Java Code Examples for net.sf.json.JSONObject#accumulate()

public static JSONObject anyConditionforInitialEvent(){
	JSONObject anycondition=new JSONObject();
	JSONArray criteriaList=new JSONArray();
	JSONObject conditionOccurrence=new JSONObject();
	JSONObject jnull=new JSONObject();
	conditionOccurrence.accumulate("ConditionOccurrence", jnull);
	criteriaList.add(conditionOccurrence);
	anycondition.accumulate("CriteriaList", criteriaList);
	JSONObject observationWindow=new JSONObject();
	observationWindow.accumulate("PriorDays", 0);
	observationWindow.accumulate("PostDays", 0);
	anycondition.accumulate("ObservationWindow", observationWindow);
	JSONObject primaryCriteriaLimit=new JSONObject();
	primaryCriteriaLimit.accumulate("Type", "First");
	anycondition.accumulate("PrimaryCriteriaLimit", primaryCriteriaLimit);
	return anycondition;
}
 

public static List<Concept> searchConceptByNameAndDomain(String entity, String domainid)
			throws UnsupportedEncodingException, IOException, ClientProtocolException {
		JSONObject queryjson = new JSONObject();
		queryjson.accumulate("QUERY", entity);
		queryjson.accumulate("DOMAIN_ID", "['" + domainid + "']");
		queryjson.accumulate("STANDARD_CONCEPT","S");//only standard concept
//		queryjson.accumulate("VOCABULARY_ID", "['SNOMED']");
		System.out.println("queryjson:" + queryjson);
		String vocabularyresult = getConcept(queryjson);
		System.out.println("vocabularyresult  length=" + vocabularyresult.length());
		Gson gson = new Gson();
		JsonArray ja = new JsonParser().parse(vocabularyresult).getAsJsonArray();
		if (ja.size() == 0) {
			System.out.println("size=" + ja.size());
			return null;
		}
		List<Concept> list = gson.fromJson(ja, new TypeToken<List<Concept>>() {
		}.getType());
		return list;
	}
 

public String extendByUMLS(String term){
	Integer conceptId=0;
	JSONObject jo=new JSONObject();
	jo.accumulate("term", term);
	String result=HttpUtil.doPost(umlsurl, jo.toString());
	JSONObject rejo=JSONObject.fromObject(result);
	if(rejo!=null){
		String aftermap=rejo.getString("term");
	if(aftermap.equals("unmapped")==false){
		return aftermap;
	}else{
		return term;
	}
	}else{
		return term;
	}
	
}
 

public String[] getCloestConceptByUsagi(String term,String domain){
	String[] res=new String[3];
	JSONObject jo=new JSONObject();
	jo.accumulate("term", StringUtil.cleanASCII(term));
	jo.accumulate("domain", domain);
	String result=HttpUtil.doPost(usagi, jo.toString());
	System.out.println(jo.toString());
	System.out.println("result="+result);
	JSONObject bestconcept=JSONObject.fromObject(result);
	System.out.println("matchScore="+bestconcept.getDouble("matchScore"));
	String matchs=String.format("%.2f", bestconcept.getDouble("matchScore")*100);
	
	JSONObject concept_jo=bestconcept.getJSONObject("concept");
	Integer cId=concept_jo.getInt("conceptId");
	String conceptname=concept_jo.getString("conceptName");
	
	res[0]=String.valueOf(cId);
	res[1]=conceptname;
	res[2]=matchs;
	return res;
}
 

public Integer createConceptByConceptName(String word,String domain) throws UnsupportedEncodingException, ClientProtocolException, IOException{
	Integer conceptId=0;
	//the most related one
	System.out.println("word=" + word);
	System.out.println("domain=" + domain);
	
	List<Concept> econceptlist = ATLASUtil.searchConceptByNameAndDomain(word, domain);
	String expression=generateConceptSetByConcepts(econceptlist);
	long t1=System.currentTimeMillis();  
	JSONObject jo=new JSONObject();
	jo.accumulate("name", word+"_created_by_"+GlobalSetting.c2qversion);
	jo.accumulate("id", 23333);
	String result=HttpUtil.doPost(conceptseturl, jo.toString());
	JSONObject rejo=JSONObject.fromObject(result);
	HttpUtil.doPut(conceptseturl+rejo.getString("id")+"/items",expression);		
	return Integer.valueOf(rejo.getString("id"));
}
 

