Merge branch 'develop' into 'master'

smaller term

See merge request !10

src/main/java/es/bsc/inb/nlp/gate/generic/component/util/AnnotationUtil.java

@@ -324,13 +324,18 @@ public  class AnnotationUtil {
 					}else {
 						first = false;
 					}
-					//add specimen to finding
-					Annotation specimen = as.get(new Integer(spe_id));
-					specimen.getFeatures().put(template_value_name, getSendCode(specimen, gate.Utils.stringFor(doc, specimen)));
-					specimen.getFeatures().put(send_code_name, getOnlySENDCode(specimen, gate.Utils.stringFor(doc, specimen)));
-					specimen.getFeatures().put(send_codelist_name, getOnlySENDCodeList(specimen, gate.Utils.stringFor(doc, specimen)));
-					specimen.getFeatures().put("ANNOTATION_TYPE",specimen.getType());
-					doc.getAnnotations(annotationSetRelationExtraction).add(specimen.getStartNode(), specimen.getEndNode(), "FINDING_"+finding_id, specimen.getFeatures());
+					try {
+						//add specimen to finding
+						Annotation specimen = as.get(new Integer(spe_id));
+						specimen.getFeatures().put(template_value_name, getSendCode(specimen, gate.Utils.stringFor(doc, specimen)));
+						specimen.getFeatures().put(send_code_name, getOnlySENDCode(specimen, gate.Utils.stringFor(doc, specimen)));
+						specimen.getFeatures().put(send_codelist_name, getOnlySENDCodeList(specimen, gate.Utils.stringFor(doc, specimen)));
+						specimen.getFeatures().put("ANNOTATION_TYPE",specimen.getType());
+						doc.getAnnotations(annotationSetRelationExtraction).add(specimen.getStartNode(), specimen.getEndNode(), "FINDING_"+finding_id, specimen.getFeatures());
+					}catch(Exception e) {
+						e.printStackTrace();
+					}
+					
 				}
 			}
 					
@@ -484,21 +489,6 @@ public  class AnnotationUtil {
 		return text;
 	}
 	
-	private static String getValueFinding(Annotation annotation, String text) {
-		String send_code = "";
-		if(annotation.getFeatures().get("MANUAL_SEND_CODE")!=null) {
-			send_code = annotation.getFeatures().get("MANUAL_SEND_CODE").toString();
-		}else if(annotation.getFeatures().get("CDISC_SEND_CODE")!=null) {
-			send_code = annotation.getFeatures().get("CDISC_SEND_CODE").toString();
-		}else if(annotation.getFeatures().get("ETOX_SEND_CODE")!=null) {
-			send_code = annotation.getFeatures().get("ETOX_SEND_CODE").toString();
-		}
-		if(!send_code.equals("")) {
-			return text+"("+send_code+")";
-		}
-		return text;
-	}
-	
 	private static String getOnlySENDCodeList(Annotation annotation, String text) {
 		String send_code = "";
 		if(annotation.getFeatures().get("MANUAL_CODELIST")!=null) {
@@ -507,6 +497,8 @@ public  class AnnotationUtil {
 			send_code = annotation.getFeatures().get("CDISC_CODELIST").toString();
 		}else if(annotation.getFeatures().get("ETOX_CODELIST")!=null) {
 			send_code = annotation.getFeatures().get("ETOX_CODELIST").toString();
+		}else if(annotation.getFeatures().get("SMALLER_TERM_CODELIST")!=null) {
+			send_code = annotation.getFeatures().get("SMALLER_TERM_CODELIST").toString();
 		}
 		return send_code;
 	}
@@ -528,6 +520,8 @@ public  class AnnotationUtil {
 			send_code = annotation.getFeatures().get("ETOX_SEND_DOMAIN_CODE").toString();
 		}else if(annotation.getFeatures().get("MANUAL_SEND_DOMAIN_CODE")!=null) {
 			send_code = annotation.getFeatures().get("MANUAL_SEND_DOMAIN_CODE").toString();
+		}else if(annotation.getFeatures().get("SMALLER_TERM_SEND_DOMAIN_CODE")!=null){
+			send_code = annotation.getFeatures().get("SMALLER_TERM_SEND_DOMAIN_CODE").toString();
 		}
 		return send_code;
 	}
@@ -547,6 +541,8 @@ public  class AnnotationUtil {
 			send_code = annotation.getFeatures().get("CDISC_SEND_CODE").toString();
 		}else if(annotation.getFeatures().get("ETOX_SEND_CODE")!=null) {
 			send_code = annotation.getFeatures().get("ETOX_SEND_CODE").toString();
+		}else if(annotation.getFeatures().get("SMALLER_TERM_SEND_CODE")!=null){
+			send_code = annotation.getFeatures().get("SMALLER_TERM_SEND_CODE").toString();
 		}
 		return send_code;