private void getTrafficSpots() {
controller.showProgressBar();
String uploadWebsite =
"http://" + controller.selectedCity.URL + "/php/trafficstatus.cache?dummy=ert43";
String[] ArrayOfData = null;
StreamConnection c = null;
InputStream s = null;
StringBuffer b = new StringBuffer();
String url = uploadWebsite;
System.out.print(url);
try {
c = (StreamConnection) Connector.open(url);
s = c.openDataInputStream();
int ch;
int k = 0;
while ((ch = s.read()) != -1) {
System.out.print((char) ch);
b.append((char) ch);
}
// System.out.println("b"+b);
try {
JSONObject ff1 = new JSONObject(b.toString());
String data1 = ff1.getString("locations");
JSONArray jsonArray1 = new JSONArray(data1);
Vector TrafficStatus = new Vector();
for (int i = 0; i < jsonArray1.length(); i++) {
System.out.println(jsonArray1.getJSONArray(i).getString(3));
double aDoubleLat = Double.parseDouble(jsonArray1.getJSONArray(i).getString(1));
double aDoubleLon = Double.parseDouble(jsonArray1.getJSONArray(i).getString(2));
System.out.println(aDoubleLat + " " + aDoubleLon);
TrafficStatus.addElement(
new LocationPointer(
jsonArray1.getJSONArray(i).getString(3),
(float) aDoubleLon,
(float) aDoubleLat,
1,
true));
}
controller.setCurrentScreen(controller.TrafficSpots(TrafficStatus));
} catch (Exception E) {
controller.setCurrentScreen(traf);
new Thread() {
public void run() {
controller.showAlert("Error in network connection.", Alert.FOREVER, AlertType.INFO);
}
}.start();
}
} catch (Exception e) {
controller.setCurrentScreen(traf);
new Thread() {
public void run() {
controller.showAlert("Error in network connection.", Alert.FOREVER, AlertType.INFO);
}
}.start();
}
}
// Grabs assets off the intarwebz and saves them to a local store/jail for hydration.
private void fetch(JSONArray args) {
String url;
String username;
String password;
String id;
try {
id = args.getString(0);
url = args.getString(1);
username = args.getString(2);
password = args.getString(3);
// Create directory for app.
local_path = "/data/data/" + ctx.getPackageName() + "/remote_app/" + id + "/";
File fp = new File(local_path);
fp.mkdirs();
if (fetchApp(url, username, password)) {
this.success(
new PluginResult(PluginResult.Status.OK, "file://" + local_path + "index.html"),
this.callback);
} else {
this.error(
new PluginResult(
PluginResult.Status.ERROR,
"Error during app saving or fetching; protocol or IO error likely."),
this.callback);
}
} catch (JSONException e) {
this.error(
new PluginResult(
PluginResult.Status.JSON_EXCEPTION,
"JSON exception during argument parsing; make sure the app ID, URL, username and password were passed as an argument."),
this.callback);
}
}
public void fillInEchoNestInfo() throws IOException, EchoNestException {
if (artist == null || title == null) {
JSONObject songProfile = null;
try {
songProfile =
EchoNestQuery.get("song", "profile", "id=" + EchoNestId + "&bucket=audio_summary");
} catch (EchoNestException e) {
}
JSONObject song = songProfile.optJSONArray("songs").optJSONObject(0);
artist = new Artist(song.optString("artist_name"), song.optString("artist_id"));
title = song.optString("title");
duration = song.optJSONObject("audio_summary").optInt("duration");
} else if (EchoNestId == null) {
String artistName = URLEncoder.encode(artist.getName(), "UTF-8");
String title = URLEncoder.encode(this.title, "UTF-8");
JSONObject songSearch = null;
try {
songSearch =
EchoNestQuery.get(
"song",
"search",
"artist="
+ artistName
+ "&title="
+ title
+ "&results=1"
+ "&bucket=audio_summary");
} catch (EchoNestException e) {
}
