HTSFSampleDAO htsfSampleDAO = mapseqDAOBean.getHTSFSampleDAO(); try { if (sequencerRunId != null) { WorkflowDAO workflowDAO = mapseqDAOBean.getWorkflowDAO(); ncgenesWorkflow = workflowDAO.findByName("NCGenes"); } catch (MaPSeqDAOException e2) { this.mapseqDAOBean.getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
for (Long id : sequencerRunIdList) { try { sequencerRunList.add(mapseqDAOBean.getSequencerRunDAO().findById(id)); } catch (MaPSeqDAOException e1) { List<HTSFSample> htsfSampleList = mapseqDAOBean.getHTSFSampleDAO().findBySequencerRunId(sr.getId()); Map<Integer, List<Double>> laneClusterDensityTotalMap = new HashMap<Integer, List<Double>>(); mapseqDAOBean.getHTSFSampleDAO().save(sample);
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; }
path = path.replace(oldSampleName, newSampleName); fileData.setPath(path); getWorkflowBeanService().getMaPSeqDAOBean().getFileDataDAO().save(fileData); getWorkflowBeanService().getMaPSeqDAOBean().getHTSFSampleDAO().save(htsfSample);
public static WorkflowRun getWorkflowRun(MaPSeqDAOBean mapseqDAOBean, String pipelineName, JSONObject jsonObject, Account account) throws JSONException { logger.info("ENTERING getWorkflowRun(Pipeline<?>, JSONObject, Account)"); WorkflowRun workflowRun = null; logger.debug("jsonObject.has(\"name\"): {}", jsonObject.has("name")); if (jsonObject.has("name")) { String workflowRunName = jsonObject.getString("name"); Workflow workflow = null; try { workflow = mapseqDAOBean.getWorkflowDAO().findByName(pipelineName); } catch (MaPSeqDAOException e) { logger.error("ERROR", e); } if (workflow == null) { logger.warn("No Workflow Found: {}", pipelineName); return null; } workflowRun = new WorkflowRun(); workflowRun.setStatus(WorkflowRunStatusType.PENDING); workflowRun.setCreator(account); workflowRun.setName(workflowRunName); workflowRun.setWorkflow(workflow); } if (workflowRun != null) { logger.debug("WorkflowRun: {}", workflowRun.toString()); } return workflowRun; }
getPipelineBeanService().getMaPSeqDAOBean().getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e1) { logger.error("Could not persist HTSFSample");
sequencerRun = mapseqDAOBean.getSequencerRunDAO().findById(guid); } catch (MaPSeqDAOException e) { e.printStackTrace(); mapseqDAOBean.getSequencerRunDAO().save(sequencerRun); } catch (MaPSeqDAOException e) { e.printStackTrace();
workflow = mapseqDAOBean.getWorkflowDAO().findByName(pipelineName); } catch (MaPSeqDAOException e) { logger.error("ERROR", e);
HTSFSampleDAO htsfSampleDAO = mapseqDAOBean.getHTSFSampleDAO(); try { if (sequencerRunId != null) { this.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();
variantCallingWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO() .findByName("NIDAUCSFVariantCalling"); } catch (MaPSeqDAOException e1) { getWorkflowBeanService().getMaPSeqDAOBean().getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
ncgenesWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO().findByName("NCGenes"); } catch (MaPSeqDAOException e1) { e1.printStackTrace();
HTSFSampleDAO htsfSampleDAO = mapseqDAOBean.getHTSFSampleDAO(); try { if (sequencerRunId != null) { this.mapseqDAOBean.getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
SequencerRunDAO sequencerRunDAO = mapseqDAOBean.getSequencerRunDAO(); for (Long sequencerRunId : sequencerRunIdList) { SequencerRun sequencerRun = sequencerRunDAO.findById(sequencerRunId); 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());
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; }
ncgenesWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO().findByName("NCGenes"); } catch (MaPSeqDAOException e1) { e1.printStackTrace(); getWorkflowBeanService().getMaPSeqDAOBean().getHTSFSampleDAO().save(htsfSample); } catch (MaPSeqDAOException e) { e.printStackTrace();
ncgenesWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO().findByName("NCGenes"); } catch (MaPSeqDAOException e1) { e1.printStackTrace();
htsfSample = mapseqDAOBean.getHTSFSampleDAO().findById(htsfSampleId); } catch (MaPSeqDAOException e1) { e1.printStackTrace();
logger.info("sequencerRun: {}", getWorkflowPlan().getSequencerRun().toString()); try { htsfSampleSet.addAll(getWorkflowBeanService().getMaPSeqDAOBean().getHTSFSampleDAO() .findBySequencerRunId(getWorkflowPlan().getSequencerRun().getId())); } catch (MaPSeqDAOException e) { ncgenesWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO().findByName("NCGenes"); } catch (MaPSeqDAOException e1) { e1.printStackTrace();
variantCallingWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO() .findByName("NIDAUCSFVariantCalling"); } catch (MaPSeqDAOException e1) {