@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();
}
}
public void sendSubmissionEmail(TnrsJob job) throws Exception {
String job_type = "";
if (job.getType() == TnrsJob.NAME_MATCH_JOB) {
job_type = " matching ";
} else {
job_type = " parsing ";
}
Email response = new HtmlEmail();
response.setHostName("localhost");
response.setSmtpPort(25);
response.setFrom("*****@*****.**");
response.setSubject("TNRS Job submission");
response.setMsg(
"Your TNRS "
+ job_type
+ " job ("
+ job.getRequest().getOriginalFilename()
+ ") was successfully submitted on "
+ dateFormat.format(new Date())
+ ". \n\n"
+ "When your list is done processing, you will receive an email notification that contains instructions regarding retrieval of your results from the TNRS website at http://tnrs.iplantcollaborative.org/.\n\n"
+ "Please contact us at [email protected] if you have any difficulty retrieving your results. \n"
+ "\n\n You can check the status of your job in the 'Retrieve results' tab of the application using your email and the following key: "
+ job.getRequest().getId()
+ ".\n\nTo update the status for your job in progress, please select the 'Retrieve results' button again. Your progress will update at this time.\n\n"
+ "Thank you, \n"
+ "iPlant Collaborative");
response.addTo(job.getRequest().getEmail());
response.send();
}
private void saveResults(
TnrsJob job,
JSONObject results,
Vector<String> ids,
Vector<String> original_names,
String session_id)
throws Exception {
if (job.getType() == TnrsJob.PARSING_JOB) {
ParsingResultsFile csv = new ParsingResultsFile(job, baseFolder);
csv.writeJsonData(results.getJSONArray("parsedNames"), ids);
} else {
MatchingResultsFile csv = new MatchingResultsFile(job, baseFolder, session_id, false);
TNRSResultsTransformer transformer = new TNRSResultsTransformer();
JSONArray results_array = transformer.transform(results, job, ids, original_names);
csv.writeJsonData(results_array, ids);
csv.close();
}
}
@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();
}
}
