mon Sep 17 00:00:00 2001
From: javi <javicorvi@gmail.com>
Date: Tue, 22 Jun 2021 16:52:28 +0200
Subject: [PATCH 04/11] export srdomain finding and validation

---
 .../api/controllers/DocumentController.java   |  10 +-
 .../rest/api/services/DocumentService.java    |   2 +-
 .../api/services/DocumentServiceImpl.java     | 172 +++++++++---------
 3 files changed, 96 insertions(+), 88 deletions(-)

diff --git a/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java b/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
index 426b2e0..db310da 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
@@ -56,15 +56,15 @@ public class DocumentController {
 		return "";
 	}
 	
-	@RequestMapping("/documents/{id}/exportFinding/{findingId}/{export_finding}")
-	public String setExportFinding(@PathVariable(value="id") Long id, @PathVariable(value="findingId") Integer findingId, @PathVariable(value="export_finding") String export_finding) {
-		documentService.setExportFinding(id, findingId, export_finding);
+	@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);
 		return "true";
 	}
 	
 	@RequestMapping("/documents/{id}/findingValidation/{findingId}/{status}")
-	public String setFindingValidation(@PathVariable(value="id") Long id, @PathVariable(value="findingId") Integer findingId, @PathVariable(value="export_finding") String export_finding) {
-		documentService.setExportFinding(id, findingId, export_finding);
+	public String setFindingValidation(@PathVariable(value="id") Long id, @PathVariable(value="findingId") Integer findingId, @PathVariable(value="status") String status) {
+		documentService.setFindingValidation(id, findingId, status);
 		return "true";
 	}
 	
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java
index 192a195..dd2f6bf 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentService.java
@@ -28,7 +28,7 @@ public interface DocumentService  {
 
 	String findFindingsEvidenceByDocumentId(Long id);
 
-	Boolean setExportFinding(Long id, Integer findingId, String export_finding);
+	Boolean setExportSRDomainFinding(Long id, Integer findingId, Boolean export_srdomain);
 	
 	Boolean setFindingValidation(Long id, Integer findingId,String status);
 }
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
index 1f4431a..0063164 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
@@ -111,9 +111,11 @@ public class DocumentServiceImpl implements DocumentService {
 		Document document = this.findByDocumentId(id);
 		Finding findingSelected = null;
 		for (Finding finding : documentAnnotations.getFindings()) {
-			if(finding.getFindingId().equals(findingId)) {
-				findingSelected = finding;
-				break;
+			if(finding.getSrDomainFindings()!=null) {
+				if(finding.getFindingId().equals(findingId)) {
+					findingSelected = finding;
+					break;
+				}
 			}
 		}
 		
@@ -145,20 +147,23 @@ public class DocumentServiceImpl implements DocumentService {
 	}
 	
