Merge branch 'develop' into 'master'

"Merge branch 'allevidence' into 'develop'"

See merge request !15

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

@@ -8,7 +8,6 @@ import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.CrossOrigin;
-import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RestController;
@@ -17,8 +16,6 @@ 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;
 
 
@@ -79,6 +76,12 @@ public class DocumentController {
 		return "true";
 	}
 	
+	@RequestMapping("/documents/{id}/srFindingValidation/{srDomainId}/{status}")
+	public String setSRFindingValidation(@PathVariable(value="id") Long id, @PathVariable(value="srDomainId") Integer srDomainId, @PathVariable(value="status") String status) {
+		documentService.setValidationSRDomainFinding(id, srDomainId, status);
+		return "true";
+	}
+	
 	@RequestMapping("/documents/{id}/findingValidation/{findingId}/{status}")
 	public String setFindingValidation(@PathVariable(value="id") Long id, @PathVariable(value="findingId") Integer findingId, @PathVariable(value="status") String status) {
 		documentService.setFindingValidation(id, findingId, status);
@@ -91,19 +94,37 @@ public class DocumentController {
 		return snippet;
 	}
 	
+	@RequestMapping("/documents/{id}/evidence/findings")
+	public String findAllFindingEvidence(@PathVariable(value="id") Long id) {
+		String snippet = documentService.findFindingsEvidenceByDocumentId(id);
+		return snippet;
+	}
+	
 	@RequestMapping("/documents/{id}/evidence/all")
 	public String findAllEvidence(@PathVariable(value="id") Long id) {
-		String snippet = documentService.findFindingsEvidenceByDocumentId(id);
+		String snippet = documentService.findAllEvidenceByDocumentId(id);
 		return snippet;
 	}
 	
+	@RequestMapping("/documents/{id}/evidence/sentences")
+	public String findSentencesEvidence(@PathVariable(value="id") Long id) {
+		String snippet = documentService.findSentencesEvidenceByDocumentId(id);
+		//String snippet = documentService.findAllEvidenceByDocumentId(id);
+		return snippet;
+	}
 	
-	@RequestMapping("/documents/{id}/finding2/{findingId}")
-	public String findFinding2(@PathVariable(value="id") Long id, @PathVariable(value="findingId") Integer findingId) {
-		String snippet = documentService.findTextSnippetByDocumentIdAndFindingId2(id, findingId);
+	@RequestMapping("/documents/{id}/text")
+	public String findDocumentText(@PathVariable(value="id") Long id) {
+		String snippet = documentService.findTextByDocumentId(id);
 		return snippet;
 	}
 	
+//	@RequestMapping("/documents/{id}/finding2/{findingId}")
+//	public String findFinding2(@PathVariable(value="id") Long id, @PathVariable(value="findingId") Integer findingId) {
+//		String snippet = documentService.findTextSnippetByDocumentIdAndFindingId2(id, findingId);
+//		return snippet;
+//	}
+	
 	@RequestMapping(value = "/documents/export/{id}")
     public ResponseEntity<byte[]> generateReport(@PathVariable("id") long documentId){
     	String filename = "Study_Report_" + documentId +".txt";

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

 package es.bsc.inb.ades.rest.api.model;
 
+import org.apache.tomcat.util.bcel.classfile.Constant;
+
+import es.bsc.inb.ades.rest.api.util.Constants;
+
 /**
  * This class describes a finding in SR-Domain format.
  * No textual evidence.
@@ -23,11 +27,16 @@ public class SRDomainFinding implements Cloneable{
 	private String SRENPHSE="";
 	private String SROBENDY="";
 	private String SRDOMAIN="";
+	private String SRDOMAIN_DESC="";
 	private String SRSPEC="";
+	private String SRSPEC_DESC="";
 	private String SRTSTCD="";
+	private String SRTSTCD_DESC="";
 	private String SRFNDG="";
+	private String SRFNDG_DESC="";
 	private String SRORES="";
 	private String SROBSV="";
+	private String SROBSV_DESC="";
 	private String SROBSQ="";
 	private String SRSEV="";
 	private String SRPCNT="";
@@ -38,6 +47,59 @@ public class SRDomainFinding implements Cloneable{
 	private Boolean export;
 	private Integer findingId;
 	private Integer srDomainId;
+	private String status="non_curated";
+	
+	
+	
+	
+	public String getStatus() {
+		return status;
+	}
+
+	public void setStatus(String status) {
+		this.status = status;
+	}
+
+	public String getSrdomain_value() {
+		if(Constants.SEND_DOMAIN_NAMES.get(SRDOMAIN)!=null) {
+			return Constants.SEND_DOMAIN_NAMES.get(SRDOMAIN) + "(" + SRDOMAIN + ")";
+		}else if(SRDOMAIN==null || SRDOMAIN.equals("")) {
+			return "";
+		}else {
+			return SRDOMAIN;
+		}
+		 
+	}
+	
+	public String getSrfndg_value() {
+		if(SRFNDG ==null || SRFNDG.equals("")) {
+			return SRORES;
+		}
+		return SRFNDG_DESC + "(" + SRFNDG + ")";
+	}
+	
+	public String getSrtstcd_value() {
+		if(SRTSTCD ==null || SRTSTCD.equals("")) {
+			return SRTSTCD_DESC;
+		}
+		return SRTSTCD_DESC + "(" + SRTSTCD + ")";
+	}
+	
+	public String getSrobsv_value() {
+		if(SROBSV ==null || SROBSV.equals("")) {
+			return SROBSV_DESC;
+		}
+		return SROBSV_DESC + "(" + SROBSV + ")";
+	}
+	
+	public String getSrspec_value() {
+		if(SRSPEC ==null || SRSPEC.equals("")) {
+			return SRSPEC_DESC;
+		}
+		return SRSPEC_DESC + "(" + SRSPEC + ")";
+	}
+	
+	
 	
