/**
* takes a query object and calls the appropriate sub component that answers the given query
*
* @param query the query that has to be answered
* @return a string in the answer exchange format that will be sent to the frontend
*/
public static String handleQuery(Query query) {
// interval search
String answer;
if (query.x_Search == null) {
// check if necessary fields are given
if (query.i_Start == -1 || query.i_End == -1) {
// query.response_format = "Wrong interval given";
return "Wrong interval given";
} else if (query.s_Chromosome == -1) {
// query.response_format = "No chromosome given";
return "No chromosome given";
} else if (query.s_Source == -1) {
// query.response_format = "No source given";
return "No source given";
}
// correct query format
else {
// Send query to IndexController
// Translation from query to intervalst.query
// needs to be unified
/*
short s_SourceNo=(short)0;
if (query.source.equals("dbSNP")) {
s_SourceNo = (short) 0;
}
if (query.source.equals("1000GenomesProject")){
s_SourceNo =(short) 1;
}
*/
Query[] q_Query = {query};
QueryAnswer temp_answer = indexController.answerQuery(q_Query);
answer = answerQuery(temp_answer);
/*
// byte temp = query.chromosome.get();
// byte[] b={temp};
//CRITICAL PART. change query format into intervallst.query . answerquery throws nullpointer
byte[] b=new byte[0];
byte[] c=new byte[0];
int i=query.position[0];
int j=query.position[1];
IntervalST.Query intervalst_query=new IntervalST.Query(1,i,j,s_SourceNo,Integer.toString(query.chromosome).getBytes(),null,null);
IntervalST.Query[] queries={intervalst_query};
IntervalST.Answer x_Result=indexController.answerQuery(queries);
System.out.println("Length of AnswerList: "+x_Result.x_List.size());
if (query.hasDetail) {
String sequence = Chromosome_reader.retrieve_sequence(i,j,Integer.toString(query.chromosome));
}
return query;
*/
}
}
// gene name search
else {
// test for prefix query
if (query.b_isPrefix) {
/*
// This needs to be replaced!
String[] genenames = GeneTranslator.completeGeneName(query.search);
*/
String[] genenames = {"FOXP2", "FOXP4"};
JSONObject obj = new JSONObject();
obj.put("source", query.s_Source);
obj.put("chromosome", query.s_Chromosome);
JSONArray names = new JSONArray();
for (int i = 0; i < genenames.length; i++) {
names.add(genenames[i]);
}
obj.put("prefix", names);
StringWriter out = new StringWriter();
try {
obj.writeJSONString(out);
} catch (IOException e) {
e.printStackTrace();
}
answer = out.toString();
} else {
if (query.x_Search == "getInitialSources") {
System.out.println("getInitialSources");
return null;
} else {
String[] interval = GeneTranslator.translateToIntervall(query.x_Search);
JSONObject pos_obj = new JSONObject();
JSONObject obj = new JSONObject();
pos_obj.put("from", Integer.valueOf(interval[0]));
pos_obj.put("to", Integer.valueOf(interval[1]));
obj.put("search", query.x_Search);
obj.put("position", pos_obj);
StringWriter out = new StringWriter();
try {
obj.writeJSONString(out);
} catch (IOException e) {
e.printStackTrace();
}
answer = out.toString();
}
}
}
// queryID_pool.add(query.queryID);
return answer;
}
/** @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse response) */
@SuppressWarnings("unchecked")
protected void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
response.setContentType("application/json");
response.setHeader("Cache-Control", "nocache");
response.setCharacterEncoding("utf-8");
PrintWriter out = response.getWriter();
StringWriter result = new StringWriter();
// get received JSON data from request
BufferedReader br = new BufferedReader(new InputStreamReader(request.getInputStream()));
String postData = "";
if (br != null) {
postData = br.readLine();
}
try {
JSONObject json = (JSONObject) new JSONParser().parse(postData);
JSONObject resultObj = new JSONObject();
JSONArray list = new JSONArray();
List<Tracking> trackingList = new ArrayList<Tracking>();
// get the website list
if (json.get("type").equals("websiteslist")) {
trackingList = trackingDao.websiteList(pool);
for (Tracking item : trackingList) {
list.add(item.getWebsite());
}
}
// render report
else if (json.get("type").equals("submit")) {
if (json.get("criteria").equals("date")) {
// render repoty by date
trackingList = trackingDao.getListByDate(pool, json.get("date").toString());