 	@Override
-	public Boolean setExportFinding(Long id, Integer findingId,String export_finding) {
+	public Boolean setExportSRDomainFinding(Long id, Integer srDomainId,Boolean export_srdomainfinding) {
 		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
-		Finding findingSelected = null;
+		SRDomainFinding sRDomainFindingSelected = null;
 		for (Annotation annotation : documentAnnotations.getRelevantSentences()) {
 			for (Finding finding : annotation.getFindings()) {
-				if(finding.getFindingId().equals(findingId)) {
-					findingSelected = finding;
-					break;
+				for (SRDomainFinding srDomainFinding : finding.getSrDomainFindings()) {
+					if(srDomainFinding.getSrDomainId().equals(srDomainId)) {
+						sRDomainFindingSelected = srDomainFinding;
+						break;
+					}
 				}
+				
 			}
 		}
-		if(findingSelected!=null) {
+		if(sRDomainFindingSelected!=null) {
 			//https://stackoverflow.com/questions/47699646/updating-replacing-a-deeply-nested-object-in-mongodb-with-spring-data-mongodb
-			findingSelected.setExport(export_finding);
+			sRDomainFindingSelected.setExport(export_srdomainfinding);
 			documentAnnotationsRepository.save(documentAnnotations);
 			return true;
 		}
@@ -266,80 +271,83 @@ public class DocumentServiceImpl implements DocumentService {
 		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"));
 		for (Finding finding : documentAnnotations.getFindings()) {
-			for (SRDomainFinding srDomainFinding : finding.getSrDomainFindings()) {
-				//STUDYID -- > Study Identifier  
-				retStr.append(id);
-				retStr.append("|");
-				//DOMAIN  -- > Domain Abbreviation, always SR 
-				retStr.append("SR");
-				retStr.append("|");
-				//SRSEQ  -- > Sequence number
-				retStr.append("");
-				retStr.append("|");
-				//SRRISK --> Effect Level Associated with a Group/Sex, NOEL, LOEL, NOAEL, LOAEL, HNSTD, STD, MTD 
-				retStr.append(srDomainFinding.getSRRISK()==null?"":srDomainFinding.getSRRISK());
-				retStr.append("|");
-				//SPGRPCD --> Sponsor-defined Group Code, group 1 , A 
-				retStr.append(srDomainFinding.getSPGRPCD()==null?"":srDomainFinding.getSPGRPCD());
-				retStr.append("|");
-				//GRPLBL --> Sponsor-defined Group Name, "low dose", "mid dose"
-				retStr.append(srDomainFinding.getGRPLBL()==null?"":srDomainFinding.getGRPLBL());
-				retStr.append("|");
-				//SRGRPDOS --> Group Dose Level, "20 mg/kg"
-				retStr.append(srDomainFinding.getSRGRPDOS()==null?"":srDomainFinding.getSRGRPDOS());
-				retStr.append("|");
-				//SRSEX -- > Sex
-				retStr.append(srDomainFinding.getSRSEX()==null?"":srDomainFinding.getSRSEX());
-				retStr.append("|");
-				//SRSTDY --> Study Day of Start of Finding
-				retStr.append("");
-				retStr.append("|");
-				//SRSTPHSE --> Study Phase of first Observation, “PRE-DOSING”, “DOSING”, “RECOVERY”
-				retStr.append("");
-				retStr.append("|");
-				//SROBSTDY --> Start Phase Day of Observation
-				retStr.append("");
-				retStr.append("|");
-				//SRENPHSE -->Study Phase of last Observation
-				retStr.append("");
-				retStr.append("|");
-				//SRDOMAIN --> Domain of Finding
-				retStr.append(srDomainFinding.getSRDOMAIN()==null?"":srDomainFinding.getSRDOMAIN());
-				retStr.append("|");
-				//SRSPEC --> Specimen of Finding
-				retStr.append(srDomainFinding.getSRSPEC()==null?"":srDomainFinding.getSRSPEC());
-				retStr.append("|");
-				//SRTSTCD --> Test Short Name
-				retStr.append(srDomainFinding.getSRTSTCD()==null?"":srDomainFinding.getSRTSTCD());
-				retStr.append("|");
-				//SRFNDG --> Finding
-				retStr.append(srDomainFinding.getSRFNDG()==null?"":srDomainFinding.getSRFNDG());
-				retStr.append("|");
-				//SRORES --> Observation (original result)
-				retStr.append(srDomainFinding.getSRORES()==null?"":srDomainFinding.getSRORES());
-				retStr.append("|");
-				//SROBSV --> Manifestation of Finding, “I” (Increase), “D” (Decrease), “P” (Present) or “A” (Absent)
-				retStr.append(srDomainFinding.getSROBSV()==null?"":srDomainFinding.getSROBSV());
-				retStr.append("|");
-				//SROBSQ --> Observation Qualifier, “R” (Reversible), “T” (Transient) or ‘none’
-				retStr.append(srDomainFinding.getSROBSQ()==null?"":srDomainFinding.getSROBSQ());
-				retStr.append("|");
-				//SRSEV --> Severity of Finding
-				retStr.append("");
-				retStr.append("|");
-				//SRPCNT --> Scale of this Finding
-				retStr.append("");
-				retStr.append("|");
-				//SRSIGF --> Statistical Significance
-				retStr.append(srDomainFinding.getSRSIGF()==null?"":srDomainFinding.getSRSIGF());
-				retStr.append("|");
-				//SRTRTEF --> Treatment-Related
-				retStr.append(srDomainFinding.getSRTRTEF()==null?"":srDomainFinding.getSRTRTEF());
-				retStr.append("|");
-				//SRCOMNT --> Comment
-				retStr.append("\n");
+			if(finding.getSrDomainFindings()!=null) {
+				for (SRDomainFinding srDomainFinding : finding.getSrDomainFindings()) {
+					//STUDYID -- > Study Identifier  
+					retStr.append(id);
+					retStr.append("|");
+					//DOMAIN  -- > Domain Abbreviation, always SR 
+					retStr.append("SR");
+					retStr.append("|");
+					//SRSEQ  -- > Sequence number
+					retStr.append("");
+					retStr.append("|");
+					//SRRISK --> Effect Level Associated with a Group/Sex, NOEL, LOEL, NOAEL, LOAEL, HNSTD, STD, MTD 
+					retStr.append(srDomainFinding.getSRRISK()==null?"":srDomainFinding.getSRRISK());
+					retStr.append("|");
+					//SPGRPCD --> Sponsor-defined Group Code, group 1 , A 
+					retStr.append(srDomainFinding.getSPGRPCD()==null?"":srDomainFinding.getSPGRPCD());
+					retStr.append("|");
+					//GRPLBL --> Sponsor-defined Group Name, "low dose", "mid dose"
+					retStr.append(srDomainFinding.getGRPLBL()==null?"":srDomainFinding.getGRPLBL());
+					retStr.append("|");
+					//SRGRPDOS --> Group Dose Level, "20 mg/kg"
+					retStr.append(srDomainFinding.getSRGRPDOS()==null?"":srDomainFinding.getSRGRPDOS());
+					retStr.append("|");
+					//SRSEX -- > Sex
+					retStr.append(srDomainFinding.getSRSEX()==null?"":srDomainFinding.getSRSEX());
+					retStr.append("|");
+					//SRSTDY --> Study Day of Start of Finding
+					retStr.append("");
+					retStr.append("|");
+					//SRSTPHSE --> Study Phase of first Observation, “PRE-DOSING”, “DOSING”, “RECOVERY”
+					retStr.append("");
+					retStr.append("|");
+					//SROBSTDY --> Start Phase Day of Observation
+					retStr.append("");
+					retStr.append("|");
+					//SRENPHSE -->Study Phase of last Observation
+					retStr.append("");
+					retStr.append("|");
+					//SRDOMAIN --> Domain of Finding
+					retStr.append(srDomainFinding.getSRDOMAIN()==null?"":srDomainFinding.getSRDOMAIN());
+					retStr.append("|");
+					//SRSPEC --> Specimen of Finding
+					retStr.append(srDomainFinding.getSRSPEC()==null?"":srDomainFinding.getSRSPEC());
+					retStr.append("|");
+					//SRTSTCD --> Test Short Name
+					retStr.append(srDomainFinding.getSRTSTCD()==null?"":srDomainFinding.getSRTSTCD());
+					retStr.append("|");
+					//SRFNDG --> Finding
+					retStr.append(srDomainFinding.getSRFNDG()==null?"":srDomainFinding.getSRFNDG());
+					retStr.append("|");
+					//SRORES --> Observation (original result)
+					retStr.append(srDomainFinding.getSRORES()==null?"":srDomainFinding.getSRORES());
+					retStr.append("|");
+					//SROBSV --> Manifestation of Finding, “I” (Increase), “D” (Decrease), “P” (Present) or “A” (Absent)
+					retStr.append(srDomainFinding.getSROBSV()==null?"":srDomainFinding.getSROBSV());
+					retStr.append("|");
+					//SROBSQ --> Observation Qualifier, “R” (Reversible), “T” (Transient) or ‘none’
+					retStr.append(srDomainFinding.getSROBSQ()==null?"":srDomainFinding.getSROBSQ());
+					retStr.append("|");
+					//SRSEV --> Severity of Finding
+					retStr.append("");
+					retStr.append("|");
+					//SRPCNT --> Scale of this Finding
+					retStr.append("");
+					retStr.append("|");
+					//SRSIGF --> Statistical Significance
+					retStr.append(srDomainFinding.getSRSIGF()==null?"":srDomainFinding.getSRSIGF());
+					retStr.append("|");
+					//SRTRTEF --> Treatment-Related
+					retStr.append(srDomainFinding.getSRTRTEF()==null?"":srDomainFinding.getSRTRTEF());
+					retStr.append("|");
+					//SRCOMNT --> Comment
+					retStr.append("\n");
+				}
 			}
 			
