@Override
public void handle(HttpExchange arg0) throws IOException {
try {
JSONObject request =
(JSONObject) JSONSerializer.toJSON(IOUtils.toString(arg0.getRequestBody()));
String email = request.getString("email");
String key = request.getString("key");
for (int i = 0; i < jobs.size(); i++) {
TnrsJob job = jobs.get(i);
if (job.getRequest().getId().equals(key) && job.getRequest().getEmail().equals(email)) {
JSONObject json = (JSONObject) JSONSerializer.toJSON(job.toJsonString());
json.put("status", "incomplete");
json.put("progress", job.progress());
HandlerHelper.writeResponseRequest(arg0, 200, json.toString(), "application/json");
return;
}
}
if (JobHelper.jobFileExists(baseFolder, email, key)) {
TnrsJob job = JobHelper.readJobInfo(baseFolder, email, key);
HandlerHelper.writeResponseRequest(arg0, 200, job.toJsonString(), "application/json");
} else {
HandlerHelper.writeResponseRequest(
arg0, 500, "No such job exists o it might have expired", "text/plain");
}
} catch (Exception ex) {
log.error(ExceptionUtils.getFullStackTrace(ex));
throw new IOException(ex);
}
}
@Override
public void handle(HttpExchange arg0) throws IOException {
try {
JSONObject json =
(JSONObject) JSONSerializer.toJSON(IOUtils.toString(arg0.getRequestBody()));
JSONObject result = new JSONObject();
String email = json.getString("email");
String key = json.getString("key");
for (int i = 0; i < jobs.size(); i++) {
TnrsJob job = jobs.get(i);
if (job.getRequest().getEmail().equals(email) && job.getRequest().getId().equals(key)) {
if (job.status().equals("failed") || job.status().equals("error")) {
result.put("type", "failed");
} else {
result.put("type", "incomplete");
double progress = job.progress();
if (job.progress() == 100.0) {
progress = 99.0;
}
result.put("progress", progress);
}
HandlerHelper.writeResponseRequest(arg0, 200, result.toString(), "application/json");
return;
}
}
String filename = baseFolder + email.replace("@", "-").replace(".", "-") + "/result" + key;
File results = new File(filename);
if (!results.exists()) {
result.put("type", "non-existent");
} else {
result.put("type", "complete");
TnrsJob job = JobHelper.readJobInfo(baseFolder, email, key);
result.put("job_type", job.getTypeString());
}
HandlerHelper.writeResponseRequest(arg0, 200, result.toString(), "application/json");
return;
} catch (Exception ex) {
log.error(ExceptionUtils.getFullStackTrace(ex));
throw new IOException(ex);
}
}
@Override
public void handle(HttpExchange arg0) throws IOException {
try {
JSONObject command =
(JSONObject) JSONSerializer.toJSON(IOUtils.toString(arg0.getRequestBody()));
String job_id = command.getString("job_id");
TnrsJob job = null;
for (TnrsJob jobc : jobs) {
if (jobc.getRequest().getId().equals(job_id)) {
job = jobc;
break;
}
}
if (job == null) {
HandlerHelper.writeResponseRequest(arg0, 500, "Invalid job identifier", "text/plain");
}
if (command.getString("command").equals("stop")) {
synchronized (job) {
job.disable();
}
} else if (command.getString("command").equals("pause")) {
synchronized (job) {
job.pause();
}
} else if (command.getString("command").equals("resume")) {
synchronized (job) {
job.resume();
}
} else {
HandlerHelper.writeResponseRequest(arg0, 500, "Wrong command", "text/plain");
return;
}
HandlerHelper.writeResponseRequest(arg0, 200, "", "text/plain");
} catch (Exception ex) {
log.error(ExceptionUtils.getFullStackTrace(ex));
}
}
@Override
public void handle(HttpExchange arg0) throws IOException {
try {
String message =
"<html><body><table border=\"1\"><tr><th>Email</th><th>Submitted at:</th><th>Progress:</th><th>Status:</th><th>Job id</th></tr>";
for (int i = 0; i < jobs.size(); i++) {
TnrsJob job = jobs.get(i);
message +=
"<tr> <td> "
+ job.getRequest().getEmail()
+ "</td><td>"
+ job.getSubmissionDate()
+ " </td><td> "
+ job.progress()
+ "% </td><td> "
+ job.status()
+ "</td><td>"
+ job.getRequest().getId()
+ "</td></tr>\n";
}
message += "</table>";
HandlerHelper.writeResponseRequest(arg0, 200, message, "text/html");
} catch (Exception ex) {
log.error(ExceptionUtils.getFullStackTrace(ex));
throw new IOException(ex);
}
}
@Override
public void handle(HttpExchange arg0) throws IOException {
try {
JSONObject json =
(JSONObject) JSONSerializer.toJSON(IOUtils.toString(arg0.getRequestBody()));
String contents = json.getString("names");
byte[] fileContents = contents.getBytes("UTF-8");
ByteArrayOutputStream byteArray = new ByteArrayOutputStream();
GZIPOutputStream gzipStr = new GZIPOutputStream(byteArray);
gzipStr.write(fileContents);
gzipStr.close();
ByteArrayOutputStream byteArray2 = new ByteArrayOutputStream();
Base64OutputStream base64 = new Base64OutputStream(byteArray2);
base64.write(byteArray.toByteArray());
base64.close();
String value = new String(byteArray2.toByteArray());
json.remove("names");
json.put("upload", value);
