Esempio n. 1
0
    @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);
      }
    }
Esempio n. 2
0
    @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);
      }
    }
Esempio n. 3
0
    @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));
      }
    }
Esempio n. 4
0
    @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);
      }
    }
Esempio n. 5
0
    @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);
      }
    }
Esempio n. 6
0
    @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);
      }
    }
Esempio n. 7
0
    @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();
      }
    }
Esempio n. 8
0
    @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);
      }
    }