JSONArray songs = songSearch.optJSONArray("songs");
if (songs.length() == 0) throw new EchoNestException(6, "No items found.");
JSONObject song = songs.optJSONObject(0);
artist = new Artist(song.optString("artist_name"), song.optString("artist_id"));
EchoNestId = song.optString("id");
duration = song.optJSONObject("audio_summary").optInt("duration");
} else if (duration == -1) {
JSONObject songProfile = null;
try {
songProfile =
EchoNestQuery.get("song", "profile", "id=" + EchoNestId + "&bucket=audio_summary");
} catch (EchoNestException e) {
}
duration =
songProfile
.optJSONArray("songs")
.optJSONObject(0)
.optJSONObject("audio_summary")
.optInt("duration");
}
}
public static boolean hasUpdate(int projectID, String version) {
try {
HttpURLConnection con =
(HttpURLConnection)
(new URL("https://api.curseforge.com/servermods/files?projectIds=" + projectID))
.openConnection();
con.setRequestMethod("GET");
con.setRequestProperty("User-Agent", "Mozilla/4.0 (compatible; JVM)");
con.setRequestProperty("Pragma", "no-cache");
con.connect();
JSONArray json = (JSONArray) JSONValue.parse(new InputStreamReader(con.getInputStream()));
String[] cdigits =
((String) ((JSONObject) json.get(json.size() - 1)).get("name"))
.toLowerCase()
.split("\\.");
String[] vdigits = version.toLowerCase().split("\\.");
int max = vdigits.length > cdigits.length ? cdigits.length : vdigits.length;
int a;
int b;
for (int i = 0; i < max; i++) {
a = b = 0;
try {
a = Integer.parseInt(cdigits[i]);
} catch (Throwable t1) {
char[] c = cdigits[i].toCharArray();
for (int j = 0; j < c.length; j++) {
a += (c[j] << ((c.length - (j + 1)) * 8));
}
}
try {
b = Integer.parseInt(vdigits[i]);
} catch (Throwable t1) {
char[] c = vdigits[i].toCharArray();
for (int j = 0; j < c.length; j++) {
b += (c[j] << ((c.length - (j + 1)) * 8));
}
}
if (a > b) {
return true;
} else if (a < b) {
return false;
} else if ((i == max - 1) && (cdigits.length > vdigits.length)) {
return true;
}
}
} catch (Throwable t) {
}
return false;
}
// El string debe estar em formato json
public boolean updateRegistry(String dataJson) {
try {
// Crea objeto json con string por parametro
JSONObject json = new JSONObject(dataJson);
// Obtiene el array de Registos
JSONArray arr = json.getJSONArray("Registry");
// Recorre el array
for (int i = 0; i < arr.length(); i++) {
// Obtiene los datos idSensor y value
int idSensor = arr.getJSONObject(i).getInt("idSensor");
int value = arr.getJSONObject(i).getInt("value");
// Recorre la configuracion de registro
for (RegistryConf reg : registryConf) {
// Se fija si el registro corresponde a esta configuracion
if (reg.getIdSensor() == idSensor) {
// Checkea el criterio para guardar, o no en la BD
// Checkea tambien si el valor es igual al anterior
if (reg.getSaveTypeString() == "ONCHANGE" && lastRead.get(idSensor) != value) {
// Actualizo la ultima lectura y guardo en la BD
lastRead.put(idSensor, value);
saveRegistry(idSensor, value);
} else if (reg.getSaveTypeString() == "ONTIME") {
// Variables auxiliares, para checkear tiempo
Long auxLong = System.currentTimeMillis() / 1000;
int now = auxLong.intValue();
int timeToSave = lastRead.get(idSensor) + reg.getValue();
// Checkea si ya es tiempo para guerdar un nuevo registro
if (now >= timeToSave) {
// Actualizo el ultimo guardado
lastRead.put(idSensor, now);
saveRegistry(idSensor, value);
}
}
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
return false;
}
/**
* Sends login command.
*
* @param capalistParam param from previous command.
* @return is command successful.
