Examples with StudyFile com.odysseusinc.arachne.portal.model.StudyFile used on opensource projects

Example 6 with StudyFile

use of com.odysseusinc.arachne.portal.model.StudyFile in project ArachneCentralAPI by OHDSI.

the class BaseStudyServiceImpl method getAllStudyFilesExceptLinks.

@Override
@PreAuthorize("hasPermission(#studyId, 'Study', " + "T(com.odysseusinc.arachne.portal.security.ArachnePermission).ACCESS_STUDY)")
public void getAllStudyFilesExceptLinks(Long studyId, String archiveName, OutputStream os) throws IOException {
    T study = studyRepository.findOne(studyId);
    Path storeFilesPath = fileService.getPath(study);
    List<StudyFile> files = study.getFiles().stream().filter(file -> StringUtils.isEmpty(file.getLink())).collect(Collectors.toList());
    fileService.archiveFiles(os, storeFilesPath, files);
}

Example 7 with StudyFile

use of com.odysseusinc.arachne.portal.model.StudyFile in project ArachneCentralAPI by OHDSI.

the class BaseStudyController method getFile.

@ApiOperation("Get file of the study.")
@RequestMapping(value = "/api/v1/study-management/studies/{studyId}/files/{fileUuid}", method = GET)
public FileDTO getFile(@PathVariable("studyId") Long studyId, @PathVariable("fileUuid") String uuid, @RequestParam(defaultValue = "true") Boolean withContent) throws PermissionDeniedException, NotExistException, IOException {
    StudyFile studyFile = studyService.getStudyFile(studyId, uuid);
    FileDTO fileDto = conversionService.convert(studyFile, StudyFileContentDTO.class);
    if (withContent) {
        fileDto = FileDtoContentHandler.getInstance(fileDto, fileService.getPathToFile(studyFile).toFile()).withPdfConverter(toPdfConverter::convert).handle();
    }
    return fileDto;
}

Example 8 with StudyFile

use of com.odysseusinc.arachne.portal.model.StudyFile in project ArachneCentralAPI by OHDSI.

the class StudyFileServiceImpl method getFileInputStream.

@Override
public InputStream getFileInputStream(AbstractStudyFile studyFile) throws FileNotFoundException {
    Objects.requireNonNull(studyFile, "File must not be null");
    final File file = getPathToFile(studyFile).toFile();
    if (!file.exists()) {
        if (!StringUtils.isEmpty(studyFile.getLink())) {
            InputStream response = getInputStream(studyFile);
            if (response != null) {
                return response;
            }
        }
        throw new FileNotFoundException();
    }
    return new FileInputStream(file);
}

Example 9 with StudyFile

use of com.odysseusinc.arachne.portal.model.StudyFile in project ArachneCentralAPI by OHDSI.

the class BaseStudyToStudyDTOConverter method convert.

@Override
public DTO convert(final S source) {
    final DTO studyDTO = createResultObject();
    studyDTO.setStatus(conversionService.convert(source.getStatus(), StudyStatusDTO.class));
    studyDTO.setTitle(source.getTitle());
    studyDTO.setType(conversionService.convert(source.getType(), StudyTypeDTO.class));
    studyDTO.setEndDate(source.getEndDate());
    studyDTO.setStartDate(source.getStartDate());
    studyDTO.setDescription(source.getDescription());
    if (!CollectionUtils.isEmpty(source.getParticipants())) {
        studyDTO.setParticipants(source.getParticipants().stream().map(link -> conversionService.convert(link, ParticipantDTO.class)).collect(Collectors.toList()));
    }
    final List<StudyDataSourceLink> foundLinks = studyService.getLinksByStudyId(source.getId(), EntityUtils.fromAttributePaths("dataSource.dataNode.dataNodeUsers.user"));
    for (final StudyDataSourceLink studyDataSourceLink : foundLinks) {
        final DataSourceDTO dataSourceDTO = conversionService.convert(studyDataSourceLink, DataSourceDTO.class);
        studyDTO.getDataSources().add(dataSourceDTO);
    }
    List<Analysis> analyses = getAnalyses(source);
    for (final Analysis analysis : analyses) {
        studyDTO.getAnalyses().add(conversionService.convert(analysis, BaseAnalysisDTO.class));
    }
    List<StudyFile> files = studyService.getFilesByStudyId(source.getId(), EntityUtils.fromAttributePaths("author"));
    for (final StudyFile studyFile : files) {
        studyDTO.getFiles().add(conversionService.convert(studyFile, StudyFileDTO.class));
    }
    studyDTO.setCreated(source.getCreated());
    studyDTO.setUpdated(source.getUpdated());
    studyDTO.setId(source.getId());
    studyDTO.setPermissions(conversionService.convert(source, PermissionsDTO.class));
    studyDTO.setPaperId(source.getPaper() == null ? null : source.getPaper().getId());
    studyDTO.setPrivacy(source.getPrivacy());
    proceedAdditionalFields(studyDTO, source);
    return studyDTO;
}