+			
 		}
 		return retStr.toString().getBytes(Charset.forName("UTF-8"));
 	}
-- 
GitLab


From f6c3b0f1c32c5c2962c865edbf54466f343c76ad Mon Sep 17 00:00:00 2001
From: javi <javicorvi@gmail.com>
Date: Wed, 23 Jun 2021 18:22:50 +0200
Subject: [PATCH 05/11] error in export

---
 .../api/services/DocumentServiceImpl.java     | 178 ++++++++----------
 1 file changed, 80 insertions(+), 98 deletions(-)

diff --git a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
index 0063164..06c4573 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
@@ -45,6 +45,8 @@ public class DocumentServiceImpl implements DocumentService {
 	@Autowired
 	public DocumentAnnotationsRepository documentAnnotationsRepository;
 	
+	static final Map<String, String> ANNOTATION_CLASS_STYLE = createMap();
+	
 	public List<Document> findAll() {
 		return documentRepository.findAllNamesByOrderByName();
 	}
@@ -85,25 +87,7 @@ public class DocumentServiceImpl implements DocumentService {
 		documentRepository.findByDocumentId(id);
 		return documentRepository.findByDocumentId(id);
 	}
-	
-	
-	static final Map<String, String> ANNOTATION_CLASS_STYLE = createMap();
-	
-//	@Override
-//	public String findTextSnippetByDocumentIdAndFindingId(Long id, Integer findingId) {
-//		Document document = this.findByDocumentId(id);
-//		Finding findingSelected = null;
-//		for (Finding finding : document.getFindings()) {
-//			if(finding.getFindingId().equals(findingId)) {
-//				findingSelected = finding;
-//				break;
-//			}
-//		}
-//		if(findingSelected!=null) {
-//			return this.generateFindingSnippet(document.getText(), findingSelected);
-//		}
-//		return "";
-//	}
+
 	
 	@Override
 	public String findTextSnippetByDocumentIdAndFindingId2(Long id, Integer findingId) {
@@ -111,12 +95,10 @@ public class DocumentServiceImpl implements DocumentService {
 		Document document = this.findByDocumentId(id);
 		Finding findingSelected = null;
 		for (Finding finding : documentAnnotations.getFindings()) {
-			if(finding.getSrDomainFindings()!=null) {
-				if(finding.getFindingId().equals(findingId)) {
+			if(finding.getFindingId().equals(findingId)) {
 					findingSelected = finding;
 					break;
 				}
-			}
 		}
 		
