/**
* tries to parse the given json message into a query object
*
* @param json_file a json that fulfills the exchange format between frontend and middleware
* @return a query object that holds the information in the json message
*/
public static Query parse(String json_file) {
try {
Query query = new Query();
Object obj = JSONValue.parse(json_file);
// System.out.println(obj);
JSONObject j = (JSONObject) obj;
// System.out.println(j);
// sources
if (j.get("source") != null) {
/*
JSONArray jArray = (JSONArray)j.get("sources");
ArrayList<String> sources = new ArrayList<String>();
for (int i = 0; i < jArray.size(); i++){
sources.add(jArray.get(i).toString());
}
*/
if (((String) (j.get("source"))).equals("dbSNP")) {
query.s_Source = (short) 0;
}
if (((String) (j.get("source"))).equals("1000GenomesProject")) {
query.s_Source = (short) 1;
}
}
// chromosome
if (j.get("chromosome") != null) {
if (((String) j.get("chromosome")).equals("X")) {
query.s_Chromosome = 23;
} else if (((String) j.get("chromosome")).equals("Y")) {
query.s_Chromosome = 24;
} else if (((String) j.get("chromosome")).equals("MT")) {
query.s_Chromosome = 25;
} else {
query.s_Chromosome = (short) Integer.parseInt((String) j.get("chromosome"));
}
}
// position
if (j.get("intervall") != null) {
JSONObject pos_obj = (JSONObject) j.get("intervall");
query.i_Start = (int) (long) pos_obj.get("from");
query.i_End = (int) (long) pos_obj.get("to");
query.i_ZoomLevel = (int) (long) pos_obj.get("size");
}
// gene search
if (j.get("search") != null) {
query.x_Search = (String) j.get("search");
}
// prefix
if (j.get("prefix") != null) {
query.b_isPrefix = (boolean) j.get("prefix");
} else {
query.b_isPrefix = false;
}
/*
// subintervals
if (j.get("subintervals") != null){
query.subintervals = (int)(long) j.get("subintervals");
}
*/
// hasDetail flag
if (j.get("hasDetail") != null) {
query.b_hasDetail = (boolean) j.get("hasDetail");
}
if (j.get("filter") != null) {
JSONObject fil_obj = (JSONObject) j.get("filter");
if (((boolean) fil_obj.get("male")) && !((boolean) fil_obj.get("female"))) {
query.s_Gender = (short) 0;
} else if (!((boolean) fil_obj.get("male")) && ((boolean) fil_obj.get("female"))) {
query.s_Gender = (short) 1;
}
query.i_RelFrq = (int) (long) fil_obj.get("relfrq");
JSONArray orig_array = (JSONArray) fil_obj.get("origin");
query.s_Country = new short[orig_array.size()];
for (int i = 0; i < orig_array.size(); i++) {
query.s_Country[i] = IndexController.getNumber((String) orig_array.get(i));
}
}
return query;
} catch (Exception e) {
System.out.println("Unknown query format");
return null;
}
/*
try{
Query query = new Query();
Integer randomID = get_random_number();
query.queryID = randomID;
queryID_pool.remove(randomID);
Object obj = JSONValue.parse(json_file);
//System.out.println(obj);
JSONObject j = (JSONObject) obj;
//System.out.println(j);
// sources
if (j.get("source") != null){
query.source = (String)j.get("source");
}
// chromosome
if (j.get("chromosome") != null){
query.chromosome = (int) (long) j.get("chromosome");
}
// position
if (j.get("intervall") != null){
JSONObject pos_obj = (JSONObject) j.get("intervall");
Integer[] pos = new Integer[2];
pos[0] = (int)(long)pos_obj.get("from");
pos[1] = (int)(long)pos_obj.get("to");
query.zoom_level = (int)(long)pos_obj.get("size");
query.position = pos;
}
// gene search
if (j.get("search") != null){
query.search = (String) j.get("search");
}
// prefix
if (j.get("prefix") != null){
query.isPrefix = (boolean)j.get("prefix");
}
else{
query.isPrefix = false;
}
// hasDetail flag
if (j.get("hasDetail") != null){
query.hasDetail = (boolean) j.get("hasDetail");
}
if (j.get("filter") != null){
Filter fil = new Filter();
JSONObject fil_obj = (JSONObject)j.get("filter");
fil.male = (boolean)fil_obj.get("male");
fil.female = (boolean) fil_obj.get("female");
fil.relfrq = (int) (long)fil_obj.get("origin");
JSONArray orig_array = (JSONArray) fil_obj.get("origin");
String[] orig = new String[orig_array.size()];
for (int i = 0; i < orig_array.size(); i++){
orig[i] = (String)orig_array.get(i);
}
fil.origin = orig;
query.filter = fil;
}
return query;
}
catch(Exception e){
System.out.println("Unknown query format");
return null;
}
*/
}