*/
@SuppressWarnings("unchecked")
private boolean sendCapas(JSONArray capalistParam) {
if (connection == null || capalistParam == null || capalistParam.isEmpty()) return false;
JSONObject obj = new JSONObject();
try {
obj.put("class", "login_capas");
obj.put("capaid", capalistParam.get(0));
obj.put("lastconnwins", "false");
obj.put("loginkind", "agent");
obj.put("state", "");
return send(obj);
} catch (Exception e) {
logger.error("Error login", e);
return false;
}
}
// Removes locally-stored app(s).
private void remove(JSONArray args) {
try {
local_path = "/data/data/" + ctx.getPackageName() + "/remote_app/" + args.getString(1) + "/";
deleteDirectory(new File(local_path));
} catch (JSONException e) {
this.error(
new PluginResult(
PluginResult.Status.ERROR,
"JSON exception during argument parsing; make sure the app ID was passed as an argument."),
this.callback);
}
}
// Loads a locally-saved app into the WebView.
private void load(JSONArray args) {
try {
local_path = "/data/data/" + ctx.getPackageName() + "/remote_app/" + args.getString(1) + "/";
this.success(
new PluginResult(PluginResult.Status.OK, "file://" + local_path + "index.html"),
this.callback);
} catch (JSONException e) {
this.error(
new PluginResult(
PluginResult.Status.ERROR,
"JSON exception during argument parsing; make sure the app ID was passed as an argument."),
this.callback);
}
}
@RequestMapping(
value = "/getCityApi",
method = {RequestMethod.GET, RequestMethod.POST})
public String getCityApi(
HttpServletRequest request,
@RequestParam(value = "locationname") String locationname,
ModelMap model) {
Map<Object, Object> map = new HashMap<Object, Object>();
JSONArray jSONArray = new JSONArray();
try {
String status = "active";
List<City> cityList = cityService.getCityApi(locationname, status);
if (cityList != null && cityList.size() > 0) {
for (int i = 0; i < cityList.size(); i++) {
City city = (City) cityList.get(i);
String cityName = (String) city.getCity();
String stateName = (String) city.getState();
int ID = (Integer) (city.getId());
JSONObject jSONObject = new JSONObject();
jSONObject.put("id", ID);
jSONObject.put("text", cityName);
jSONArray.put(jSONObject);
}
utilities.setSuccessResponse(response, jSONArray.toString());
} else {
throw new ConstException(ConstException.ERR_CODE_NO_DATA, ConstException.ERR_MSG_NO_DATA);
}
} catch (Exception ex) {
logger.error("getCity :" + ex.getMessage());
utilities.setErrResponse(ex, response);
}
model.addAttribute("model", jSONArray.toString());
return "home";
}
public static JSONValue parseJSONValue(ParseState parseState) {
if (parseState.skipWhite()) {
char c = parseState.current();
switch (c) {
case '{':
return JSONObject.parseJSON(parseState);
case '"':
return JSONString.parseJSON(parseState);
case '[':
return JSONArray.parseJSON(parseState);
case 'n':
return JSONNull.parseJSON(parseState);
case 't':
case 'f':
return JSONBoolean.parseJSON(parseState);
default:
if ((c >= '0' && c <= '9') || c == '-' || c == '.' || c == 'N') // NaN ok
return JSONNumber.parseJSON(parseState);
break;
}
}
return null;
}
public Map getTaskMapBatch(String objectId) throws Exception {
Map map = new HashMap();
String apiURL = "https://rally1.rallydev.com/slm/webservice/1.34/adhoc";
String requestJSON =
"{"
+ "\"task\" : \"/task?query=(ObjectID%20=%20"
+ objectId
+ ")&fetch=true\","
+ "\"userstory\" : \"/hierarchicalrequirement?query=(ObjectID%20=%20${task.WorkProduct.ObjectID})&fetch=FormattedID\","
+ "\"timeentryitem\":\"/timeentryitem?query=(Task.ObjectID%20=%20"