 		if(findingSelected!=null) {
@@ -270,84 +252,84 @@ public class DocumentServiceImpl implements DocumentService {
 		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"));
-		for (Finding finding : documentAnnotations.getFindings()) {
-			if(finding.getSrDomainFindings()!=null) {
-				for (SRDomainFinding srDomainFinding : finding.getSrDomainFindings()) {
-					//STUDYID -- > Study Identifier  
-					retStr.append(id);
-					retStr.append("|");
-					//DOMAIN  -- > Domain Abbreviation, always SR 
-					retStr.append("SR");
-					retStr.append("|");
-					//SRSEQ  -- > Sequence number
-					retStr.append("");
-					retStr.append("|");
-					//SRRISK --> Effect Level Associated with a Group/Sex, NOEL, LOEL, NOAEL, LOAEL, HNSTD, STD, MTD 
-					retStr.append(srDomainFinding.getSRRISK()==null?"":srDomainFinding.getSRRISK());
-					retStr.append("|");
-					//SPGRPCD --> Sponsor-defined Group Code, group 1 , A 
-					retStr.append(srDomainFinding.getSPGRPCD()==null?"":srDomainFinding.getSPGRPCD());
-					retStr.append("|");
-					//GRPLBL --> Sponsor-defined Group Name, "low dose", "mid dose"
-					retStr.append(srDomainFinding.getGRPLBL()==null?"":srDomainFinding.getGRPLBL());
-					retStr.append("|");
-					//SRGRPDOS --> Group Dose Level, "20 mg/kg"
-					retStr.append(srDomainFinding.getSRGRPDOS()==null?"":srDomainFinding.getSRGRPDOS());
-					retStr.append("|");
-					//SRSEX -- > Sex
-					retStr.append(srDomainFinding.getSRSEX()==null?"":srDomainFinding.getSRSEX());
-					retStr.append("|");
-					//SRSTDY --> Study Day of Start of Finding
-					retStr.append("");
-					retStr.append("|");
-					//SRSTPHSE --> Study Phase of first Observation, “PRE-DOSING”, “DOSING”, “RECOVERY”
-					retStr.append("");
-					retStr.append("|");
-					//SROBSTDY --> Start Phase Day of Observation
-					retStr.append("");
-					retStr.append("|");
-					//SRENPHSE -->Study Phase of last Observation
-					retStr.append("");
-					retStr.append("|");
-					//SRDOMAIN --> Domain of Finding
-					retStr.append(srDomainFinding.getSRDOMAIN()==null?"":srDomainFinding.getSRDOMAIN());
-					retStr.append("|");
-					//SRSPEC --> Specimen of Finding
-					retStr.append(srDomainFinding.getSRSPEC()==null?"":srDomainFinding.getSRSPEC());
-					retStr.append("|");
-					//SRTSTCD --> Test Short Name
-					retStr.append(srDomainFinding.getSRTSTCD()==null?"":srDomainFinding.getSRTSTCD());
-					retStr.append("|");
-					//SRFNDG --> Finding
-					retStr.append(srDomainFinding.getSRFNDG()==null?"":srDomainFinding.getSRFNDG());
-					retStr.append("|");
-					//SRORES --> Observation (original result)
-					retStr.append(srDomainFinding.getSRORES()==null?"":srDomainFinding.getSRORES());
-					retStr.append("|");
-					//SROBSV --> Manifestation of Finding, “I” (Increase), “D” (Decrease), “P” (Present) or “A” (Absent)
-					retStr.append(srDomainFinding.getSROBSV()==null?"":srDomainFinding.getSROBSV());
-					retStr.append("|");
-					//SROBSQ --> Observation Qualifier, “R” (Reversible), “T” (Transient) or ‘none’
-					retStr.append(srDomainFinding.getSROBSQ()==null?"":srDomainFinding.getSROBSQ());
-					retStr.append("|");
-					//SRSEV --> Severity of Finding
-					retStr.append("");
-					retStr.append("|");
-					//SRPCNT --> Scale of this Finding
-					retStr.append("");
-					retStr.append("|");
-					//SRSIGF --> Statistical Significance
-					retStr.append(srDomainFinding.getSRSIGF()==null?"":srDomainFinding.getSRSIGF());
-					retStr.append("|");
-					//SRTRTEF --> Treatment-Related
-					retStr.append(srDomainFinding.getSRTRTEF()==null?"":srDomainFinding.getSRTRTEF());
-					retStr.append("|");
-					//SRCOMNT --> Comment
-					retStr.append("\n");
+		for (Annotation relevantSentences : documentAnnotations.getRelevantSentences()) {
+			for (Finding finding : relevantSentences.getFindings()) {
+				if(finding.getSrDomainFindings()!=null) {
+					for (SRDomainFinding srDomainFinding : finding.getSrDomainFindings()) {
+						//STUDYID -- > Study Identifier  
+						retStr.append(id);
+						retStr.append("|");
+						//DOMAIN  -- > Domain Abbreviation, always SR 
+						retStr.append("SR");
+						retStr.append("|");
+						//SRSEQ  -- > Sequence number
+						retStr.append("");
+						retStr.append("|");
+						//SRRISK --> Effect Level Associated with a Group/Sex, NOEL, LOEL, NOAEL, LOAEL, HNSTD, STD, MTD 
+						retStr.append(srDomainFinding.getSRRISK()==null?"":srDomainFinding.getSRRISK());
+						retStr.append("|");
+						//SPGRPCD --> Sponsor-defined Group Code, group 1 , A 
+						retStr.append(srDomainFinding.getSPGRPCD()==null?"":srDomainFinding.getSPGRPCD());
+						retStr.append("|");
+						//GRPLBL --> Sponsor-defined Group Name, "low dose", "mid dose"
+						retStr.append(srDomainFinding.getGRPLBL()==null?"":srDomainFinding.getGRPLBL());
+						retStr.append("|");
+						//SRGRPDOS --> Group Dose Level, "20 mg/kg"
+						retStr.append(srDomainFinding.getSRGRPDOS()==null?"":srDomainFinding.getSRGRPDOS());
+						retStr.append("|");
+						//SRSEX -- > Sex
+						retStr.append(srDomainFinding.getSRSEX()==null?"":srDomainFinding.getSRSEX());
+						retStr.append("|");
+						//SRSTDY --> Study Day of Start of Finding
+						retStr.append("");
+						retStr.append("|");
+						//SRSTPHSE --> Study Phase of first Observation, “PRE-DOSING”, “DOSING”, “RECOVERY”
+						retStr.append("");
+						retStr.append("|");
+						//SROBSTDY --> Start Phase Day of Observation
+						retStr.append("");
+						retStr.append("|");
+						//SRENPHSE -->Study Phase of last Observation
+						retStr.append("");
+						retStr.append("|");
+						//SRDOMAIN --> Domain of Finding
+						retStr.append(srDomainFinding.getSRDOMAIN()==null?"":srDomainFinding.getSRDOMAIN());
+						retStr.append("|");
+						//SRSPEC --> Specimen of Finding
+						retStr.append(srDomainFinding.getSRSPEC()==null?"":srDomainFinding.getSRSPEC());
+						retStr.append("|");
+						//SRTSTCD --> Test Short Name
+						retStr.append(srDomainFinding.getSRTSTCD()==null?"":srDomainFinding.getSRTSTCD());
+						retStr.append("|");
+						//SRFNDG --> Finding
+						retStr.append(srDomainFinding.getSRFNDG()==null?"":srDomainFinding.getSRFNDG());
+						retStr.append("|");
+						//SRORES --> Observation (original result)
+						retStr.append(srDomainFinding.getSRORES()==null?"":srDomainFinding.getSRORES());
+						retStr.append("|");
+						//SROBSV --> Manifestation of Finding, “I” (Increase), “D” (Decrease), “P” (Present) or “A” (Absent)
+						retStr.append(srDomainFinding.getSROBSV()==null?"":srDomainFinding.getSROBSV());
+						retStr.append("|");
+						//SROBSQ --> Observation Qualifier, “R” (Reversible), “T” (Transient) or ‘none’
+						retStr.append(srDomainFinding.getSROBSQ()==null?"":srDomainFinding.getSROBSQ());
+						retStr.append("|");
+						//SRSEV --> Severity of Finding
+						retStr.append("");
+						retStr.append("|");
+						//SRPCNT --> Scale of this Finding
+						retStr.append("");
+						retStr.append("|");
+						//SRSIGF --> Statistical Significance
+						retStr.append(srDomainFinding.getSRSIGF()==null?"":srDomainFinding.getSRSIGF());
+						retStr.append("|");
+						//SRTRTEF --> Treatment-Related
+						retStr.append(srDomainFinding.getSRTRTEF()==null?"":srDomainFinding.getSRTRTEF());
+						retStr.append("|");
+						//SRCOMNT --> Comment
+						retStr.append("\n");
+					}
 				}
 			}
-			
-			
 		}
 		return retStr.toString().getBytes(Charset.forName("UTF-8"));
 	}
-- 
GitLab


From 1fe1c23e8c97c60b21136c7d8d315c6b31923744 Mon Sep 17 00:00:00 2001
From: jcorvi <javier.corvi@bsc.es>
Date: Thu, 12 Aug 2021 14:04:36 +0000
Subject: [PATCH 06/11] Update .gitlab-ci.yml

