Examples of SequencerInterrogator

uk.ac.bbsrc.tgac.miso.core.service.integration.strategy.interrogator.SequencerInterrogator
This class represents an entry point that couples a SequencerInterrogationStrategy to a SequencerReference, so that reference can be interrogated by that strategy. In this way, each mechanism that can be employed by a strategy has to be wrapped up with a SequencerReference. @author Rob Davey @since 0.0.2

Examples of uk.ac.bbsrc.tgac.miso.core.service.integration.strategy.interrogator.SequencerInterrogator

    if (sr != null) {
      if (!sr.getPlatform().getPlatformType().equals(PlatformType.LS454)) {
        throw new IOException("Trying to interrogate a " + sr.getPlatform().getPlatformType().getKey() + " sequencer reference with a 454 strategy");
      }
      try {
        SequencerInterrogator context = SequencerInterrogatorFactory.getSequencerInterrogator(sr);


        model.put("stats", context.listAllStatus());
        model.put("referenceName", sr.getName());
        model.put("referenceId", sr.getId());
      }
      catch (InterrogationException e) {
        model.put("error", MisoWebUtils.generateErrorDivMessage("Cannot retrieve status information for the given sequencer reference: " + sr.getName(), e.getMessage()));

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Examples of uk.ac.bbsrc.tgac.miso.core.service.integration.strategy.interrogator.SequencerInterrogator

    if (sr != null) {
      if (!sr.getPlatform().getPlatformType().equals(PlatformType.LS454)) {
        throw new IOException("Trying to interrogate a " + sr.getPlatform().getPlatformType().getKey() + " sequencer reference with a 454 strategy");
      }
      try {
        SequencerInterrogator context = SequencerInterrogatorFactory.getSequencerInterrogator(sr);
        Status status = context.getRunStatus(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);

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Examples of uk.ac.bbsrc.tgac.miso.core.service.integration.strategy.interrogator.SequencerInterrogator

   * @return SequencerInterrogator
   * @throws InterrogationException when an unsupported PlatformType is specified 
   */
  public static SequencerInterrogator getSequencerInterrogator(SequencerReference sr) throws InterrogationException {
    if (sr.getPlatform().getPlatformType().equals(PlatformType.ILLUMINA)) {
      return new SequencerInterrogator(new IlluminaSequencerInterrogationStrategy(), sr);
    }
    else if (sr.getPlatform().getPlatformType().equals(PlatformType.LS454)) {
      return new SequencerInterrogator(new LS454SequencerInterrogationStrategy(), sr);
    }
    else if (sr.getPlatform().getPlatformType().equals(PlatformType.SOLID)) {
      return new SequencerInterrogator(new SolidSequencerInterrogationStrategy(), sr);
    }
    else if (sr.getPlatform().getPlatformType().equals(PlatformType.IONTORRENT)) {
      //return new SequencerInterrogator(new SolidSequencerInterrogationStrategy(), sr);
      throw new InterrogationException("Unsupported PlatformType");
    }

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