+ objectId
+ ")&fetch=Values\","
+ "\"timespent\":\"${timeentryitem.Values.Hours}\""
+ "}";
log.info("apiURL=" + apiURL);
log.info("requestJSON=" + requestJSON);
String responseJSON = postRallyXML(apiURL, requestJSON);
// log.info("responseJSON="+responseJSON);
// Map jsonMap=JsonUtil.jsonToMap(responseJSON);
JSONParser parser = new JSONParser();
Map jsonMap = (Map) parser.parse(responseJSON);
// log.info("jsonMap="+jsonMap);
String taskObjId = "";
String taskFormattedId = "";
String taskName = "";
String estimate = "";
String toDo = "";
String taskState = "";
String taskOwner = "";
String userstoryFormattedId = "";
// Get task info
JSONObject taskMap = (JSONObject) jsonMap.get("task");
JSONArray taskArray = (JSONArray) taskMap.get("Results");
if (taskArray != null && taskArray.size() > 0) {
JSONObject taskInfo = (JSONObject) taskArray.get(0);
// log.info("taskMap="+taskMap);
// log.info("taskInfo="+taskInfo);
taskObjId = (taskInfo.get("ObjectID")).toString();
taskFormattedId = (taskInfo.get("FormattedID")).toString();
taskState = (taskInfo.get("State")).toString();
Object taskNameObj = taskInfo.get("Name");
taskName = taskNameObj == null ? "" : taskNameObj.toString();
Object estimateObject = taskInfo.get("Estimate");
estimate = estimateObject == null ? "" : estimateObject.toString();
Object toDoObject = taskInfo.get("ToDo");
toDo = toDoObject == null ? "" : toDoObject.toString();
JSONObject ownerMap = (JSONObject) taskInfo.get("Owner");
log.info("ownerMap=" + ownerMap);
if (ownerMap != null) {
taskOwner = (String) ownerMap.get("_refObjectName");
if (taskOwner == null) {
taskOwner = "";
}
}
}
// Get user story info
JSONObject userstoryMap = (JSONObject) jsonMap.get("userstory");
JSONArray userstoryArray = (JSONArray) userstoryMap.get("Results");
if (userstoryArray != null && userstoryArray.size() > 0) {
JSONObject userstoryInfo = (JSONObject) userstoryArray.get(0);
userstoryFormattedId = (userstoryInfo.get("FormattedID")).toString();
log.info("userstoryFormattedId=" + userstoryFormattedId);
}
// Calculate timeSpent
JSONArray timeSpentList = (JSONArray) jsonMap.get("timespent");
log.info("timeSpentList=" + timeSpentList);
double timeSpent = 0.0;
for (int i = 0; i < timeSpentList.size(); i++) {
String timeSpentString = (String) timeSpentList.get(i);
if (timeSpentString != null) {
timeSpent += Double.parseDouble(timeSpentString);
}
}
map.put("type", "task");
map.put("formattedId", taskFormattedId);
map.put("usId", userstoryFormattedId);
map.put("name", taskName);
map.put("taskStatus", taskState);
map.put("owner", taskOwner);
map.put("taskEstimateTotal", estimate);
map.put("taskRemainingTotal", toDo);
map.put("taskTimeSpentTotal", "" + timeSpent);
return map;
}
public Map getUserStoryTaskMap(String timeEntryItemRef) throws Exception {
Map taskMap = new HashMap();
String[] objectIdArr = timeEntryItemRef.split("/");
String objectId = objectIdArr[objectIdArr.length - 1];
log.info("objectId=" + objectId);
String apiURL = "https://rally1.rallydev.com/slm/webservice/1.34/adhoc";
String requestJSON =
"{"
+ "\"timeentryitem\" : \"/timeentryitem?query=(ObjectID%20=%20"
+ objectId
+ ")&fetch=true\","
+ "\"task\" : \"/task?query=(ObjectID%20=%20${timeentryitem.Task.ObjectID})&fetch=true\","
+ "\"userstory\" : \"/hierarchicalrequirement?query=(ObjectID%20=%20${task.WorkProduct.ObjectID})&fetch=true\","
+ "\"defect\" : \"/defect?query=(ObjectID%20=%20${task.WorkProduct.ObjectID})&fetch=true\""
+ "}";
log.info("apiURL=" + apiURL);
log.info("requestJSON=" + requestJSON);