---
 .gitlab-ci.yml | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 54d6515..af566f4 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,8 +6,11 @@ stages:
 build_docker_image:
   stage: build
   script:
-    - docker login -u javicorvi -p $DOCKER_PASS
-    - docker build -t $DOCKER_BUILD .
-    - docker push $DOCKER_BUILD
+    #- docker login -u javicorvi -p $DOCKER_PASS
+    #- docker build -t registry.gitlab.bsc.es/ .
+    #- docker push $DOCKER_BUILD
+    - docker login -u gitlab-ci-token -p $CI_BUILD_TOKEN registry.gitlab.bsc.es
+    - docker build -t registry.gitlab.bsc.es/inb/etransafe/pretox-rest-api:develop .
+    - docker push registry.gitlab.bsc.es/inb/etransafe/pretox-rest-api:develop
   tags:
     - build
-- 
GitLab


From d13f8631a4677d098e7ab1ce947f8bfe7f1b0a10 Mon Sep 17 00:00:00 2001
From: jcorvi <javier.corvi@bsc.es>
Date: Wed, 29 Sep 2021 10:06:39 +0000
Subject: [PATCH 07/11] Update .gitlab-ci.yml

---
 .gitlab-ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index af566f4..70a6e6d 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -8,7 +8,7 @@ build_docker_image:
   script:
     #- docker login -u javicorvi -p $DOCKER_PASS
     #- docker build -t registry.gitlab.bsc.es/ .
-    #- docker push $DOCKER_BUILD
+    #- docker push $DOCKER_BUILD 
     - docker login -u gitlab-ci-token -p $CI_BUILD_TOKEN registry.gitlab.bsc.es
     - docker build -t registry.gitlab.bsc.es/inb/etransafe/pretox-rest-api:develop .
     - docker push registry.gitlab.bsc.es/inb/etransafe/pretox-rest-api:develop
-- 
GitLab


From cf19ecf7a1c1a986c5ecfa8fe9617154774b6cf3 Mon Sep 17 00:00:00 2001
From: jcorvi <javier.corvi@bsc.es>
Date: Wed, 29 Sep 2021 10:11:47 +0000
Subject: [PATCH 08/11] Update .gitlab-ci.yml

---
 .gitlab-ci.yml | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 70a6e6d..1b1a027 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,6 +1,8 @@
 variables:
-  DOCKER_USER: javicorvi
-  DOCKER_BUILD: $DOCKER_USER/$CI_PROJECT_NAME:$CI_COMMIT_REF_NAME
+  #DOCKER_USER: javicorvi
+  #DOCKER_BUILD: $DOCKER_USER/$CI_PROJECT_NAME:$CI_COMMIT_REF_NAME
+  DOCKER_REGISTRY: registry.gitlab.bsc.es
+  IMAGE_FULL_PATH: $DOCKER_REGISTRY/$CI_PROJECT_NAME:$CI_COMMIT_REF_NAME
 stages:
   - build
 build_docker_image:
@@ -9,8 +11,12 @@ build_docker_image:
     #- docker login -u javicorvi -p $DOCKER_PASS
     #- docker build -t registry.gitlab.bsc.es/ .
     #- docker push $DOCKER_BUILD 
-    - docker login -u gitlab-ci-token -p $CI_BUILD_TOKEN registry.gitlab.bsc.es
-    - docker build -t registry.gitlab.bsc.es/inb/etransafe/pretox-rest-api:develop .
-    - docker push registry.gitlab.bsc.es/inb/etransafe/pretox-rest-api:develop
+
+    #- docker login -u gitlab-ci-token -p $CI_BUILD_TOKEN $DOCKER_REGISTRY
+    #- docker build -t registry.gitlab.bsc.es/inb/etransafe/pretox-rest-api:develop .
+    #- docker push registry.gitlab.bsc.es/inb/etransafe/pretox-rest-api:develop
+     - docker login -u gitlab-ci-token -p $CI_BUILD_TOKEN $DOCKER_REGISTRY
+     - docker build -t $IMAGE_FULL_PATH .
+     - docker push $IMAGE_FULL_PATH
   tags:
     - build
-- 
GitLab


From 38d6aeab78eef216670dc215f669cdb567674624 Mon Sep 17 00:00:00 2001
From: jcorvi <javier.corvi@bsc.es>
Date: Wed, 29 Sep 2021 10:18:45 +0000
Subject: [PATCH 09/11] Update .gitlab-ci.yml

---
 .gitlab-ci.yml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 1b1a027..1c94154 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,8 +1,11 @@
 variables:
   #DOCKER_USER: javicorvi
   #DOCKER_BUILD: $DOCKER_USER/$CI_PROJECT_NAME:$CI_COMMIT_REF_NAME
+  
   DOCKER_REGISTRY: registry.gitlab.bsc.es
-  IMAGE_FULL_PATH: $DOCKER_REGISTRY/$CI_PROJECT_NAME:$CI_COMMIT_REF_NAME
+  #any doubts regarind gitlab ci cd enviroment variables go to 
+  #https://docs.gitlab.com/ee/ci/variables/predefined_variables.html
+  IMAGE_FULL_PATH: $DOCKER_REGISTRY/$CI_PROJECT_PATH:$CI_COMMIT_REF_NAME
 stages:
   - build
 build_docker_image:
-- 
GitLab


From e24606cc4925dfbb19e5c2fc765ec6c832cee9a4 Mon Sep 17 00:00:00 2001
From: Javi Corvi <javicorvi@gmail.com>
Date: Thu, 7 Oct 2021 15:56:45 +0200
Subject: [PATCH 10/11] development

