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; }
WorkflowPlan workflowPlan = pipelineExecutor.getPipeline().getWorkflowPlan(); if (workflowPlan != null) { WorkflowRun workflowRun = workflowPlan.getWorkflowRun(); if (workflowRun != null) { Account creator = workflowRun.getCreator(); StringBuilder sb = new StringBuilder(); sb.append(String.format("WorkflowRun Name: %s%n", workflowRun.getName())); if (workflowPlan.getSequencerRun() != null) { sb.append(String.format("SequencerRun Name: %s%n", workflowPlan .getSequencerRun().getName())); if (workflowPlan.getHTSFSamples() != null) { for (HTSFSample sample : workflowPlan.getHTSFSamples()) { sb.append(String.format("HTSFSample Name: %s%n", sample.getName()));
WorkflowRun workflowRun = workflowPlan.getWorkflowRun(); SequencerRun sequencerRun = workflowPlan.getSequencerRun(); if (sequencerRun != null) { logger.debug("sequencerRun.getId().toString(): {}", sequencerRun.getId().toString());
@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); }
try { WorkflowRun workflowRun = workflowRunDAO.findById(pipelineExecutor.getPipeline().getWorkflowPlan() .getWorkflowRun().getId()); pipelineExecutor.getPipeline().getWorkflowPlan().setWorkflowRun(workflowRun);
.findById(getWorkflowPlan().getWorkflowRun().getId()); workflowRun.setStartDate(new Date()); workflowRun.setCondorDAGClusterId(jobNode.getCluster());
File baseDir = new File(getWorkflowPlan().getSequencerRun().getBaseDirectory()); File sequencerRunDir = new File(baseDir, getWorkflowPlan().getSequencerRun().getName()); File dataDir = new File(sequencerRunDir, "Data"); File intensitiesDir = new File(dataDir, "Intensities"); try { htsfSampleList = getWorkflowBeanService().getMaPSeqDAOBean().getHTSFSampleDAO() .findBySequencerRunId(getWorkflowPlan().getSequencerRun().getId()); } catch (MaPSeqDAOException e) { e.printStackTrace(); .addArgument(ConfigureBCLToFastqCLI.OUTPUTDIR, unalignedDir.getAbsolutePath()); Set<EntityAttribute> srEntityAttributeSet = getWorkflowPlan().getSequencerRun().getAttributes(); copy2Job.addArgument(CopyCLI.SOURCE, source2File.getAbsolutePath()); File r2FastqFile = new File(casavaOutputDirectory, String.format("%s_%s_L%03d_R%d.fastq.gz", getWorkflowPlan().getSequencerRun().getName(), htsfSample.getBarcode(), laneIndex, 2)); copy2Job.addArgument(CopyCLI.DESTINATION, r2FastqFile.getAbsolutePath()); copy2Job.addArgument(CopyCLI.MIMETYPE, MimeType.FASTQ.toString());
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) { e.printStackTrace(); if (getWorkflowPlan().getHTSFSamples() != null) { htsfSampleSet.addAll(getWorkflowPlan().getHTSFSamples());
if (getWorkflowPlan().getSequencerRun() != null) { logger.info("sequencerRun: {}", getWorkflowPlan().getSequencerRun().toString()); try { htsfSampleSet.addAll(getWorkflowBeanService().getMaPSeqDAOBean().getHTSFSampleDAO() .findBySequencerRunId(getWorkflowPlan().getSequencerRun().getId())); } catch (MaPSeqDAOException e) { e.printStackTrace(); 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().getSequencerRun() != null) { logger.info("sequencerRun: {}", getWorkflowPlan().getSequencerRun().toString()); try { htsfSampleSet.addAll(getPipelineBeanService().getMaPSeqDAOBean().getHTSFSampleDAO() .findBySequencerRunId(getWorkflowPlan().getSequencerRun().getId())); } catch (MaPSeqDAOException e) { e.printStackTrace(); if (getWorkflowPlan().getHTSFSamples() != null) { htsfSampleSet.addAll(getWorkflowPlan().getHTSFSamples());
if (getWorkflowPlan().getSequencerRun() == null && getWorkflowPlan().getHTSFSamples() == null) if (getWorkflowPlan().getSequencerRun() != null) logger.info("sequencerRun: {}", getWorkflowPlan().getSequencerRun().toString()); .findBySequencerRunId(getWorkflowPlan().getSequencerRun().getId())); if (getWorkflowPlan().getHTSFSamples() != null) htsfSampleSet.addAll(getWorkflowPlan().getHTSFSamples());