String responseJSON = postRallyXML(apiURL, requestJSON);
// Bypass"%;" to avoid exception
responseJSON = responseJSON.replace("%;", ";");
responseJSON = responseJSON.replace("%", "");
Map jsonMap = JsonUtil.jsonToMap(responseJSON);
String usRef = "";
String usName = "";
String usFormattedId = "";
String usPlanEstimate = "";
String usTaskEstimateTotal = "";
String usTaskRemainingTotal = "";
String usState = "";
String usOwner = "";
Map usMap = new HashMap();
// Get user story info
JSONObject userstoryMap = (JSONObject) jsonMap.get("userstory");
JSONArray userstoryArray = (JSONArray) userstoryMap.get("Results");
if (userstoryArray == null || userstoryArray.size() == 0) {
userstoryMap = (JSONObject) jsonMap.get("defect");
userstoryArray = (JSONArray) userstoryMap.get("Results");
}
if (userstoryArray != null && userstoryArray.size() > 0) {
JSONObject userstoryInfo = (JSONObject) userstoryArray.get(0);
// log.info("userstoryInfo="+userstoryInfo);
usRef = (userstoryInfo.get("_ref")).toString();
usFormattedId = (userstoryInfo.get("FormattedID")).toString();
usName = (userstoryInfo.get("Name")).toString();
usState = (userstoryInfo.get("ScheduleState")).toString();
if (userstoryInfo.get("PlanEstimate") != null)
usPlanEstimate = (userstoryInfo.get("PlanEstimate")).toString();
if (userstoryInfo.get("TaskEstimateTotal") != null)
usTaskEstimateTotal = (userstoryInfo.get("TaskEstimateTotal")).toString();
if (userstoryInfo.get("TaskRemainingTotal") != null)
usTaskRemainingTotal = (userstoryInfo.get("TaskRemainingTotal")).toString();
JSONObject ownerMap = (JSONObject) userstoryInfo.get("Owner");
if (ownerMap != null) {
usOwner = (String) ownerMap.get("_refObjectName");
if (usOwner == null) {
usOwner = "";
}
}
}
Map usDetailMap = new HashMap();
usDetailMap.put("usFormattedId", usFormattedId);
usDetailMap.put("usName", usName);
usDetailMap.put("usPlanEstimate", usPlanEstimate);
usDetailMap.put("usTaskEstimateTotal", usTaskEstimateTotal);
usDetailMap.put("usTaskRemainingTotal", usTaskRemainingTotal);
usDetailMap.put("usOwner", usOwner);
usDetailMap.put("usState", usState);
usMap.put(usRef, usDetailMap);
// log.info("usMap="+usMap);
String taskObjId = "";
String taskFormattedId = "";
String taskName = "";
String estimate = "";
String toDo = "";
String taskState = "";
String taskOwner = "";
String projectName = "";
String iterationName = "";
String workProductRef = "";
List taskList = new ArrayList();
// Get task info
JSONObject taskJsonMap = (JSONObject) jsonMap.get("task");
JSONArray taskArray = (JSONArray) taskJsonMap.get("Results");
if (taskArray != null && taskArray.size() > 0) {
for (int i = 0; i < taskArray.size(); i++) {
JSONObject taskInfo = (JSONObject) taskArray.get(0);
// log.info("taskMap="+taskMap);
// log.info("taskInfo="+taskInfo);
taskObjId = (taskInfo.get("ObjectID")).toString();
taskFormattedId = (taskInfo.get("FormattedID")).toString();
taskState = (taskInfo.get("State")).toString();
Object taskNameObj = taskInfo.get("Name");
taskName = taskNameObj == null ? "" : taskNameObj.toString();
Object estimateObject = taskInfo.get("Estimate");
estimate = estimateObject == null ? "" : estimateObject.toString();
Object toDoObject = taskInfo.get("ToDo");
toDo = toDoObject == null ? "" : toDoObject.toString();
JSONObject ownerMap = (JSONObject) taskInfo.get("Owner");
// log.info("ownerMap="+ownerMap);
if (ownerMap != null) {
taskOwner = (String) ownerMap.get("_refObjectName");
if (taskOwner == null) {
taskOwner = "";
}
}