---
 pom.xml                                       |  5 +++-
 .../api/controllers/DocumentController.java   |  7 ++++++
 .../ades/rest/api/security/WebController.java |  4 ++--
 .../basic/inmemory/AuthenticationBean.java    | 24 +++++++++++++++++++
 .../BasicAuthenticationController.java        | 17 +++++++++++++
 .../basic/inmemory/SecurityConfig.java        | 24 +++++++++++++++++++
 .../resources/application-prod.properties     |  5 ++--
 src/main/resources/application.properties     |  3 ++-
 8 files changed, 83 insertions(+), 6 deletions(-)
 create mode 100644 src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/AuthenticationBean.java
 create mode 100644 src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/BasicAuthenticationController.java
 create mode 100644 src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/SecurityConfig.java

diff --git a/pom.xml b/pom.xml
index 4563bf9..e875981 100644
--- a/pom.xml
+++ b/pom.xml
@@ -51,7 +51,10 @@
             <artifactId>spring-boot-devtools</artifactId>
             <optional>true</optional>
         </dependency>
-      	
+      	<dependency>
+			<groupId>org.springframework.boot</groupId>
+			<artifactId>spring-boot-starter-security</artifactId>
+		</dependency>
       	
 <!--       	<dependency>
 			<groupId>org.springframework.boot</groupId>
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java b/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
index 27c71b5..1e1b309 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
@@ -1,5 +1,6 @@
 package es.bsc.inb.ades.rest.api.controllers;
 
+import java.security.Principal;
 import java.util.List;
 
 import org.springframework.beans.factory.annotation.Autowired;
@@ -7,6 +8,7 @@ import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
+import org.springframework.ui.Model;
 import org.springframework.web.bind.annotation.CrossOrigin;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
@@ -23,6 +25,11 @@ public class DocumentController {
 	@Autowired
 	public DocumentService documentService;
 	
+	@RequestMapping("/api/v1/basicauth")
+    public String validateLogin(Model model, Principal principal) {
+        return "login correct";
+    }
+	
 	@RequestMapping("/documents/")
     public List<Document> findAll() {
         return documentService.findAll();
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/security/WebController.java b/src/main/java/es/bsc/inb/ades/rest/api/security/WebController.java
index fc69e4c..b675377 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/security/WebController.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/security/WebController.java
@@ -9,9 +9,9 @@ import java.security.Principal;
 @Controller
 public class WebController {
    
-    @RequestMapping("/")
+    @RequestMapping("/api/v1/nada")
     public String index(Model model, Principal principal) {
-        return "index";
+        return "login correct";
     }
     @GetMapping("/greeting")
     public String greeting(@RequestParam(name="name", required=false, defaultValue="World") String name, Model model) {
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/AuthenticationBean.java b/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/AuthenticationBean.java
new file mode 100644
index 0000000..7f26752
--- /dev/null
+++ b/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/AuthenticationBean.java
@@ -0,0 +1,24 @@
+package es.bsc.inb.ades.rest.api.security.basic.inmemory;
+
+public class AuthenticationBean {
+
+    private String message;
+
+    public AuthenticationBean(String message) {
+        this.message = message;
+    }
+
+    public String getMessage() {
+        return message;
+    }
+
+    public void setMessage(String message) {
+        this.message = message;
+    }
+
+    @Override
+    public String toString() {
+        return String.format("HelloWorldBean [message=%s]", message);
+    }
+
+}
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/BasicAuthenticationController.java b/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/BasicAuthenticationController.java
new file mode 100644
index 0000000..352acdb
--- /dev/null
+++ b/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/BasicAuthenticationController.java
@@ -0,0 +1,17 @@
+package es.bsc.inb.ades.rest.api.security.basic.inmemory;
+
+import org.springframework.web.bind.annotation.CrossOrigin;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.RestController;
+
+//Controller
+@CrossOrigin(origins={ "http://localhost:3000", "http://localhost:4200", "http://localhost:8081" })
+@RestController
+public class BasicAuthenticationController {
+
+  @GetMapping(path = "/basicauth")
+  public AuthenticationBean helloWorldBean() {
+      //throw new RuntimeException("Some Error has Happened! Contact Support at ***-***");
+      return new AuthenticationBean("You are authenticated");
+  }   
+}
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/SecurityConfig.java b/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/SecurityConfig.java
new file mode 100644
index 0000000..9cb1d90
--- /dev/null
+++ b/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/SecurityConfig.java
@@ -0,0 +1,24 @@
+package es.bsc.inb.ades.rest.api.security.basic.inmemory;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.http.HttpMethod;
+import org.springframework.security.config.annotation.authentication.builders.AuthenticationManagerBuilder;
+import org.springframework.security.config.annotation.web.builders.HttpSecurity;
+import org.springframework.security.config.annotation.web.configuration.WebSecurityConfigurerAdapter;
+
+@Configuration
+public class SecurityConfig extends WebSecurityConfigurerAdapter {
+	@Override
+	protected void configure(HttpSecurity http) throws Exception {
+		http.csrf().disable().
+
+				authorizeRequests().antMatchers(HttpMethod.OPTIONS, "/**").permitAll().anyRequest().authenticated()
+				.and().httpBasic();
+	}
+
+	@Autowired
+	public void configureGlobal(AuthenticationManagerBuilder auth) throws Exception {
+		auth.inMemoryAuthentication().withUser("admin").password("{noop}password").roles("USER");
+	}
+}
diff --git a/src/main/resources/application-prod.properties b/src/main/resources/application-prod.properties
index 840722d..289eaea 100644
--- a/src/main/resources/application-prod.properties
+++ b/src/main/resources/application-prod.properties
@@ -1,5 +1,6 @@
 spring.application.name =ades_rest_api
 #Spring Boot Port
 server.port = ${SERVER_PORT}
-#ADES Database
-spring.data.mongodb.uri=${MONGO_URI}/etransafe
+#PRETOX Database
+spring.data.mongodb.uri=${MONGO_URI}
+
diff --git a/src/main/resources/application.properties b/src/main/resources/application.properties
index 559622b..8da406d 100644
--- a/src/main/resources/application.properties
+++ b/src/main/resources/application.properties
@@ -3,7 +3,8 @@ spring.application.name =ades_rest_api
 #server.port = ${SERVER_PORT}
 server.port = 8090
 #ADES Database
-spring.data.mongodb.uri=mongodb://localhost:27017/etransafe
+#spring.data.mongodb.uri=mongodb://localhost:27017/etransafe
+spring.data.mongodb.uri=mongodb://etransafe_rw:etransafe_rw2019!@mdb-login.bsc.es:27017/etransafe
 #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
 
