Merge branch 'allevidence' of https://gitlab.bsc.es/inb/etransafe/pretox-rest-api into allevidence

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

@@ -76,6 +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);
@@ -88,15 +94,22 @@ 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;
 	}
 	

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.
@@ -40,8 +44,31 @@ public class SRDomainFinding implements Cloneable{
 	private String SRTRTEF="";
 	private String SRCOMNT="";
 
+	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() {
-		return SRDOMAIN_DESC + "(" + SRDOMAIN + ")";
+		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() {
@@ -72,9 +99,7 @@ public class SRDomainFinding implements Cloneable{
 		return SRSPEC_DESC + "(" + SRSPEC + ")";
 	}
 	
-	private Boolean export;
-	private Integer findingId;
-	private Integer srDomainId;
+	
 	
 	public String getSTUDYID() {
 		return STUDYID;

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

@@ -30,12 +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/services/DocumentServiceImpl.java

@@ -128,8 +128,34 @@ public class DocumentServiceImpl implements DocumentService {
 		return false;
 	}
 	
+	@Override
+	public Boolean setValidationSRDomainFinding(Long id, Integer srDomainFindingId, String status) {
+		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
+		SRDomainFinding srDomainFindingelected = null;
+		for (Annotation annotation : documentAnnotations.getRelevantSentences()) {
+			for (Finding finding : annotation.getFindings()) {
+				for (SRDomainFinding srDomainFinding : finding.getSrDomainFindings()) {
+					if(srDomainFinding.getSrDomainId().equals(srDomainFindingId)) {
+						srDomainFindingelected = srDomainFinding;
+						break;
+					}
+				}
+				
+			}
+		}
+		if(srDomainFindingelected!=null) {
+			//https://stackoverflow.com/questions/47699646/updating-replacing-a-deeply-nested-object-in-mongodb-with-spring-data-mongodb
+			srDomainFindingelected.setStatus(status);
+			documentAnnotationsRepository.save(documentAnnotations);
+			createTracking(id, "admin",  Action.ACCEPT, srDomainFindingelected.getTrackingSummary());
+			return true;
+		}
+		return false;
+	}
+	
 	@Override
 	public Boolean setExportSRDomainFinding(Long id, Integer srDomainId,Boolean export_srdomainfinding) {
+		System.out.println("Entra:"+srDomainId);
 		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
 		SRDomainFinding sRDomainFindingSelected = null;
 		for (Annotation annotation : documentAnnotations.getRelevantSentences()) {
@@ -189,10 +215,20 @@ public class DocumentServiceImpl implements DocumentService {
 	 * Get Findings evidence from a document
 	 */
 	public String findFindingsEvidenceByDocumentId(Long id) {
+		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
+		Document document = this.findByDocumentId(id);
+		return this.generateAllFindingsEvidenceSnippet(document.getText(), documentAnnotations.getRelevantSentences());
+	}
+	
+	/**
+	 * Get Findings evidence from a document
+	 */
+	public String findAllEvidenceByDocumentId(Long id) {
 		DocumentAnnotations documentAnnotations = this.findDocumentAnnotationsByDocumentId(id);
 		Document document = this.findByDocumentId(id);
 		return this.generateAllEvidenceSnippet(document.getText(), documentAnnotations.getRelevantSentences());
 	}
+	
 	/**
 	 * Get relevant sentences evidence from a document
 	 */
@@ -610,6 +646,98 @@ public class DocumentServiceImpl implements DocumentService {
 		int a = 1;
 		int r = 1;
 		for (Annotation sentenceAnnotation : sentences) {
+			JsonArray values_sentence = new JsonArray();
+			//values_sentence.add("T"+t);
+			values_sentence.add("S"+sentenceAnnotation.getId());
+			values_sentence.add("RELEVANT_SENTENCE");
+			JsonArray offste_sentence = new JsonArray();
+			JsonArray offste2_sentence = new JsonArray();
+			offste_sentence.add(sentenceAnnotation.getStartOffset());
+			offste_sentence.add(sentenceAnnotation.getEndOffset());
+			offste2_sentence.add(offste_sentence);
+			values_sentence.add(offste2_sentence);
+			entities.add(values_sentence);
+			t++;
+			if(sentenceAnnotation.getFindings()!=null) {
+				for (Finding findingSelected : sentenceAnnotation.getFindings()) {
+					List<Annotation> all = findingSelected.generateSortedAnnotationsAll();
+					String id_finding = "";
+					for (Annotation annotation : all) {
+						JsonArray values = new JsonArray();
+						String type = annotation.getFeature("ANNOTATION_TYPE");
+						//String id = "T"+t;
+						String id = "E"+annotation.getId();
+						
+						//TODO source
+//						String source = annotation.getFeature("SOURCES");
+//						if(source!=null && !source.equals("")) {
+//							id = id + " - SOURCE: " + source;
+//						}
+//						values.add("T"+t+ " - SOURCE: " + source);
+						
+						values.add(id);
+						values.add(type);
+						JsonArray offste = new JsonArray();
+						JsonArray offste2 = new JsonArray();
+						offste.add(annotation.getStartOffset());
+						offste.add(annotation.getEndOffset());
+						offste2.add(offste);
+						values.add(offste2);
+						entities.add(values);
+						if(type.equals("FINDING") || type.equals("STUDY_TESTCD") ) {
+							id_finding = "T"+t;
+							JsonArray values_a = new JsonArray();
+							values_a.add("A"+a);
+							values_a.add("Notorious");
+							values_a.add(id_finding);
+							attributes.add(values_a);
+							a++;
+						}else {
+							JsonArray values_r = new JsonArray();
+							values_r.add("R"+r);
+							values_r.add("Relation");
+							JsonArray values_r_e = new JsonArray();
+							JsonArray values_r_e_v = new JsonArray();
+							values_r_e_v.add("Entity");
+							values_r_e_v.add(id_finding);
+							values_r_e.add(values_r_e_v);
+							JsonArray values_r_e_v_2 = new JsonArray();
+							values_r_e_v_2.add("Subentity");
+							values_r_e_v_2.add("T"+t);
+							values_r_e.add(values_r_e_v_2);
+							values_r.add(values_r_e);
+							relations.add(values_r);
+							r++;
+						}
+						t++;
+					}
+				}
+			}
+			
+		}
+		findings_evidence.add("entities", entities);
+		findings_evidence.add("attributes", attributes);
+		findings_evidence.add("relations", relations);
+		return gsonBuilder.toJson(findings_evidence).toString();
+	}
+	
+	/**
+	 * Generate the evidence of view all button.  
+	 * @param text
+	 * @param findingSelected
+	 * @return
+	 */
+	private String generateAllFindingsEvidenceSnippet(String text, List<Annotation> sentences) {
+		Gson gsonBuilder = new GsonBuilder().create();
+		JsonObject findings_evidence = new JsonObject();
+		findings_evidence.addProperty("text", text);
+		JsonArray entities = new JsonArray();
+		JsonArray attributes = new JsonArray();
+		JsonArray relations = new JsonArray();
+		int t = 1;
+		int a = 1;
+		int r = 1;
+		for (Annotation sentenceAnnotation : sentences) {
 //			JsonArray values_sentence = new JsonArray();
 //			values_sentence.add("T"+t);
 //			values_sentence.add("PRETOX_RELEVANT_SENTENCE");

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");
+	    
+	}};
+	
+	
 }