 	public String getSTUDYID() {
 		return STUDYID;
@@ -156,9 +218,9 @@ public class SRDomainFinding implements Cloneable{
 	public String getSROBSV() {
 		return SROBSV;
 	}
-	public void setSROBSV(String sROBSV) {
-		SROBSV = sROBSV;
-	}
+	
+	
+	
 	public String getSROBSQ() {
 		return SROBSQ;
 	}
@@ -195,10 +257,41 @@ public class SRDomainFinding implements Cloneable{
 	public void setSRCOMNT(String sRCOMNT) {
 		SRCOMNT = sRCOMNT;
 	}
+	public void setSRDOMAIN_DESC(String sRDOMAIN_DESC) {
+		SRDOMAIN_DESC = sRDOMAIN_DESC;
+	}
+	public void setSROBSV(String sROBSV) {
+		SROBSV = sROBSV;
+	}
 	
+	public String getSRDOMAIN_DESC() {
+		return SRDOMAIN_DESC;
+	}
 	
-	
-	
+	public String getSRSPEC_DESC() {
+		return SRSPEC_DESC;
+	}
+	public void setSRSPEC_DESC(String sRSPEC_DESC) {
+		SRSPEC_DESC = sRSPEC_DESC;
+	}
+	public String getSRTSTCD_DESC() {
+		return SRTSTCD_DESC;
+	}
+	public void setSRTSTCD_DESC(String sRTSTCD_DESC) {
+		SRTSTCD_DESC = sRTSTCD_DESC;
+	}
+	public String getSRFNDG_DESC() {
+		return SRFNDG_DESC;
+	}
+	public void setSRFNDG_DESC(String sRFNDG_DESC) {
+		SRFNDG_DESC = sRFNDG_DESC;
+	}
+	public String getSROBSV_DESC() {
+		return SROBSV_DESC;
+	}
+	public void setSROBSV_DESC(String sROBSV_DESC) {
+		SROBSV_DESC = sROBSV_DESC;
+	}
 	public Boolean getExport() {
 		if(export==null)return true;
 		return export;

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

@@ -6,7 +6,6 @@ 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  {
@@ -17,7 +16,7 @@ public interface DocumentService  {
 
 	Document findByDocumentId2(Long id);
 	
-	String findTextSnippetByDocumentIdAndFindingId2(Long id, Integer findingId);
+	//String findTextSnippetByDocumentIdAndFindingId2(Long id, Integer findingId);
 	
 	String findFindingEvidenceByDocumentIdAndFindingId(Long id, Integer findingId);
 	
@@ -31,8 +30,16 @@ public interface DocumentService  {
 
 	String findFindingsEvidenceByDocumentId(Long id);
 	
+	String findAllEvidenceByDocumentId(Long id);
+	
+	String findSentencesEvidenceByDocumentId(Long id);
+	
+	String findTextByDocumentId(Long id);
+	
 	Boolean setExportSRDomainFinding(Long id, Integer findingId, Boolean export_srdomain);
 	
+	Boolean setValidationSRDomainFinding(Long id, Integer srDomainFindingId,String status);
+	
 	Boolean setFindingValidation(Long id, Integer findingId,String status);
 	
 	Status moveDocument(Long id, Status status);

src/main/java/es/bsc/inb/ades/rest/api/util/Constants.java

 package es.bsc.inb.ades.rest.api.util;
 
+import java.util.HashMap;
+import java.util.Map;
+
 public class Constants {
 
 	public static int  SLICE_START = 1000;
@@ -7,4 +10,26 @@ public class Constants {
 	public static int POINTS_INT = 5;
 	public static String POINTS = ".....";
 	
+	
+	public static Map<String, String> SEND_DOMAIN_NAMES = new HashMap<String, String>(){{
+	    put("LB", "Laboratory Test Results");
+	    put("BW", "Body Weight");
+	    put("BG", "Body Weight Gain");
+	    put("CV", "Cardiovascular Domain");
+	    put("CL", "Clinical");
+	    put("DD", "Death Diagnosis");
+	    put("EG", "ECG Test Results");
+	    put("FM", "Fetal Measurements");
+	    put("FW", "Food And Water");
+	    put("FX", "Fetal Pathology Findings");
+	    put("MA", "Macroscopic Findings");
+	    put("MI", "Microscopic Findings");
+	    put("OM", "Organ Measurements");
+	    put("RE", "Respiratory Findings");
+	    put("TF", "Tumor Findings");
+	    put("VS", "Vital Signs");
+	    
+	}};
+	
+	
 }