-- 
GitLab


From 3ae8d83926b9fa63058f1c04a5f28fb2540bdc4f Mon Sep 17 00:00:00 2001
From: Javi Corvi <javicorvi@gmail.com>
Date: Fri, 8 Oct 2021 00:31:39 +0200
Subject: [PATCH 11/11] rest api development

---
 .../api/controllers/DocumentController.java   |  10 +-
 .../ades/rest/api/model/SRDomainFinding.java  |   1 +
 .../BasicAuthenticationController.java        |   2 +-
 .../basic/inmemory/SecurityConfig.java        |   3 +-
 .../api/services/DocumentServiceImpl.java     | 145 +++++++++---------
 5 files changed, 80 insertions(+), 81 deletions(-)

diff --git a/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java b/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
index 1e1b309..78e0231 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/controllers/DocumentController.java
@@ -1,6 +1,5 @@
 package es.bsc.inb.ades.rest.api.controllers;
 
-import java.security.Principal;
 import java.util.List;
 
 import org.springframework.beans.factory.annotation.Autowired;
@@ -8,28 +7,23 @@ import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
-import org.springframework.ui.Model;
 import org.springframework.web.bind.annotation.CrossOrigin;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
 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.services.DocumentService;
 
 
 @RestController
-@CrossOrigin
+@CrossOrigin()
 public class DocumentController {
 	
 	@Autowired
 	public DocumentService documentService;
 	
-	@RequestMapping("/api/v1/basicauth")
-    public String validateLogin(Model model, Principal principal) {
-        return "login correct";
-    }
-	
 	@RequestMapping("/documents/")
     public List<Document> findAll() {
         return documentService.findAll();
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/model/SRDomainFinding.java b/src/main/java/es/bsc/inb/ades/rest/api/model/SRDomainFinding.java
index 57fa5a5..8fd8423 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/model/SRDomainFinding.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/model/SRDomainFinding.java
@@ -200,6 +200,7 @@ public class SRDomainFinding implements Cloneable{
 	
 	
 	public Boolean getExport() {
+		if(export==null)return true;
 		return export;
 	}
 	public void setExport(Boolean export) {
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/BasicAuthenticationController.java b/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/BasicAuthenticationController.java
index 352acdb..0140397 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/BasicAuthenticationController.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/BasicAuthenticationController.java
@@ -5,7 +5,7 @@ import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.RestController;
 
 //Controller
-@CrossOrigin(origins={ "http://localhost:3000", "http://localhost:4200", "http://localhost:8081" })
+@CrossOrigin()
 @RestController
 public class BasicAuthenticationController {
 
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/SecurityConfig.java b/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/SecurityConfig.java
index 9cb1d90..0eeddfa 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/SecurityConfig.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/security/basic/inmemory/SecurityConfig.java
@@ -11,7 +11,8 @@ import org.springframework.security.config.annotation.web.configuration.WebSecur
 public class SecurityConfig extends WebSecurityConfigurerAdapter {
 	@Override
 	protected void configure(HttpSecurity http) throws Exception {
-		http.csrf().disable().
+		        http.cors().and().csrf().disable().
+		        //http.csrf().disable().
 