JSONObject workProductMap = (JSONObject) taskInfo.get("WorkProduct");
// log.info("workProductMap="+workProductMap);
if (workProductMap != null) {
workProductRef = (String) workProductMap.get("_ref");
if (workProductRef == null) {
workProductRef = "";
}
}
JSONObject projectMap = (JSONObject) taskInfo.get("Project");
// log.info("projectMap="+projectMap);
if (projectMap != null) {
projectName = (String) projectMap.get("_refObjectName");
if (projectName == null) {
projectName = "";
}
}
JSONObject iterationMap = (JSONObject) taskInfo.get("Iteration");
// log.info("iterationMap="+iterationMap);
if (iterationMap != null) {
iterationName = (String) iterationMap.get("_refObjectName");
if (iterationName == null) {
iterationName = "";
}
}
taskMap.put("taskFormattedId", taskFormattedId);
taskMap.put("taskName", taskName);
taskMap.put("taskState", taskState);
taskMap.put("owner", taskOwner);
taskMap.put("taskEstimate", estimate);
taskMap.put("taskRemaining", toDo);
taskMap.put("projectName", projectName);
taskMap.put("iterationName", iterationName);
Map map = (Map) usMap.get(workProductRef);
taskMap.put("usName", map.get("usFormattedId") + " " + map.get("usName"));
log.info("taskMap=" + taskMap);
} // for taskArray
}
return taskMap;
}
public double getTimeSpentByTask(String taskNo) throws Exception {
double timeSpent = 0.0D;
String apiURL = "https://rally1.rallydev.com/slm/webservice/1.34/adhoc";
String requestJSON =
"{"
+ "\"task\" : \"/task?query=(FormattedID%20=%20"
+ taskNo
+ ")&fetch=true\","
+ "\"timeentryitem\":\"/timeentryitem?query=(Task.FormattedID%20=%20"
+ taskNo
+ ")&fetch=Values\","
+ "\"timespent\":\"${timeentryitem.Values.Hours}\""
+ "}";
log.info("apiURL=" + apiURL);
log.info("requestJSON=" + requestJSON);
String responseJSON = postRallyXML(apiURL, requestJSON);
// log.info("responseJSON="+responseJSON);
// Map jsonMap=JsonUtil.jsonToMap(responseJSON);
JSONParser parser = new JSONParser();
Map jsonMap = (Map) parser.parse(responseJSON);
/*
//log.info("jsonMap="+jsonMap);
String taskObjId="";
String taskFormattedId="";
String taskName="";
String estimate="";
String toDo="";
String taskState="";
String taskOwner="";
String userstoryFormattedId="";
//Get task info
JSONObject taskMap=(JSONObject)jsonMap.get("task");
JSONArray taskArray=(JSONArray)taskMap.get("Results");
if(taskArray!=null && taskArray.size()>0) {
JSONObject taskInfo=(JSONObject)taskArray.get(0);
//log.info("taskMap="+taskMap);
//log.info("taskInfo="+taskInfo);
taskObjId=(taskInfo.get("ObjectID")).toString();
taskFormattedId=(taskInfo.get("FormattedID")).toString();
taskState=(taskInfo.get("State")).toString();
Object taskNameObj=taskInfo.get("Name");
taskName=taskNameObj==null ? "" : taskNameObj.toString();
Object estimateObject=taskInfo.get("Estimate");
estimate=estimateObject==null ? "" : estimateObject.toString();
Object toDoObject=taskInfo.get("ToDo");
toDo=toDoObject==null ? "" : toDoObject.toString();
JSONObject ownerMap=(JSONObject)taskInfo.get("Owner");
log.info("ownerMap="+ownerMap);
if(ownerMap!=null) {
taskOwner=(String)ownerMap.get("_refObjectName");
if(taskOwner==null) {
taskOwner="";
}
}
}
//Get user story info
JSONObject userstoryMap=(JSONObject)jsonMap.get("userstory");
JSONArray userstoryArray=(JSONArray)userstoryMap.get("Results");
if(userstoryArray!=null && userstoryArray.size()>0) {
JSONObject userstoryInfo=(JSONObject)userstoryArray.get(0);
userstoryFormattedId=(userstoryInfo.get("FormattedID")).toString();
log.info("userstoryFormattedId="+userstoryFormattedId);
}
*/
