public String createSampleSheet(Run run, User user) { final List<String> columns = getColumns().collect(Collectors.toList()); return header(run) + Stream.concat(// Stream.of(String.join(",", columns)), // run.getSequencerPartitionContainers().stream()// .flatMap(container -> container.getPartitions().stream())// .filter(partition -> partition.getPool() != null)// .flatMap(partition -> createRowsForPartition(run, user, columns, partition))) .collect(Collectors.joining("\n")); }
posDto.setRun(run == null ? null : asDto(run)); posDto.setPools(run == null ? Collections.emptyList() : run.getSequencerPartitionContainers().stream()//
containerSerialNumber, container.getPartitions().size(), laneCount)); if (target.getSequencerPartitionContainers().stream().noneMatch(c -> c.getId() == container.getId())) { target.addSequencerPartitionContainer(container, position); updatePartitionContents(getLaneContents, container);
@Override public Long create(Run run) throws IOException { authorizationManager.throwIfNotWritable(run); validateChanges(null, run); saveContainers(run); run.setChangeDetails(authorizationManager.getCurrentUser()); loadChildEntities(run); run.setSecurityProfile(securityProfileStore.get(securityProfileStore.save(run.getSecurityProfile()))); run.setName(generateTemporaryName()); Run saved = save(run); makeContainerChangesChangeLog(saved, Collections.emptyList(), saved.getSequencerPartitionContainers()); return saved.getId(); }
private void applyChanges(Run target, Run source) throws IOException { validateChanges(target, source); target.setAlias(source.getAlias()); target.setAccession(source.getAccession()); target.setDescription(source.getDescription()); target.setFilePath(source.getFilePath()); target.setHealth(source.getHealth()); target.setStartDate(source.getStartDate()); target.setCompletionDate(source.getCompletionDate()); target.setMetrics(source.getMetrics()); makeContainerChangesChangeLog(target, target.getSequencerPartitionContainers(), source.getSequencerPartitionContainers()); applyContainerChanges(target, source); target.setSequencingParameters(source.getSequencingParameters()); target.setSequencer(source.getSequencer()); if (isIlluminaRun(target)) { applyIlluminaChanges((IlluminaRun) target, (IlluminaRun) source); } else if (isLS454Run(target)) { applyLS454Changes((LS454Run) target, (LS454Run) source); } else if (isSolidRun(target)) { applySolidChanges((SolidRun) target, (SolidRun) source); } else if (isOxfordNanoporeRun(target)) { applyOxfordNanoporeChanges((OxfordNanoporeRun) target, (OxfordNanoporeRun) source); } }
dto.setContainers(asContainerDtos(from.getSequencerPartitionContainers(), includeContainerPartitions, includePoolContents));