} else if (json.get("criteria").equals("daterange")) {
// render repoty by date range
trackingList =
trackingDao.getListByDateRange(
pool, json.get("fromdate").toString(), json.get("todate").toString());
} else if (json.get("criteria").equals("website")) {
// render repoty by website
String website = (json.get("website") == null ? "" : json.get("website").toString());
trackingList = trackingDao.getListByWebsite(pool, website);
}
for (Tracking item : trackingList) {
JSONObject trackingObj = new JSONObject();
trackingObj.put("date", item.getDate());
trackingObj.put("website", item.getWebsite());
trackingObj.put("visit", item.getVisit());
list.add(trackingObj);
}
}
resultObj.put("result", list);
resultObj.writeJSONString(result);
// finally output the json string
out.print(result.toString());
} catch (ParseException | SQLException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
/**
* parses an answer object into the json exchange format for an answer
*
* @param answer the answer object that should be translated
* @return json string in the exchange format between frontend and middleware
*/
public static String answerQuery(QueryAnswer answer) {
JSONObject obj = new JSONObject();
obj.put("source", answer.source);
// add chromosome attribute to json answer
obj.put("chromosome", answer.chromosome);
JSONObject from_to = new JSONObject();
from_to.put("from", answer.position[0]);
from_to.put("to", answer.position[1]);
obj.put("position", from_to);
String response;
if (answer.hasDetail) {
JSONObject details = new JSONObject();
details.put("refseq", answer.refseq);
// create json_array for found mutations
JSONArray mutations_array = new JSONArray();
for (IntervalST.Mutation x : answer.mutations) {
// json object for single mutation, that was found
JSONObject mut = new JSONObject();
// name of mutation, need to convert from byte array to string
mut.put("name", new String(x.b_RefName));
// json object for position of mutation's interval, with "to" and "from" as attributes
JSONObject mut_pos = new JSONObject();
mut_pos.put("from", x.i_Low);
mut_pos.put("to", x.i_High);
mut.put("position", mut_pos);
// json object for metadata
JSONObject meta = new JSONObject();
// json object for gender
JSONObject gender = new JSONObject();
// -1 for no filter on gender, 0 for male and 1 for female
if (x.s_Gender == -1) {
gender.put("m", true);
gender.put("w", true);
} else if (x.s_Gender == 0) {
gender.put("m", true);
gender.put("w", false);
} else if (x.s_Gender == 1) {
gender.put("m", false);
gender.put("w", true);
} else {
gender = null;
}
meta.put("gender", gender);
// add country
meta.put("origin", IndexController.getCountry(x.s_Country));
// downloadtime
meta.put("downloadtime", x.s_Date);
// add metadata json object to mutation json object
mut.put("metadata", meta);
// add sequence of basis pairs, first need to convert integer to string
if (answer.chromosome == 23) {
mut.put("mutationseq", Chromosome_reader.retrieve_sequence(x.i_Low, x.i_High, "X"));
} else if (answer.chromosome == 24) {
mut.put("mutationseq", Chromosome_reader.retrieve_sequence(x.i_Low, x.i_High, "Y"));
} else if (answer.chromosome == 25) {
mut.put("mutationseq", Chromosome_reader.retrieve_sequence(x.i_Low, x.i_High, "MT"));
} else {
mut.put(
"mutationseq",
Chromosome_reader.retrieve_sequence(x.i_Low, x.i_High, answer.chromosome.toString()));
}
// add json object for mutation x to json array for all mutations that were found
mutations_array.add(mut);
}
details.put("mutations", mutations_array);
obj.put("details", details);
StringWriter out = new StringWriter();
try {
obj.writeJSONString(out);
} catch (IOException e) {
e.printStackTrace();
}
response = out.toString();
} else {
obj.put("details", null);
// function to count occurrences of mutations in subintervals
Integer[] counts = count_mutations(answer);
JSONArray mutation_counts = new JSONArray();
for (int i = 0; i < counts.length; i++) {
mutation_counts.add(counts[i]);
}
obj.put("graph", mutation_counts);
StringWriter out = new StringWriter();
try {
obj.writeJSONString(out);
} catch (IOException e) {
e.printStackTrace();
}
response = out.toString();
}
if (response != null) {
return response;
} else {
return "Something went wrong while creating answer";
}
}