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

Example 1 with SubmissionGroup

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

the class ArachnePermissionEvaluator method addPermissions.

public boolean addPermissions(ArachneUser user, HasArachnePermissions hasPermissionsObj) {
    Set<ArachnePermission> allPermissions = getAllPermissions(hasPermissionsObj, user);
    hasPermissionsObj.setPermissions(allPermissions);
    if (hasPermissionsObj instanceof Analysis) {
        final Analysis analysis = (Analysis) hasPermissionsObj;
        final List<SubmissionGroup> submissionGroups = analysis.getSubmissionGroups();
        if (!CollectionUtils.isEmpty(submissionGroups)) {
            submissionGroups.forEach(submissionGroup -> submissionGroup.getSubmissions().forEach(submission -> {
                final Set<ArachnePermission> submissionPermissions = getAllPermissions(submission, user);
                submission.setPermissions(submissionPermissions);
            }));
        }
        final List<AnalysisFile> files = analysis.getFiles();
        if (!CollectionUtils.isEmpty(files)) {
            files.forEach(file -> {
                final Set<ArachnePermission> filePermissions = getAllPermissions(file, user);
                file.setPermissions(filePermissions);
            });
        }
    }
    return true;
}

Example 2 with SubmissionGroup

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

the class AnalysisHelper method createSubmission.

public static List<Submission> createSubmission(BaseSubmissionService submissionService, List<Long> datasourceIds, IUser user, Analysis analysis) throws IOException, NotExistException, NoExecutableFileException, ValidationException {
    final List<Submission> submissions = new LinkedList<>();
    // removes datasourceId duplicates
    Set<Long> datasourceIdSet = new HashSet<>(datasourceIds);
    SubmissionGroup submissionGroup = submissionService.createSubmissionGroup(user, analysis);
    for (Long datasourceId : datasourceIdSet) {
        submissions.add(submissionService.createSubmission(user, analysis, datasourceId, submissionGroup));
    }
    return submissions;
}

Example 3 with SubmissionGroup

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

the class BaseSubmissionServiceImpl method createSubmissionGroup.

@Override
public SubmissionGroup createSubmissionGroup(IUser user, Analysis analysis) throws IOException, NoExecutableFileException {
    checkBeforeCreateSubmissionGroup(analysis);
    List<SubmissionFile> files = new LinkedList<>();
    SubmissionGroup submissionGroup = new SubmissionGroup();
    submissionGroup.setAnalysis(analysis);
    submissionGroup.setAnalysisType(analysis.getType());
    submissionGroup.setAuthor(user);
    Date now = new Date();
    submissionGroup.setCreated(now);
    submissionGroup.setUpdated(now);
    submissionGroup.setFiles(files);
    submissionGroup = submissionGroupRepository.save(submissionGroup);
    Path submissionGroupFolder = analysisHelper.getSubmissionGroupFolder(submissionGroup);
    if (Files.notExists(submissionGroupFolder)) {
        Files.createDirectories(submissionGroupFolder);
    }
    for (AnalysisFile analysisFile : analysis.getFiles()) {
        SubmissionFile submissionFile = new SubmissionFile();
        String storeFilesPath = fileStorePath + File.separator + "content";
        String uuid = UUID.randomUUID().toString();
        submissionFile.setSubmissionGroup(submissionGroup);
        submissionFile.setContentType(analysisFile.getContentType());
        submissionFile.setCreated(analysisFile.getCreated());
        submissionFile.setUpdated(analysisFile.getUpdated());
        submissionFile.setLabel(analysisFile.getLabel());
        submissionFile.setRealName(analysisFile.getRealName());
        submissionFile.setEntryPoint(analysisFile.getEntryPoint());
        submissionFile.setUuid(uuid);
        submissionFile.setAuthor(analysisFile.getAuthor());
        submissionFile.setVersion(analysisFile.getVersion());
        submissionFile.setAntivirusStatus(analysisFile.getAntivirusStatus());
        submissionFile.setAntivirusDescription(analysisFile.getAntivirusDescription());
        Boolean isExecutable = analysisFile.getExecutable();
        submissionFile.setExecutable(isExecutable != null && isExecutable);
        Path analysisFileContent = Paths.get(storeFilesPath, analysis.getStudy().getId().toString(), analysis.getId().toString(), analysisFile.getUuid());
        Path submissionFileContent = submissionGroupFolder.resolve(uuid);
        Path target = Files.copy(analysisFileContent, submissionFileContent, StandardCopyOption.REPLACE_EXISTING);
        try (InputStream in = Files.newInputStream(target)) {
            String checksum = DigestUtils.md5DigestAsHex(in);
            submissionFile.setChecksum(checksum);
        }
        files.add(submissionFile);
    }
    submissionFileRepository.save(files);
    submissionGroup.setChecksum(calculateMD5Hash(submissionGroupFolder, files));
    submissionGroupRepository.save(submissionGroup);
    return submissionGroup;
}

