sampleDescriptor.setAttribute("refname", experiment.getLibrary().getSample().getAlias()); sampleDescriptor.setAttribute("refcenter", centreName); if (!isStringEmptyOrNull(experiment.getLibrary().getSample().getAccession())) { sampleDescriptor.setAttribute("accession", experiment.getLibrary().getSample().getAccession()); if (!isStringEmptyOrNull(experiment.getLibrary().getAlias())) { libraryName.setTextContent(experiment.getLibrary().getAlias()); } else { libraryName.setTextContent(experiment.getLibrary().getName()); libraryStrategy.setTextContent(experiment.getLibrary().getLibraryStrategyType().getName()); libraryDescriptor.appendChild(libraryStrategy); librarySource.setTextContent(experiment.getLibrary().getSample().getSampleType()); libraryDescriptor.appendChild(librarySource); librarySelection.setTextContent(experiment.getLibrary().getLibrarySelectionType().getName()); libraryDescriptor.appendChild(librarySelection); if (experiment.getLibrary().getPaired()) { layout = xml.getOwnerDocument().createElementNS(null, "PAIRED"); if (experiment.getLibrary().getDnaSize() != null) { layout.setAttribute("NOMINAL_LENGTH", experiment.getLibrary().getDnaSize().toString()); } else { layout.setAttribute("NOMINAL_LENGTH", "0");
public static ExperimentDto asDto(@Nonnull Experiment from) { ExperimentDto dto = new ExperimentDto(); dto.setId(from.getId()); dto.setAccession(from.getAccession()); dto.setAlias(from.getAlias()); dto.setDescription(from.getDescription()); dto.setName(from.getName()); dto.setInstrumentModel(asDto(from.getInstrumentModel())); dto.setLibrary(asDto(from.getLibrary(), false)); dto.setPartitions(from.getRunPartitions().stream() .map(entry -> new ExperimentDto.RunPartitionDto(asDto(entry.getRun()), asDto(entry.getPartition()))).collect(Collectors.toList())); dto.setStudy(asDto(from.getStudy())); dto.setTitle(from.getTitle()); return dto; }
experiment.setName(DbUtils.generateTemporaryName()); experiment.setInstrumentModel(platformService.get(experiment.getInstrumentModel().getId())); experiment.setLibrary(libraryService.get(experiment.getLibrary().getId())); experiment.setStudy(studyService.get(experiment.getStudy().getId())); experiment.setChangeDetails(authorizationManager.getCurrentUser()); original.setName(experiment.getName()); original.setInstrumentModel(platformService.get(experiment.getInstrumentModel().getId())); original.setLibrary(libraryService.get(experiment.getLibrary().getId())); original.setStudy(studyService.get(experiment.getStudy().getId())); original.setSecurityProfile(securityStore.getSecurityProfileById(experiment.getSecurityProfile().getProfileId()));