job.getParams().put("path", dbAdaptorFactory.getCatalogFileDBAdaptor().get(job.getOutDir().getUid(), QueryOptions.empty()).first().getId()); } catch (CatalogDBException e) {
parameters.append(JobDBAdaptor.QueryParams.OUT_DIR.key(), outDir); } catch (CatalogException e) { logger.error("Cannot find file {}. Error: {}", job.getOutDir().getPath(), e.getMessage()); throw e;
fileIdsReferencedInJobs.add(job.getOutDir().getUid()); jobMap.put(job.getUid(), job); Job job = jobMap.get(jobAux.getUid()); File outDir = job.getOutDir(); if (outDir == null || outDir.getUid() <= 0) { logger.error("Unexpected error: Output directory from job not found?"); throw new CatalogException("Internal error. Please, report to the OpenCGA administrators."); if (!relatedFileMap.containsKey(job.getOutDir().getUid())) { logger.error("Unexpected error: Deleted output directory was apparently not found in the map of job associated files"); throw new CatalogException("Internal error. Please, report to the OpenCGA administrators.");
@Override public Document convertToStorageType(Job object) { Document document = super.convertToStorageType(object); document.put("uid", object.getUid()); document.put("studyUid", object.getStudyUid()); document.put("outDir", convertFileToDocument(object.getOutDir())); document.put("input", convertFilesToDocument(object.getInput())); document.put("output", convertFilesToDocument(object.getOutput())); return document; }
job.setUserId(userId); job.setRelease(catalogManager.getStudyManager().getCurrentRelease(study, userId)); job.setOutDir(job.getOutDir() != null && StringUtils.isNotEmpty(job.getOutDir().getPath()) ? job.getOutDir() : null); if (job.getOutDir() != null) { String fileName = StringUtils.isNotEmpty(job.getOutDir().getPath()) ? job.getOutDir().getPath() : job.getOutDir().getName(); File file = catalogManager.getFileManager().smartResolutor(study.getUid(), fileName, userId); authorizationManager.checkFilePermission(study.getUid(), file.getUid(), userId, FileAclEntry.FilePermissions.WRITE);