Package uk.ac.bbsrc.tgac.miso.core.data

Examples of uk.ac.bbsrc.tgac.miso.core.data.SequencerReference

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  }

  @RequestMapping(value = "/solid/{referenceId}/{runName}", method = RequestMethod.GET)
  public ModelAndView solidStats(@PathVariable(value = "referenceId") Long referenceId, @PathVariable(value = "runName") String runName, ModelMap model) throws IOException {
    model.put("platformtype", PlatformType.SOLID);
    SequencerReference sr = requestManager.getSequencerReferenceById(referenceId);
    if (sr != null) {
      if (!sr.getPlatform().getPlatformType().equals(PlatformType.SOLID)) {
        throw new IOException("Trying to interrogate a " + sr.getPlatform().getPlatformType().getKey() + " sequencer reference with an SOLiD strategy");
      }

      try {
        Status status = requestManager.getStatusByRunName(runName);
        if (status != null) {
          model.put("referenceName", sr.getName());
          model.put("referenceId", sr.getId());
          model.put("runId", requestManager.getRunByAlias(runName).getId());
          model.put("runName", runName);
          model.put("runStatus", status);

          InputStream in = StatsController.class.getResourceAsStream("/status/xsl/solid/statusXml.xsl");
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  }

  @RequestMapping(value = "/pacbio/{referenceId}", method = RequestMethod.GET)
  public ModelAndView pacbioStats(@PathVariable(value = "referenceId") Long referenceId, ModelMap model) throws IOException {
    model.put("platformtype", PlatformType.PACBIO.getKey().toLowerCase());
    SequencerReference sr = requestManager.getSequencerReferenceById(referenceId);
    if (sr != null) {
      if (!sr.getPlatform().getPlatformType().equals(PlatformType.PACBIO)) {
        throw new IOException("Trying to interrogate a " + sr.getPlatform().getPlatformType().getKey() + " sequencer reference with a PacBio strategy");
      }
      model.put("stats", requestManager.listAllStatusBySequencerName(sr.getName()));
      model.put("referenceName", sr.getName());
      model.put("referenceId", sr.getId());
    }
    else {
      model.put("error", "Cannot retrieve the given sequencer reference: " + referenceId);
    }
    return new ModelAndView("/pages/viewStats.jsp", model);
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  }

  @RequestMapping(value = "/pacbio/{referenceId}/{runName}", method = RequestMethod.GET)
  public ModelAndView pacbioStats(@PathVariable(value = "referenceId") Long referenceId, @PathVariable(value = "runName") String runName, ModelMap model) throws IOException {
    model.put("platformtype", PlatformType.PACBIO);
    SequencerReference sr = requestManager.getSequencerReferenceById(referenceId);
    if (sr != null) {
      if (!sr.getPlatform().getPlatformType().equals(PlatformType.PACBIO)) {
        throw new IOException("Trying to interrogate a " + sr.getPlatform().getPlatformType().getKey() + " sequencer reference with a PacBio strategy");
      }

//      try {
        Status status = requestManager.getStatusByRunName(runName);
        if (status != null) {
          model.put("referenceName", sr.getName());
          model.put("referenceId", sr.getId());
          model.put("runId", requestManager.getRunByAlias(runName).getId());
          model.put("runName", runName);
          model.put("runStatus", status);

          /*
 
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    try {
      if (json.has("server") && !json.get("server").equals("")) {
        InetAddress i = InetAddress.getByName(json.getString("server"));
        String name = json.getString("name");
        Platform p = requestManager.getPlatformById(json.getInt("platform"));
        SequencerReference sr = new SequencerReferenceImpl(name, i, p);
        sr.setAvailable(i.isReachable(2000));
        log.info(sr.toString());
        requestManager.saveSequencerReference(sr);
        return JSONUtils.SimpleJSONResponse("Saved successfully");
      }
    }
    catch (Exception e) {
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Related Classes of uk.ac.bbsrc.tgac.miso.core.data.SequencerReference

  • uk.ac.bbsrc.tgac.miso.spring.ajax.SequencerReferenceControllerHelperService
  • uk.ac.bbsrc.tgac.miso.sqlstore.SQLSequencerReferenceDAO
  • uk.ac.bbsrc.tgac.miso.sqlstore.SQLSequencerReferenceDAO$SequencerReferenceMapper
  • uk.ac.bbsrc.tgac.miso.webapp.controller.StatsController
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