@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);
}
}
private void sendNormalCompletionEmail(TnrsJob job) throws Exception {
EmailAttachment attachment = new EmailAttachment();
attachment.setPath(JobHelper.createJobInfoFile(job));
attachment.setDisposition(EmailAttachment.ATTACHMENT);
attachment.setDescription("Job information");
attachment.setName(job.getRequest().getFilename() + " " + job.getRequest().getId() + ".txt");
MultiPartEmail response = new MultiPartEmail();
response.setHostName(properties.getProperty("org.iplantc.tnrs.mail.host"));
response.setSmtpPort(Integer.parseInt(properties.getProperty("org.iplantc.tnrs.mail.port")));
response.setFrom("*****@*****.**");
response.setSubject("TNRS Job completion");
response.setMsg(
"Your TNRS "
+ job.getTypeString()
+ " job for the file "
+ job.getRequest().getOriginalFilename()
+ " completed on "
+ dateFormat.format(new Date())
+ ".Details describing the settings applied for this job are attached to this email. You may wish to retain this for your records. \n\n Your results will be available for 7 days, after which they will be deleted from our system. \n\n"
+ "To view your results, go to the TNRS website at http://tnrs.iplantcollaborative.org, select the \"Retrieve results\" tab, and enter your email address and the following submission key:\n\n"
+ job.getRequest().getId()
+ "\n\n"
+ "Please contact us at [email protected] if you have any difficulty retrieving your results.\n"
+ "\n"
+ "Thank you,\n"
+ "iPlant Collaborative");
response.addTo(job.getRequest().getEmail());
response.attach(attachment);
response.send();
}
@Override
public void run() {
try {
StopWatch stp2 = new StopWatch();
stp2.start();
JSONObject json = new JSONObject();
job.setStatus("running");
if (job.progress() == 100.0) {
finalizeJob(job);
return;
}
Vector<String> ids = new Vector<String>();
Vector<String> original_names = new Vector<String>();
String data = job.getNextDataBatch();
if (data == null || data.equals("")) return;
String[] lines = data.split("\n");
if (job.containsId()) {
for (int i = 0; i < lines.length; i++) {
if (lines[i].trim().equals("")) continue;
ids.add(NameUtil.getNameId(lines[i]));
}
}
for (int i = 0; i < lines.length; i++) {
original_names.add(NameUtil.processName(lines[i], job.containsId()));
}
String names = NameUtil.CleanNames(lines, job);
if (names.equals("")) return;
if (job.getType() == TnrsJob.NAME_MATCH_JOB) {
TaxamatchInterface taxa_match = new TaxamatchInterface(tnrsBaseUrl);
String result = taxa_match.queryTaxamatch(names, job);
json = (JSONObject) JSONSerializer.toJSON(result);
} else if (job.getType() == TnrsJob.PARSING_JOB) {
json = gni_interface.parseNames(names);
}
if (job.outstandingNames() == 0) {
JobHelper.persistJobInfo(baseFolder, job);
}
saveResults(job, json, ids, original_names, "");
job.setStatus("idle");
stp2.stop();
log.info("overall :" + stp2.toString());
} catch (Exception ex) {
log.error(ExceptionUtils.getFullStackTrace(ex));
job.setStatus("failed");
ex.printStackTrace();
}
}
/**
* Checks if the map scale is valid
*
* @return <code>true</code> if map scale is valid; <code>false</code> otherwise.
*/
protected boolean validateMapScales() {
return JobHelper.isRequestScalesInRange(
this.session.getMapScales(),
(int) this.session.getLocation().getZoom(),
layer,
session.getLocation().getSrs());
}
@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);
}
}
/**
* This main loop iterates over the submitted jobs and creates the corresponding threads that will
* carry the execution of each job segment.
*/
@Override
public void run() {
try {
int jobno = 0;
while (true) {
sleep(20);
synchronized (jobs) {
if (jobs.size() == 0) {
continue;
}
}
TnrsJob job = jobs.get(jobno % jobs.size());
if (job.status().equalsIgnoreCase("idle")) {
ExecutionThread thread = new ExecutionThread(job);
threads.add(thread);
thread.start();
} else if (job.status().equalsIgnoreCase("stopped")) {
jobs.remove(job);
JobHelper.cleanJobData(baseFolder, job);
jobno = 0;
continue;
} else if (job.status().equals("failed")) {
sendFailedJobEmail(job);
job.setStatus("error");
}
jobno++;
if (jobs.size() == 200) {
for (int i = 0; i < threads.size(); i++) {
threads.elementAt(i).join();
}
jobno = 0;
threads.clear();
}
sleep(10);
}
} catch (Exception e) {
log.error(ExceptionUtils.getFullStackTrace(e));
e.printStackTrace();
}
}
@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();
}
}
void waitTillJobHasFinished() {
jobHelper.waitTillJobHasFinished();
}