more improvement in study and specimen

dictionaries/postprocessing-and-lexical-rules-matching/stop_words_finding_hpath.lst

@@ -9,7 +9,6 @@ treatment-related
 treatment related
 alteration
 unilateral
-basophilic tubules
 mature
 lymphoid tissue
 bile

jape_rules/main.jape

@@ -50,6 +50,7 @@ relation-extraction/finding_group
 relation-extraction/finding_dose
 relation-extraction/finding_closest_sex
 relation-extraction/finding_specimen_advance
+relation-extraction/studytestcd_specimen_advance
 relation-extraction/finding_specimen
 relation-extraction/finding_manifestation
 relation-extraction/studytest_manifestation

jape_rules/postprocessing-and-lexical-rules-matching/remove_manifestation_findings_false_positive_no_finding.jape

@@ -24,8 +24,8 @@ Rule: delete_rule
 		AnnotationSet sentenceFields = inputAS.get(sentence.getStartNode().getOffset(), sentence.getEndNode().getOffset());	
 		AnnotationSet annotations_type = sentenceFields.get(types);
 		if(annotations_type==null || annotations_type.size()==0){
-			System.out.println("MANIFESTATION ALONE: " + stringFor(doc, manifestation));
-			System.out.println(stringFor(doc, sentence));
+			//System.out.println("MANIFESTATION ALONE: " + stringFor(doc, manifestation));
+			//System.out.println(stringFor(doc, sentence));
 			outputAS.remove(manifestation);
 		}
 	}

jape_rules/relation-extraction/finding_specimen_advance.jape

@@ -23,11 +23,11 @@ Rule: finding_specimen_advance
 			gate.AnnotationSet  specimen_entities = lookup.get("SPECIMEN");
 			gate.AnnotationSet  man_entities = lookup.get("FINDING");
 			gate.Annotation  finding_change = man_entities.iterator().next();
-			
+			String content = stringFor(doc, lookup.firstNode().getOffset(),lookup.lastNode().getOffset());
 			//System.out.println("FINDING:" + stringFor(doc, finding_change));
+			//System.out.println(content);
 			gate.FeatureMap features = finding_change.getFeatures();
- 			String content = stringFor(doc, lookup.firstNode().getOffset(),lookup.lastNode().getOffset());
- 		    features.put("text", stringFor(doc, finding_change));
+ 			features.put("text", stringFor(doc, finding_change));
 			features.put("rule", "FINDING_SPECIMEN");
 			Boolean first = true;
 			String spe_ids = "";

jape_rules/relation-extraction/studytestcd_specimen_advance.jape

+//this rule annotates findings orientated to detect MANIFESTATION OF FINDING Changes in a specimen
+Imports: {
+import static gate.Utils.*;
+}
+Phase:secondphase
+Input: Token STUDY_TESTCD SPECIMEN
+Options: control = appelt
+Rule: finding_specimen_advance
+(
+({SPECIMEN} {STUDY_TESTCD}) | 
+({STUDY_TESTCD} ({Token})[0,3] {Token.pos=="IN"} ({Token.pos=="DT"})? {SPECIMEN} (({Token.root==","} | {Token.root=="and"}) {SPECIMEN})[0,8]) 
+) :finding_specimen_advance
+-->
+{
+    gate.AnnotationSet lookup = (gate.AnnotationSet) bindings.get("finding_specimen_advance");
+	gate.Annotation ann = (gate.Annotation) lookup.iterator().next();
+	gate.AnnotationSet  sentence_set = outputAS.get("Sentence",ann.getStartNode().getOffset(), ann.getEndNode().getOffset());
+	gate.Annotation  sentence = sentence_set.iterator().next();
+	//System.out.println("finding_specimen_advance");
+	//System.out.println(stringFor(doc, sentence));
+	try{
+			//System.out.println(doc.getName());
+			gate.AnnotationSet  specimen_entities = lookup.get("SPECIMEN");
+			gate.AnnotationSet  man_entities = lookup.get("STUDY_TESTCD");
+			gate.Annotation  finding_change = man_entities.iterator().next();
+			String content = stringFor(doc, lookup.firstNode().getOffset(),lookup.lastNode().getOffset());
+			//System.out.println("FINDING:" + stringFor(doc, finding_change));
+			System.out.println(content);
+			gate.FeatureMap features = finding_change.getFeatures();
+ 			features.put("text", stringFor(doc, finding_change));
+			features.put("rule", "STUDY_TESTCD_SPECIMEN");
+			Boolean first = true;
+			String spe_ids = "";
+			for (Annotation spe : specimen_entities) {
+				//System.out.println("SPECIMEN:" + stringFor(doc, spe));
+				if(first){
+					spe_ids = spe.getId().toString();
+					first=false;
+				}else{
+					spe_ids = spe_ids+","+spe.getId().toString();
+				}
+			}
+			features.put("SPECIMEN", spe_ids);
+			//System.out.println(stringFor(doc, lookup.firstNode().getOffset(),lookup.lastNode().getOffset()));
+			//outputAS.add(finding_change.getStartNode().getOffset(),finding_change.getEndNode().getOffset(), "FINDING", features);
+			outputAS.add(lookup.firstNode().getOffset(),lookup.lastNode().getOffset(), "STUDY_TEST_2", features);
+		}catch(InvalidOffsetException e){
+			throw new LuckyException(e);
+	}
+}
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