WorkflowDAO workflowDAO = mapseqDAOBean.getWorkflowDAO(); ncgenesWorkflow = workflowDAO.findByName("NCGenes"); } catch (MaPSeqDAOException e2) {
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; }
workflow = mapseqDAOBean.getWorkflowDAO().findByName(pipelineName); } catch (MaPSeqDAOException e) { logger.error("ERROR", e);
variantCallingWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO() .findByName("NIDAUCSFVariantCalling"); } catch (MaPSeqDAOException e1) {
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();
ncgenesWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO().findByName("NCGenes"); } catch (MaPSeqDAOException e1) { e1.printStackTrace();
variantCallingWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO() .findByName("NIDAUCSFVariantCalling"); } catch (MaPSeqDAOException e1) {
Workflow ncgenesWorkflow = null; try { ncgenesWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO().findByName("NCGenes"); } catch (MaPSeqDAOException e1) { e1.printStackTrace();
ncgenesWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO().findByName("NCGenes"); } catch (MaPSeqDAOException e1) { e1.printStackTrace();
variantCallingWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO() .findByName("NIDAUCSFVariantCalling"); } catch (MaPSeqDAOException e1) {
ncgenesWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO().findByName("NCGenes"); } catch (MaPSeqDAOException e1) { e1.printStackTrace();
alignmentWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO() .findByName("ChIPSeqAlignment"); } catch (MaPSeqDAOException e1) {
alignmentWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO() .findByName("FAIRESeqAlignment"); } catch (MaPSeqDAOException e1) {
alignmentWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO() .findByName("NIDANAAlignment"); } catch (MaPSeqDAOException e1) {
ncgenesWorkflow = getWorkflowBeanService().getMaPSeqDAOBean().getWorkflowDAO().findByName("NCGenes"); } catch (MaPSeqDAOException e1) { e1.printStackTrace();