/**
 * inclusion :flag = true ; exclusion : flag=false;
 * neg
 * temporal 1 has history of 
 * 
 * */

public static JSONObject setCriteriaUnit(int index,boolean neg,boolean flag,String type,int temporal){
	JSONObject criteriaunit = new JSONObject();
	JSONObject occurrence = new JSONObject();
	JSONObject startwindow = new JSONObject();
	JSONObject criteria = new JSONObject();
	criteria = setCriteria(type, index);
	if (neg^flag == true) {
		occurrence = setOccurrence(2, 1);	
	}else {
		occurrence = setOccurrence(0, 0);
	}
	startwindow = setTemporalWindow(temporal);
	criteriaunit.accumulate("Criteria", criteria);
	criteriaunit.accumulate("StartWindow", startwindow);
	criteriaunit.accumulate("Occurrence", occurrence);
	return criteriaunit;
}
 

public static List<Concept> searchConceptByNameAndDomain(String entity, String domainid)
		throws UnsupportedEncodingException, IOException, ClientProtocolException {
	JSONObject queryjson = new JSONObject();
	queryjson.accumulate("QUERY", entity);
	queryjson.accumulate("DOMAIN_ID", "['" + domainid + "']");
	queryjson.accumulate("STANDARD_CONCEPT", "S");// only standard concept
	System.out.println("queryjson:" + queryjson);
	String vocabularyresult = getConcept(queryjson);
	System.out.println("vocabularyresult  length=" + vocabularyresult.length());
	Gson gson = new Gson();
	JsonArray ja = new JsonParser().parse(vocabularyresult).getAsJsonArray();
	if (ja.size() == 0) {
		return null;
	}
	List<Concept> list = gson.fromJson(ja, new TypeToken<List<Concept>>() {
	}.getType());
	return list;
}
 

/**
 * index 1: has history of 
 * index 2: has 
 * */
public static JSONObject setTemporalWindow(int index) {
	JSONObject window = new JSONObject();
	JSONObject start = new JSONObject();
	JSONObject end = new JSONObject();
	if(index ==1){
		start.accumulate("Coeff", -1);
		// start.accumulate("Count", 0);
		end.accumulate("Coeff", "1");
		// end.accumulate("Count", 0);
		//end.accumulate("Days", "0");	
	}
	window.accumulate("Start", start);
	window.accumulate("End", end);
	return window;
}
 

public static List<Concept> searchConceptByName(String entity)
		throws UnsupportedEncodingException, IOException, ClientProtocolException {
	JSONObject queryjson = new JSONObject();
	queryjson.accumulate("QUERY", entity);
	System.out.println("queryjson:" + queryjson);
	String vocabularyresult = getConcept(queryjson);
	System.out.println("vocabularyresult  length=" + vocabularyresult.length());
	Gson gson = new Gson();
	JsonArray ja = new JsonParser().parse(vocabularyresult).getAsJsonArray();
	if (ja.size() == 0) {
		System.out.println("size=" + ja.size());
		return null;
	}
	List<Concept> list = gson.fromJson(ja, new TypeToken<List<Concept>>() {
	}.getType());
	return list;
}
 

public List<String> resolve(String text){
	JSONObject jo=new JSONObject();
	jo.accumulate("entity", text);
	String result=HttpUtil.doPost(reconurl, jo.toString());
	JSONArray array = JSONArray.fromObject(result);
	List<String> list=new ArrayList<String>();
	for(Object obj :array){
		list.add((String) obj);
	}
	return list;
}
 

public JSONArray defaultInitialEvent() {
	JSONArray jacriterialist = new JSONArray();
	JSONObject jo = new JSONObject();
	// JSONObject jnull=new JSONObject();
	JSONObject jvo = new JSONObject();
	jvo.accumulate("VisitSourceConcept", null);
	jvo.accumulate("First", null);
	jo.accumulate("VisitOccurrence", jvo);

