.getSequencerRun().getName())); if (workflowPlan.getHTSFSamples() != null) { for (HTSFSample sample : workflowPlan.getHTSFSamples()) { sb.append(String.format("HTSFSample Name: %s%n", sample.getName()));
public Set<HTSFSample> getAggregateHTSFSampleSet() throws PipelineException { Set<HTSFSample> htsfSampleSet = new HashSet<HTSFSample>(); if (getWorkflowPlan().getSequencerRun() == null && getWorkflowPlan().getHTSFSamples() == null) { logger.error("Don't have either sequencerRun and htsfSample"); throw new PipelineException("Don't have either sequencerRun and htsfSample"); } if (getWorkflowPlan().getSequencerRun() != null) { logger.info("sequencerRun: {}", getWorkflowPlan().getSequencerRun().toString()); try { htsfSampleSet.addAll(getPipelineBeanService().getMaPSeqDAOBean().getHTSFSampleDAO() .findBySequencerRunId(getWorkflowPlan().getSequencerRun().getId())); } catch (MaPSeqDAOException e) { logger.error("problem getting HTSFSamples"); } } if (getWorkflowPlan().getHTSFSamples() != null) { htsfSampleSet.addAll(getWorkflowPlan().getHTSFSamples()); } return htsfSampleSet; }
if (getWorkflowPlan().getSequencerRun() == null && getWorkflowPlan().getHTSFSamples() == null) { logger.error("Don't have either sequencerRun and htsfSample"); throw new PipelineException("Don't have either sequencerRun and htsfSample"); if (getWorkflowPlan().getHTSFSamples() != null) { htsfSampleSet.addAll(getWorkflowPlan().getHTSFSamples());
if (getWorkflowPlan().getHTSFSamples() != null) { logger.info("htsfSampleSet.size(): {}", htsfSampleSet.size()); htsfSampleSet.addAll(getWorkflowPlan().getHTSFSamples());
if (getWorkflowPlan().getSequencerRun() == null && getWorkflowPlan().getHTSFSamples() == null) { logger.error("Don't have either sequencerRun and htsfSample"); throw new PipelineException("Don't have either sequencerRun and htsfSample"); if (getWorkflowPlan().getHTSFSamples() != null) { htsfSampleSet.addAll(getWorkflowPlan().getHTSFSamples());
if (getWorkflowPlan().getSequencerRun() == null && getWorkflowPlan().getHTSFSamples() == null) if (getWorkflowPlan().getHTSFSamples() != null) htsfSampleSet.addAll(getWorkflowPlan().getHTSFSamples());