 				authorizeRequests().antMatchers(HttpMethod.OPTIONS, "/**").permitAll().anyRequest().authenticated()
 				.and().httpBasic();
diff --git a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
index 06c4573..708879a 100644
--- a/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
+++ b/src/main/java/es/bsc/inb/ades/rest/api/services/DocumentServiceImpl.java
@@ -256,77 +256,80 @@ public class DocumentServiceImpl implements DocumentService {
 			for (Finding finding : relevantSentences.getFindings()) {
 				if(finding.getSrDomainFindings()!=null) {
 					for (SRDomainFinding srDomainFinding : finding.getSrDomainFindings()) {
-						//STUDYID -- > Study Identifier  
-						retStr.append(id);
-						retStr.append("|");
-						//DOMAIN  -- > Domain Abbreviation, always SR 
-						retStr.append("SR");
-						retStr.append("|");
-						//SRSEQ  -- > Sequence number
-						retStr.append("");
-						retStr.append("|");
-						//SRRISK --> Effect Level Associated with a Group/Sex, NOEL, LOEL, NOAEL, LOAEL, HNSTD, STD, MTD 
-						retStr.append(srDomainFinding.getSRRISK()==null?"":srDomainFinding.getSRRISK());
-						retStr.append("|");
-						//SPGRPCD --> Sponsor-defined Group Code, group 1 , A 
-						retStr.append(srDomainFinding.getSPGRPCD()==null?"":srDomainFinding.getSPGRPCD());
-						retStr.append("|");
-						//GRPLBL --> Sponsor-defined Group Name, "low dose", "mid dose"
-						retStr.append(srDomainFinding.getGRPLBL()==null?"":srDomainFinding.getGRPLBL());
-						retStr.append("|");
-						//SRGRPDOS --> Group Dose Level, "20 mg/kg"
-						retStr.append(srDomainFinding.getSRGRPDOS()==null?"":srDomainFinding.getSRGRPDOS());
-						retStr.append("|");
-						//SRSEX -- > Sex
-						retStr.append(srDomainFinding.getSRSEX()==null?"":srDomainFinding.getSRSEX());
-						retStr.append("|");
-						//SRSTDY --> Study Day of Start of Finding
-						retStr.append("");
-						retStr.append("|");
-						//SRSTPHSE --> Study Phase of first Observation, “PRE-DOSING”, “DOSING”, “RECOVERY”
-						retStr.append("");
-						retStr.append("|");
-						//SROBSTDY --> Start Phase Day of Observation
-						retStr.append("");
-						retStr.append("|");
-						//SRENPHSE -->Study Phase of last Observation
-						retStr.append("");
-						retStr.append("|");
-						//SRDOMAIN --> Domain of Finding
-						retStr.append(srDomainFinding.getSRDOMAIN()==null?"":srDomainFinding.getSRDOMAIN());
-						retStr.append("|");
-						//SRSPEC --> Specimen of Finding
-						retStr.append(srDomainFinding.getSRSPEC()==null?"":srDomainFinding.getSRSPEC());
-						retStr.append("|");
-						//SRTSTCD --> Test Short Name
-						retStr.append(srDomainFinding.getSRTSTCD()==null?"":srDomainFinding.getSRTSTCD());
-						retStr.append("|");
-						//SRFNDG --> Finding
-						retStr.append(srDomainFinding.getSRFNDG()==null?"":srDomainFinding.getSRFNDG());
-						retStr.append("|");
-						//SRORES --> Observation (original result)
-						retStr.append(srDomainFinding.getSRORES()==null?"":srDomainFinding.getSRORES());
-						retStr.append("|");
-						//SROBSV --> Manifestation of Finding, “I” (Increase), “D” (Decrease), “P” (Present) or “A” (Absent)
-						retStr.append(srDomainFinding.getSROBSV()==null?"":srDomainFinding.getSROBSV());
-						retStr.append("|");
-						//SROBSQ --> Observation Qualifier, “R” (Reversible), “T” (Transient) or ‘none’
-						retStr.append(srDomainFinding.getSROBSQ()==null?"":srDomainFinding.getSROBSQ());
-						retStr.append("|");
-						//SRSEV --> Severity of Finding
-						retStr.append("");
-						retStr.append("|");
-						//SRPCNT --> Scale of this Finding
-						retStr.append("");
-						retStr.append("|");
-						//SRSIGF --> Statistical Significance
-						retStr.append(srDomainFinding.getSRSIGF()==null?"":srDomainFinding.getSRSIGF());
-						retStr.append("|");
-						//SRTRTEF --> Treatment-Related
-						retStr.append(srDomainFinding.getSRTRTEF()==null?"":srDomainFinding.getSRTRTEF());
-						retStr.append("|");
-						//SRCOMNT --> Comment
-						retStr.append("\n");
+						if(srDomainFinding.getExport()) {
+							//STUDYID -- > Study Identifier  
+							retStr.append(id);
+							retStr.append("|");
+							//DOMAIN  -- > Domain Abbreviation, always SR 
+							retStr.append("SR");
+							retStr.append("|");
+							//SRSEQ  -- > Sequence number
+							retStr.append(srDomainFinding.getSRSEQ());
+							retStr.append("|");
+							//SRRISK --> Effect Level Associated with a Group/Sex, NOEL, LOEL, NOAEL, LOAEL, HNSTD, STD, MTD 
+							retStr.append(srDomainFinding.getSRRISK()==null?"":srDomainFinding.getSRRISK());
+							retStr.append("|");
+							//SPGRPCD --> Sponsor-defined Group Code, group 1 , A 
+							retStr.append(srDomainFinding.getSPGRPCD()==null?"":srDomainFinding.getSPGRPCD());
+							retStr.append("|");
+							//GRPLBL --> Sponsor-defined Group Name, "low dose", "mid dose"
+							retStr.append(srDomainFinding.getGRPLBL()==null?"":srDomainFinding.getGRPLBL());
+							retStr.append("|");
+							//SRGRPDOS --> Group Dose Level, "20 mg/kg"
+							retStr.append(srDomainFinding.getSRGRPDOS()==null?"":srDomainFinding.getSRGRPDOS());
+							retStr.append("|");
+							//SRSEX -- > Sex
+							retStr.append(srDomainFinding.getSRSEX()==null?"":srDomainFinding.getSRSEX());
+							retStr.append("|");
+							//SRSTDY --> Study Day of Start of Finding
+							retStr.append("");
+							retStr.append("|");
+							//SRSTPHSE --> Study Phase of first Observation, “PRE-DOSING”, “DOSING”, “RECOVERY”
+							retStr.append("");
+							retStr.append("|");
+							//SROBSTDY --> Start Phase Day of Observation
+							retStr.append("");
+							retStr.append("|");
+							//SRENPHSE -->Study Phase of last Observation
+							retStr.append("");
+							retStr.append("|");
+							//SRDOMAIN --> Domain of Finding
+							retStr.append(srDomainFinding.getSRDOMAIN()==null?"":srDomainFinding.getSRDOMAIN());
+							retStr.append("|");
+							//SRSPEC --> Specimen of Finding
+							retStr.append(srDomainFinding.getSRSPEC()==null?"":srDomainFinding.getSRSPEC());
+							retStr.append("|");
+							//SRTSTCD --> Test Short Name
+							retStr.append(srDomainFinding.getSRTSTCD()==null?"":srDomainFinding.getSRTSTCD());
+							retStr.append("|");
+							//SRFNDG --> Finding
+							retStr.append(srDomainFinding.getSRFNDG()==null?"":srDomainFinding.getSRFNDG());
+							retStr.append("|");
+							//SRORES --> Observation (original result)
+							retStr.append(srDomainFinding.getSRORES()==null?"":srDomainFinding.getSRORES());
+							retStr.append("|");
+							//SROBSV --> Manifestation of Finding, “I” (Increase), “D” (Decrease), “P” (Present) or “A” (Absent)
+							retStr.append(srDomainFinding.getSROBSV()==null?"":srDomainFinding.getSROBSV());
+							retStr.append("|");
+							//SROBSQ --> Observation Qualifier, “R” (Reversible), “T” (Transient) or ‘none’
+							retStr.append(srDomainFinding.getSROBSQ()==null?"":srDomainFinding.getSROBSQ());
+							retStr.append("|");
+							//SRSEV --> Severity of Finding
+							retStr.append("");
+							retStr.append("|");
+							//SRPCNT --> Scale of this Finding
+							retStr.append("");
+							retStr.append("|");
+							//SRSIGF --> Statistical Significance
+							retStr.append(srDomainFinding.getSRSIGF()==null?"":srDomainFinding.getSRSIGF());
+							retStr.append("|");
+							//SRTRTEF --> Treatment-Related
+							retStr.append(srDomainFinding.getSRTRTEF()==null?"":srDomainFinding.getSRTRTEF());
+							retStr.append("|");
+							//SRCOMNT --> Comment
+							retStr.append("\n");
+						}
+						
 					}
 				}
 			}
-- 
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