	jacriterialist.add(jo);
	return jacriterialist;
}
 

public JSONObject formualteCohortQuery(Document doc) {
	List<Integer> conceptsetIds=extractConceptsetByDoc(doc);
	CdmCohort omopcohort=translateByDoc(doc);
	JSONObject cohort = new JSONObject();
	//Merge All criteria to one criteria 
	CdmCriteria initial_criteria=new CdmCriteria();
	List<CdmCriterion> clist=new ArrayList<CdmCriterion>();
	for(CdmCriteria c:omopcohort.getInitial_event()){
		if(c!=null){
			clist.addAll(c.getClist());
		}
	}
	StringBuffer initialeventtext=new StringBuffer();
	for(CdmCriteria cdmc:omopcohort.getInitial_event()){
		initialeventtext.append(cdmc.getText());
	}
	initial_criteria.setText(initialeventtext.toString());
	initial_criteria.setInitialevent(true);
	initial_criteria.setIncluded(true);
	initial_criteria.setClist(clist);
	initial_criteria.setPriorDays(omopcohort.getDaysBefore());
	initial_criteria.setPostDays(omopcohort.getDaysAfter());
	initial_criteria.setLimitTo(omopcohort.getLimitTo());
	initial_criteria.setOccurenceStart(omopcohort.getOccurrenceStart());
	cohort.accumulate("ConceptSets", formulateConceptSet(conceptsetIds));
	// initial events
	cohort.accumulate("PrimaryCriteria", formulatePrimaryCriteria(initial_criteria));
	if(initial_criteria.getText()!=null &&initial_criteria.getText().length() >0){
		System.out.println("=>additional criteria");
		cohort.accumulate("AdditionalCriteria", formulateOneCdmCriteria(initial_criteria));
	}
	cohort.accumulate("QualifiedLimit", formulateQualifiedLimit());
	cohort.accumulate("ExpressionLimit", formulateExpressionLimit());
	// other criteria
	cohort.accumulate("InclusionRules", formulateInclusionRules(omopcohort.getAdditional_criteria()));
	// set null for CensoringCriteria and CollapseSettings
	cohort.accumulate("CensoringCriteria", formulateCensoringCriteria());
	cohort.accumulate("CollapseSettings", formulateCollapseSettings());
	return cohort;
}
 

public JSONObject translateTemporal(TemporalConstraint temporal) {
	JSONObject temporalwindow = new JSONObject();
	JSONObject start = new JSONObject();
	JSONObject end = new JSONObject();
	if (temporal == null) {
		start.accumulate("Coeff", -1);
		end.accumulate("Coeff", 1);
		temporalwindow.accumulate("Start", start);
		temporalwindow.accumulate("End", end);
	} else {
		if (temporal.getStart_days() != null && temporal.getEnd_days() != null) {
			start.accumulate("Days", temporal.getStart_days());
			start.accumulate("Coeff", temporal.getStart_offset());
			temporalwindow.accumulate("Start", start);
			end.accumulate("Days", temporal.getEnd_days());
			end.accumulate("Coeff", temporal.getEnd_offset());
			temporalwindow.accumulate("End", end);
		} else if (temporal.getStart_days() == null && temporal.getEnd_days() != null) {
			start.accumulate("Coeff", -1);
			temporalwindow.accumulate("Start", start);
			end.accumulate("Days", temporal.getEnd_days());
			end.accumulate("Coeff", temporal.getEnd_offset());
			temporalwindow.accumulate("End", end);
		} else if (temporal.getStart_days() != null && temporal.getEnd_days() == null) {
			start.accumulate("Days", temporal.getStart_days());
			start.accumulate("Coeff", temporal.getStart_offset());
			end.accumulate("Coeff", 1);
			temporalwindow.accumulate("Start", start);
			temporalwindow.accumulate("End", end);
		}
	}
	return temporalwindow;
}
 

public static Integer createConceptSetByConceptName(String conceptsetname,String word,String domain) throws UnsupportedEncodingException, ClientProtocolException, IOException{			
	//the most related one		
	List<Concept> econceptlist = searchConceptByNameAndDomain(word, domain);				
	String expression=generateConceptSetByConcepts(econceptlist);
	JSONObject jo=new JSONObject();
	jo.accumulate("name", conceptsetname);
	jo.accumulate("id", 1);
	String result=HttpUtil.doPost(conceptseturl, jo.toString());
	JSONObject rejo=JSONObject.fromObject(result);
	HttpUtil.doPut(conceptseturl+rejo.getString("id")+"/items",expression);		
	return Integer.valueOf(rejo.getString("id"));
}
 

public static JSONObject setCriteria(String type, int conceptsetid) {
	JSONObject criteriatype = new JSONObject();
	JSONObject codesetId = new JSONObject();
	codesetId.accumulate("CodesetId", conceptsetid);
	if (type.equals("Condition")) {
		criteriatype.accumulate("ConditionOccurrence", codesetId);
	} else if (type.equals("Drug")) {
		criteriatype.accumulate("DrugExposure", codesetId);
	} else if (type.equals("Observation")) {
		criteriatype.accumulate("Observation", codesetId);
	} else if (type.equals("Procedure_Device")) {
		criteriatype.accumulate("DeviceExposure", codesetId);
	}
	return criteriatype;
}
 

public static JSONObject querybyconceptSetid(int conceptid){
	JSONObject jot=new JSONObject();
   	String re2=HttpUtil.doGet("http://api.ohdsi.org/WebAPI/conceptset/"+conceptid);
   	JSONObject jore2=JSONObject.fromObject(re2);
   	jot.accumulateAll(jore2);
   	String re3=HttpUtil.doGet("http://api.ohdsi.org/WebAPI/conceptset/"+conceptid+"/expression");
   	
