/**
* 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 Servlet#init() */
public void init() throws ServletException {
int success = geneTranslator.buildGeneTranslator();
indexController = new IndexController();
}
/** Servlet implementation class QueryReceiver */
@WebServlet("/QueryReceiver")
public class QueryReceiver extends GenericServlet {
private static final long serialVersionUID = 1L;
/** @see GenericServlet#GenericServlet() */
static GeneTranslator geneTranslator = new GeneTranslator();
int success = geneTranslator.buildGeneTranslator();
static IndexController indexController;
static HashSet<Integer> queryID_pool = new HashSet<Integer>(10000);
public static class Filter {
boolean male;
boolean female;
Integer relfrq;
String[] origin;
}
/*
public static class Query{
public short source;
public short chromosome;
public int from;
public int to;
public int zoom_level;
public boolean hasDetail;
public boolean isPrefix;
public String search;
public String[] origin;
public short gender;
public int relfrq;
Query() {
this.from = -1;
this.to = -1;
this.zoom_level = -1;
this.source = (short) -1;
this.gender = (short) -1;
this.relfrq = -1;
this.chromosome = -1;
}
}
*/
/**
* 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;
}
*/
}
/**
* counts the subintervals of the mutations in the answer object
*
* @param answer an answer object that was generated through a query
* @return Integer array holding the amount of mutations that intersect the subintervals
*/
public static Integer[] count_mutations(QueryAnswer answer) {
Integer[] pos = answer.position;
float interval_length = pos[1] - pos[0];
int subinterval_length = answer.zoom_level;
int number_subints = (int) Math.ceil(interval_length / subinterval_length);
Integer[] counts = new Integer[number_subints];
for (int i = 0; i < counts.length; i++) {
counts[i] = 0;
}
int[] subint_left_boundaries = new int[number_subints];
int left = pos[0];
for (int i = 0; i < number_subints; i++) {
subint_left_boundaries[i] = left + i * subinterval_length;
}
for (IntervalST.Mutation mut : answer.mutations) {
int mut_low = mut.i_Low;
int mut_high = mut.i_High;
int last_index = subint_left_boundaries.length - 1;
for (int i = 0; i < last_index; i++) {
int lower = Math.max(subint_left_boundaries[i], mut_low);
int higher = Math.min(subint_left_boundaries[i + 1], mut_high);
if (lower <= higher) {
counts[i]++;
}
}
if (mut_high >= subint_left_boundaries[last_index]) {
counts[last_index]++;
}
}
return counts;
}
/**
* 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";
}
}
/**
* 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 Servlet#init() */
public void init() throws ServletException {
int success = geneTranslator.buildGeneTranslator();
indexController = new IndexController();
}
/** @see Servlet#service(ServletRequest request, ServletResponse response) */
public void service(ServletRequest request, ServletResponse response)
throws ServletException, IOException {
// TODO Auto-generated method stub
String input_string = request.getParameter("text");
PrintWriter out = response.getWriter();
Query parsed_query = parse(input_string);
// Wrong input format -> null returned in parse function
if (parsed_query == null) {
String message = "Unknown query format";
out.write(message.toCharArray());
}
// correct input format
else {
String answer = handleQuery(parsed_query);
out.write(answer);
}
}
}