HttpClient client = new HttpClient();
PostMethod post =
new PostMethod(
"http://"
+ properties.getProperty("org.iplantc.tnrs.servicesHost")
+ "/tnrs-svc/upload");
post.setRequestEntity(new StringRequestEntity(json.toString(), "text/plain", "UTF-8"));
client.executeMethod(post);
HandlerHelper.writeResponseRequest(arg0, 200, "", "text/plain");
} catch (Exception ex) {
log.error(ExceptionUtils.getFullStackTrace(ex));
ex.printStackTrace();
throw new IOException(ex);
}
}
@Override
public void handle(HttpExchange arg0) throws IOException {
try {
JSONObject json = new JSONObject();
JSONArray array = new JSONArray();
for (int i = 0; i < jobs.size(); i++) {
JSONObject job_info = new JSONObject();
TnrsJob job = jobs.get(i);
job_info.put("email", job.getRequest().getEmail());
job_info.put("progress", job.progress());
array.add(job_info);
}
json.put("jobs", array);
HandlerHelper.writeResponseRequest(arg0, 200, json.toString(), "application/json");
} catch (Exception ex) {
log.error(ExceptionUtils.getFullStackTrace(ex));
throw new IOException(ex);
}
}
@Override
public void handle(HttpExchange arg0) throws IOException {
try {
JSONObject json =
(JSONObject) JSONSerializer.toJSON(IOUtils.toString(arg0.getRequestBody()));
String email = json.getString("email");
String key = json.getString("key");
String session_id = json.getString("session_id");
TnrsJob job = JobHelper.readJobInfo(baseFolder, email, key);
if (job.getType() == TnrsJob.PARSING_JOB) {
ParsingResultsFile results = new ParsingResultsFile(job, baseFolder);
results.createFileForDownload(properties.getProperty("org.iplantc.folder.tmp"));
} else {
MatchingResultsFile results = new MatchingResultsFile(job, baseFolder, session_id, false);
results.createFileForDownload(
properties.getProperty("org.iplantc.tnrs.folder.tmp"), json);
results.close();
}
String url = servicesUrl + "getcsv?id=" + key;
HandlerHelper.writeResponseRequest(arg0, 200, url, null);
} catch (Exception ex) {
log.error(ExceptionUtils.getFullStackTrace(ex));
ex.printStackTrace();
}
}
@Override
public void handle(HttpExchange arg0) throws IOException {
try {
String request = IOUtils.toString(arg0.getRequestBody());
JSONObject datas = (JSONObject) JSONSerializer.toJSON(request);
UUID uid = UUID.randomUUID();
HashMap<String, String> info = new HashMap<String, String>();
info.put("email", datas.getString("email"));
info.put("institution", "");
info.put("name", "");
info.put("sensitivity", datas.getString("sensitivity"));
info.put("has_id", datas.getString("has_id"));
info.put("id", uid.toString().replace("-", ""));
info.put("type", datas.getString("type"));
info.put("sources", datas.getString("sources"));
info.put("classification", datas.getString("classification"));
info.put("match_to_rank", datas.getString("match_to_rank"));
/**
* *
*
* <p>To be replaced by better code
*/
byte[] data = null;
if (datas.has("upload")) {
data =
IOUtils.toByteArray(
new GZIPInputStream(
new Base64InputStream(
new ByteArrayInputStream(datas.getString("upload").getBytes()))));
} else if (datas.has("names")) {
data = datas.getString("names").getBytes();
} else {
HandlerHelper.writeResponseRequest(arg0, 500, "Invalid request!", null);
return;
}
UniversalDetector detector = new UniversalDetector(null);
detector.handleData(data, 0, data.length);
detector.dataEnd();
String content = "";
String encoding = detector.getDetectedCharset();
if (encoding != null) {
if (encoding.equals("WINDOWS-1252")) {
encoding = "ISO-8859-1";
ByteArrayOutputStream t = new ByteArrayOutputStream();
OutputStreamWriter wr = new OutputStreamWriter(t, "UTF-8");
wr.write(new String(data, encoding));
wr.close();
content = t.toString("UTF-8");
} else {
content = new String(data, "UTF-8");
}
} else {
content = new String(data, "UTF-8");
}
info.put("upload", content);
/** */
JSONObject json = createJSONJobRequest(info);
json.put("submitted_date", new Date().toString().replace(":", ""));
json.put("original", datas.getString("file_name"));
json.put("sensitivity", datas.getString("sensitivity"));
TnrsJob job = submitJob(json.toString());
job.setTaxonomic(datas.getBoolean("taxonomic"));
job.setEmail(!info.containsKey("noemail"));
job.setSources(info.get("sources"));
job.setClassification(info.get("classification"));
job.setAllowPartial(Boolean.parseBoolean(info.get("match_to_rank")));
log.info(job.getRequest().getId() + " " + job.getRequest().getEmail());
HandlerHelper.writeResponseRequest(arg0, 200, job.getRequest().getId(), null);
if (info.get("email").trim().equals("*****@*****.**") || !job.email()) return;
try {
sendSubmissionEmail(job);
} catch (Exception ex) {
log.error(ExceptionUtils.getFullStackTrace(ex));
ex.printStackTrace();
}
} catch (Exception ex) {
log.error(ExceptionUtils.getFullStackTrace(ex));
ex.printStackTrace();
throw new IOException(ex);
}
}