Example 4 with SubmissionGroup

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

the class BaseSubmissionServiceImpl method getSubmissionAllFiles.

@Override
public void getSubmissionAllFiles(Long submissionGroupId, String archiveName, OutputStream os) throws IOException {
    SubmissionGroup submissionGroup = submissionGroupRepository.findOne(submissionGroupId);
    Path storeFilesPath = analysisHelper.getSubmissionGroupFolder(submissionGroup);
    try (ZipOutputStream zos = new ZipOutputStream(os)) {
        for (SubmissionFile submissionFile : submissionGroup.getFiles()) {
            String realName = submissionFile.getRealName();
            Path file = storeFilesPath.resolve(submissionFile.getUuid());
            if (Files.notExists(file)) {
                file = legacyAnalysisHelper.getOldSubmissionFile(submissionFile).orElseThrow(FileNotFoundException::new);
            }
            if (Files.exists(file)) {
                ZipUtil.addZipEntry(zos, realName, file);
            }
        }
    }
}

Example 5 with SubmissionGroup

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

the class BaseSubmissionServiceImpl method getSubmissionGroups.

@Override
@PreAuthorize("hasPermission(#submissoinGroupSearch.analysisId,  'Analysis', " + "T(com.odysseusinc.arachne.portal.security.ArachnePermission).ACCESS_STUDY)")
@PostAuthorize("@ArachnePermissionEvaluator.addPermissionsToSubmissions(principal, returnObject )")
public Page<SubmissionGroup> getSubmissionGroups(SubmissionGroupSearch submissoinGroupSearch) {
    final SubmissionGroupSpecification submissionGroupSpecification = new SubmissionGroupSpecification(submissoinGroupSearch);
    final Integer page = submissoinGroupSearch.getPage();
    final PageRequest pageRequest = new PageRequest(page == null ? 0 : page - 1, submissoinGroupSearch.getPageSize(), new Sort(Sort.Direction.DESC, "created"));
    final Page<SubmissionGroup> submissionGroups = submissionGroupRepository.findAll(submissionGroupSpecification, pageRequest);
    final List<SubmissionGroup> content = submissionGroups.getContent();
    final Map<Long, SubmissionGroup> submissionGroupMap = content.stream().collect(Collectors.toMap(SubmissionGroup::getId, sg -> {
        sg.setSubmissions(new ArrayList<>());
        return sg;
    }));
    final Set<Long> submissionGroupIds = submissionGroupMap.keySet();
    if (!CollectionUtils.isEmpty(submissionGroupIds)) {
        final SubmissionSpecification<T> submissionSpecification = SubmissionSpecification.<T>builder(submissionGroupIds).withStatuses(submissoinGroupSearch.getSubmissionStatuses()).withDataSourceIds(submissoinGroupSearch.getDataSourceIds()).hasInsight(submissoinGroupSearch.getHasInsight()).showHidden(submissoinGroupSearch.getShowHidden()).build();
        submissionRepository.findAll(submissionSpecification).forEach(s -> submissionGroupMap.get(s.getSubmissionGroup().getId()).getSubmissions().add(s));
    }
    return submissionGroups;
}