// Calculate timeSpent
JSONArray timeSpentList = (JSONArray) jsonMap.get("timespent");
log.info("timeSpentList=" + timeSpentList);
// double timeSpent=0.0;
for (int i = 0; i < timeSpentList.size(); i++) {
String timeSpentString = (String) timeSpentList.get(i);
if (timeSpentString != null) {
timeSpent += Double.parseDouble(timeSpentString);
}
}
return timeSpent;
}
/**
* 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;
}
*/
}
/**
* 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";
}
}
/** @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();
}
}
/**
* 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;
}
@Override
public void onComplete(String response, Object state) {
try {
Log.i(TAG, response);
json = Util.parseJson(response);
// photos are in the form of a json array
child = json.getJSONArray("data");
int total = child.length();
// contains links to photos
links = new ArrayList<String>(total);
// adds link to each photo to our list after replacing the "https" from url
// DownloadManager does not support https in gingerbread
for (int i = 0; i < total; i++) {
photo_json = child.getJSONObject(i);
if (dl_high_res_pics) {
JSONArray image_set = photo_json.getJSONArray("images");
// highest resolution picture has the index zero in the images jsonarray
JSONObject highest_res_pic = image_set.getJSONObject(0);
String http_replaced =
highest_res_pic.getString("source").replaceFirst("https", "http");
links.add(i, http_replaced);
} else {
// source property of the json object points to the photo's link
String http_replaced = photo_json.getString("source").replaceFirst("https", "http");
links.add(i, http_replaced);
}
}
download_photos.this.runOnUiThread(
new Runnable() {
public void run() {
// mytask = new DownloadImageTask();
// mytask.execute(links);
// start downloading using asynctask
// new DownloadImageTask().execute(links);
// downloadThread.setPath(path);
// downloadThread.setWholeTasks(links.size());
if (resume_file.exists()) {
initial_value = readProgress()[0];
final_value = links.size();
// case if the task is already completed
if (initial_value == final_value) {
completed = true;
resume_pause.setVisibility(View.GONE);
progress_download.setMax(final_value);
progress_download.setProgress(0); // bug in progress bar
progress_download.setProgress(initial_value);
progress_text.setText("Completed.");
mtext.setText(
getText(R.string.download_textview_message_1)
+ " "
+ path.toString()
+ ". ");
}
// case if some of the photos are already downloaded
else {
progress_download.setMax(links.size());
// progress_download.setProgress(0); //bug in progress bar
progress_download.setProgress(initial_value);
// N.B if i= initial_value -1, then one image will be downloaded again. so to
// save cost we start with i = initial_value
for (int i = initial_value; i < links.size(); i++) {
mtext.setText(
getText(R.string.download_textview_message_1)
+ " "
+ path.toString()
+ ". ");
// downloadThread.setRunningTask(i + 1);
downloadThread.enqueueDownload(
new DownloadTask(
links.get(i), path, i + 1, final_value, download_photos.this));
}
}
}
// case if the task is entirely new task
else {
for (int i = 0; i < links.size(); i++) {
mtext.setText(
getText(R.string.download_textview_message_1)
+ " "
+ path.toString()
+ ". ");
// downloadThread.setRunningTask(i + 1);
downloadThread.enqueueDownload(
new DownloadTask(
links.get(i), path, i + 1, links.size(), download_photos.this));
}
}
}
});
} catch (JSONException ex) {
Log.e(TAG, "JSONEXception : " + ex.getMessage());
}
}