public static Platform getPlatform(MaPSeqDAOBean mapseqDAOBean, JSONObject jsonObject) throws JSONException { logger.info("ENTERING getPlatform(MaPSeqDAOBean, JSONObject)"); Platform platform = null; if (jsonObject.has("guid")) { Long guid = jsonObject.getLong("guid"); try { platform = mapseqDAOBean.getPlatformDAO().findById(guid); } catch (MaPSeqDAOException e) { e.printStackTrace(); } } if (platform == null) { logger.warn("No Platform found"); return null; } logger.debug("Found Platform: {}", platform.toString()); return platform; }
public static Platform getPlatform(MaPSeqDAOBean mapseqDAOBean, JSONObject jsonObject) throws JSONException { logger.info("ENTERING getPlatform(MaPSeqDAOBean, JSONObject)"); Platform platform = null; if (jsonObject.has("guid")) { Long guid = jsonObject.getLong("guid"); try { platform = mapseqDAOBean.getPlatformDAO().findById(guid); } catch (MaPSeqDAOException e) { e.printStackTrace(); } } if (platform == null) { logger.warn("No Platform found"); return null; } logger.debug("Found Platform: {}", platform.toString()); return platform; }
clazz.getName(), workflowId); } catch (MaPSeqDAOException e) { e.printStackTrace();
e.printStackTrace(); } catch (MaPSeqDAOException e) { e.printStackTrace();
ncgenesWorkflow = workflowDAO.findByName("NCGenes"); } catch (MaPSeqDAOException e2) { e2.printStackTrace(); this.mapseqDAOBean.getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
this.mapseqDAOBean.getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
this.mapseqDAOBean.getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
e.printStackTrace(); } catch (Exception e) { e.printStackTrace();
.findByName("NIDAUCSFVariantCalling"); } catch (MaPSeqDAOException e1) { e1.printStackTrace(); getWorkflowBeanService().getMaPSeqDAOBean().getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
htsfSample = mapseqDAOBean.getHTSFSampleDAO().findById(htsfSampleId); } catch (MaPSeqDAOException e1) { e1.printStackTrace(); return;
ncgenesWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO().findByName("NCGenes"); } catch (MaPSeqDAOException e1) { e1.printStackTrace();
ncgenesWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO().findByName("NCGenes"); } catch (MaPSeqDAOException e1) { e1.printStackTrace();
ncgenesWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO().findByName("NCGenes"); } 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();
htsfSample = mapseqDAOBean.getHTSFSampleDAO().findById(guid); } catch (MaPSeqDAOException e) { e.printStackTrace(); mapseqDAOBean.getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
sequencerRun = mapseqDAOBean.getSequencerRunDAO().findById(guid); } catch (MaPSeqDAOException e) { e.printStackTrace(); mapseqDAOBean.getSequencerRunDAO().save(sequencerRun); } catch (MaPSeqDAOException e) { e.printStackTrace();
sequencerRun = mapseqDAOBean.getSequencerRunDAO().findById(guid); } catch (MaPSeqDAOException e) { e.printStackTrace(); mapseqDAOBean.getSequencerRunDAO().save(sequencerRun); } catch (MaPSeqDAOException e) { e.printStackTrace();
.findBySequencerRunId(getWorkflowPlan().getSequencerRun().getId())); } catch (MaPSeqDAOException e) { e.printStackTrace(); ncgenesWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO().findByName("NCGenes"); } catch (MaPSeqDAOException e1) { e1.printStackTrace();
@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); }
.findBySequencerRunId(getWorkflowPlan().getSequencerRun().getId())); } catch (MaPSeqDAOException e) { e.printStackTrace();