getPipelineBeanService().getMaPSeqDAOBean().getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e1) { logger.error("Could not persist HTSFSample");
List<HTSFSample> htsfSampleList = mapseqDAOBean.getHTSFSampleDAO().findBySequencerRunId(sr.getId()); Map<Integer, List<Double>> laneClusterDensityTotalMap = new HashMap<Integer, List<Double>>(); mapseqDAOBean.getHTSFSampleDAO().save(sample);
HTSFSampleDAO htsfSampleDAO = mapseqDAOBean.getHTSFSampleDAO(); try { if (sequencerRunId != null) { this.mapseqDAOBean.getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
HTSFSampleDAO htsfSampleDAO = mapseqDAOBean.getHTSFSampleDAO(); try { if (sequencerRunId != null) { this.mapseqDAOBean.getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
HTSFSampleDAO htsfSampleDAO = mapseqDAOBean.getHTSFSampleDAO(); try { if (sequencerRunId != null) { this.mapseqDAOBean.getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
List<HTSFSample> htsfSampleList = mapseqDAOBean.getHTSFSampleDAO().findBySequencerRunId(sr.getId()); mapseqDAOBean.getHTSFSampleDAO().save(sample); System.out.println(String.format("Successfully saved sample: %s", sample.getId())); logger.info(sample.toString());
getWorkflowBeanService().getMaPSeqDAOBean().getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
htsfSample = mapseqDAOBean.getHTSFSampleDAO().findById(htsfSampleId); } catch (MaPSeqDAOException e1) { e1.printStackTrace();
getWorkflowBeanService().getMaPSeqDAOBean().getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
htsfSample = mapseqDAOBean.getHTSFSampleDAO().findById(guid); } catch (MaPSeqDAOException e) { e.printStackTrace(); mapseqDAOBean.getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
getWorkflowBeanService().getMaPSeqDAOBean().getHTSFSampleDAO().save(htsfSample);
htsfSample = mapseqDAOBean.getHTSFSampleDAO().findById(guid); } catch (MaPSeqDAOException e) { e.printStackTrace(); mapseqDAOBean.getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
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; }
logger.info("sequencerRun: {}", getWorkflowPlan().getSequencerRun().toString()); try { htsfSampleSet.addAll(getWorkflowBeanService().getMaPSeqDAOBean().getHTSFSampleDAO() .findBySequencerRunId(getWorkflowPlan().getSequencerRun().getId())); } catch (MaPSeqDAOException e) {
logger.info("sequencerRun: {}", getWorkflowPlan().getSequencerRun().toString()); try { htsfSampleSet.addAll(getPipelineBeanService().getMaPSeqDAOBean().getHTSFSampleDAO() .findBySequencerRunId(getWorkflowPlan().getSequencerRun().getId())); } catch (MaPSeqDAOException e) {
@Override public void postRun() throws WorkflowException { List<HTSFSample> htsfSampleList = null; try { htsfSampleList = getWorkflowBeanService().getMaPSeqDAOBean().getHTSFSampleDAO() .findBySequencerRunId(getWorkflowPlan().getSequencerRun().getId()); } catch (MaPSeqDAOException e) { e.printStackTrace(); } if (htsfSampleList == null) { logger.warn("htsfSampleList was null"); return; } List<Long> sequencerRunIdList = new ArrayList<Long>(); sequencerRunIdList.add(getWorkflowPlan().getSequencerRun().getId()); SaveDemultiplexedStatsAttributesRunnable saveDemultiplexedStatsAttributesRunnable = new SaveDemultiplexedStatsAttributesRunnable(); saveDemultiplexedStatsAttributesRunnable.setMapseqDAOBean(getWorkflowBeanService().getMaPSeqDAOBean()); saveDemultiplexedStatsAttributesRunnable.setSequencerRunIdList(sequencerRunIdList); Executors.newSingleThreadExecutor().execute(saveDemultiplexedStatsAttributesRunnable); SaveObservedClusterDensityAttributesRunnable saveObservedClusterDensityAttributesRunnable = new SaveObservedClusterDensityAttributesRunnable(); saveObservedClusterDensityAttributesRunnable.setMapseqDAOBean(getWorkflowBeanService().getMaPSeqDAOBean()); saveObservedClusterDensityAttributesRunnable.setMapseqConfigurationService(getWorkflowBeanService() .getMaPSeqConfigurationService()); saveObservedClusterDensityAttributesRunnable.setSequencerRunIdList(sequencerRunIdList); Executors.newSingleThreadExecutor().execute(saveObservedClusterDensityAttributesRunnable); }
logger.info("sequencerRun: {}", getWorkflowPlan().getSequencerRun().toString()); try { htsfSampleSet.addAll(getPipelineBeanService().getMaPSeqDAOBean().getHTSFSampleDAO() .findBySequencerRunId(getWorkflowPlan().getSequencerRun().getId())); } catch (MaPSeqDAOException e) {
htsfSampleSet.addAll(getPipelineBeanService().getMaPSeqDAOBean().getHTSFSampleDAO() .findBySequencerRunId(getWorkflowPlan().getSequencerRun().getId()));
htsfSampleList = getWorkflowBeanService().getMaPSeqDAOBean().getHTSFSampleDAO() .findBySequencerRunId(getWorkflowPlan().getSequencerRun().getId()); } catch (MaPSeqDAOException e) {