   	JSONObject expression=JSONObject.fromObject(re3);
   	jot.accumulate("expression",expression);
   	
   	return jot;
}
 

public JSONObject formulateQualifiedLimit() {
	JSONObject qualifiedlimit = new JSONObject();
	qualifiedlimit.accumulate("Type", "First");
	return qualifiedlimit;
}
 

public JSONObject formulateExpressionLimit() {
	JSONObject expressionlimit = new JSONObject();
	expressionlimit.accumulate("Type", "First");
	return expressionlimit;
}
 

public static JSONObject setOccurrence(int type, int count) {
	JSONObject jsonob = new JSONObject();
	jsonob.accumulate("Type", type);
	jsonob.accumulate("Count", count);
	return jsonob;
}
 

public JSONArray formulateDemographic(List<CdmCriterion> criteria_list){
	JSONArray demographicarr = new JSONArray();
	for (CdmCriterion cdmcriterion : criteria_list) {
		if(cdmcriterion.getDomain().equals("Demographic")){
			//age
			if(cdmcriterion.getOrginialtext().toLowerCase().contains("age")){
				JSONObject jo=new JSONObject();
				if(cdmcriterion.getAttributes()!=null){
					String agerangestr=cdmcriterion.getAttributes().get("age_range");
					System.out.println("==???age???==");
					List<Double> m=NumericConvert.recognizeNumbersAdvanced(agerangestr);
					if(m!=null){
						System.out.println("m_size="+m.size());
						System.out.println("number="+m.get(0));
						System.err.println("Age str="+agerangestr);
						agerangestr=agerangestr.toLowerCase();
						if(m.size()==1 && 
								(
										(agerangestr.indexOf(">")!=-1 &&agerangestr.indexOf("<")==-1&&agerangestr.indexOf("=")==-1)
										||
										(agerangestr.indexOf("older") !=-1&&agerangestr.indexOf("younger") ==-1)
								)
							)
						{
							System.out.println("gt-==?");
							jo.accumulate("Value",m.get(0));
							jo.accumulate("Op", "gt");
						}else if(m.size()==1 && 
									(
											(agerangestr.indexOf("<")!=-1 &&agerangestr.indexOf(">")==-1&&agerangestr.indexOf("=")==-1)
											||
											(agerangestr.indexOf("younger") !=-1&&agerangestr.indexOf("older") ==-1)
									)
								)
						{
							jo.accumulate("Value",m.get(0));
							jo.accumulate("Op", "lt");
						}else if(m.size()==2){
							jo.accumulate("Value",m.get(0));
							jo.accumulate("Extent",m.get(1));
							jo.accumulate("Op", "bt");
						}else if(m.size()==1 && ((agerangestr.indexOf("≤")!=-1 )||(agerangestr.indexOf("at most")!=-1)||((agerangestr.indexOf("<")!=-1)&&(agerangestr.indexOf("=")!=-1)))){
							jo.accumulate("Value",m.get(0));
							jo.accumulate("Op", "lte");
						}else if(m.size()==1 && ((agerangestr.indexOf("≥")!=-1 )||(agerangestr.indexOf("at least")!=-1)||((agerangestr.indexOf(">")!=-1)&&(agerangestr.indexOf("=")!=-1)))){
							jo.accumulate("Value",m.get(0));
							jo.accumulate("Op", "gte");
						}
					}
				}
				JSONObject agejson=new JSONObject();
				agejson.accumulate("Age", jo);
				demographicarr.add(agejson);
			}
			System.out.println("gender===>");
			if(Arrays.asList(GenderGroup.maletriggers).contains(cdmcriterion.getOrginialtext().trim().toLowerCase())||Arrays.asList(GenderGroup.femaletriggers).contains(cdmcriterion.getOrginialtext().trim().toLowerCase())){
				JSONArray genderarr=new JSONArray();
				JSONObject genderjson=new JSONObject();
				if(Arrays.asList(GenderGroup.maletriggers).contains(cdmcriterion.getOrginialtext().trim().toLowerCase())){
					genderarr.add(setMale());
				}
				if(Arrays.asList(GenderGroup.femaletriggers).contains(cdmcriterion.getOrginialtext().trim().toLowerCase())){
					genderarr.add(setFeMale());
				}
				genderjson.accumulate("Gender", genderarr);
				demographicarr.add(genderjson);
			}
		}
	}
	return demographicarr;
}