workflowRun = new WorkflowRun(); workflowRun.setStatus(WorkflowRunStatusType.PENDING); workflowRun.setCreator(account); workflowRun.setCreationDate(date); workflowRun.setModificationDate(date); workflowRun.setName(workflowRunName); workflowRun.setWorkflow(workflow); logger.debug("WorkflowRun: {}", workflowRun.toString());
try { WorkflowRun workflowRun = workflowRunDAO.findById(pipelineExecutor.getPipeline().getWorkflowPlan() .getWorkflowRun().getId()); logger.debug(workflowRun.toString()); logger.info("changing status from : {} to {}", workflowRun.getStatus().getState(), status.getState()); workflowRun.setStatus(status); Date date = new Date(); case DONE: case FAILED: if (workflowRun.getStartDate() == null) { workflowRun.setStartDate(date); workflowRun.setEndDate(date); break; case RUNNING: if (workflowRun.getStartDate() == null) { workflowRun.setStartDate(date); logger.debug(workflowRun.toString()); pipelineExecutor.getPipeline().getWorkflowPlan().setWorkflowRun(workflowRun);
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; }
.findById(getWorkflowPlan().getWorkflowRun().getId()); workflowRun.setStartDate(new Date()); workflowRun.setCondorDAGClusterId(jobNode.getCluster()); workflowRun.setSubmitDirectory(jobNode.getSubmitFile().getParentFile().getAbsolutePath()); WorkflowRunDAO workflowRunDAO = getPipelineBeanService().getMaPSeqDAOBean().getWorkflowRunDAO(); workflowRunDAO.save(workflowRun);
WorkflowRun workflowRun = workflowPlan.getWorkflowRun(); if (workflowRun != null) { Account creator = workflowRun.getCreator(); if (creator != null) { String toEmailAddress = creator.getEmailAddress(); .getPipeline().getName())); 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
job.addArgument("--workflowRunId", workflowRun.getId().toString()); if (workflowRun.getCreator() != null) { job.addArgument("--accountId", workflowRun.getCreator().getId().toString());