Examples with NotNull javax.validation.constraints.NotNull used on opensource projects

Example 61 with NotNull

use of javax.validation.constraints.NotNull in project mica2 by obiba.

the class DatasetDtos method asDtoBuilder.

@NotNull
Mica.DatasetDto.Builder asDtoBuilder(@NotNull HarmonizationDataset dataset, boolean asDraft, boolean studySummary) {
    Mica.DatasetDto.Builder builder = asBuilder(dataset);
    builder.setVariableType(DatasetVariable.Type.Dataschema.name());
    Mica.HarmonizedDatasetDto.Builder hbuilder = Mica.HarmonizedDatasetDto.newBuilder();
    if (dataset.hasHarmonizationTable() && !Strings.isNullOrEmpty(dataset.getHarmonizationTable().getStudyId()) && isStudyTablePermitted(asDraft, "harmonization", dataset.getHarmonizationTable().getStudyId())) {
        hbuilder.setHarmonizationTable(createHarmonizationLinkDtoFromHarmonizationTable(dataset.getHarmonizationTable(), asDraft));
    }
    if (!dataset.getStudyTables().isEmpty()) {
        dataset.getStudyTables().stream().filter(studyTable -> isStudyTablePermitted(asDraft, "individual", studyTable.getStudyId())).forEach(studyTable -> hbuilder.addStudyTables(asDto(studyTable, studySummary)));
    }
    if (!dataset.getHarmonizationTables().isEmpty()) {
        dataset.getHarmonizationTables().stream().filter(studyTable -> isStudyTablePermitted(asDraft, "harmonization", studyTable.getStudyId())).forEach(harmonizationTable -> hbuilder.addHarmonizationTables(asDto(harmonizationTable, studySummary)));
    }
    builder.setExtension(Mica.HarmonizedDatasetDto.type, hbuilder.build());
    Mica.PermissionsDto permissionsDto = permissionsDtos.asDto(dataset);
    if (asDraft) {
        HarmonizationDatasetState state = harmonizationDatasetStateRepository.findOne(dataset.getId());
        if (state != null) {
            builder.setPublished(state.isPublished());
            builder.setExtension(Mica.EntityStateDto.datasetState, entityStateDtos.asDto(state).setPermissions(permissionsDto).build());
        }
    }
    builder.setPermissions(permissionsDto);
    return builder;
}

Example 62 with NotNull

use of javax.validation.constraints.NotNull in project mica2 by obiba.

the class DatasetDtos method asContingencyDto.

public Mica.DatasetVariableContingencyDto.Builder asContingencyDto(@NotNull OpalTable opalTable, DatasetVariable variable, DatasetVariable crossVariable, @Nullable Search.QueryResultDto results) {
    Mica.DatasetVariableContingencyDto.Builder crossDto = Mica.DatasetVariableContingencyDto.newBuilder();
    if (opalTable instanceof StudyTable)
        crossDto.setStudyTable(asDto((StudyTable) opalTable, true));
    else if (opalTable instanceof HarmonizationStudyTable)
        crossDto.setHarmonizationStudyTable(asDto((HarmonizationStudyTable) opalTable));
    Mica.DatasetVariableAggregationDto.Builder allAggBuilder = Mica.DatasetVariableAggregationDto.newBuilder();
    if (results == null) {
        allAggBuilder.setN(0);
        allAggBuilder.setTotal(0);
        crossDto.setAll(allAggBuilder);
        return crossDto;
    }
    allAggBuilder.setTotal(results.getTotalHits());
    MicaConfig micaConfig = micaConfigService.getConfig();
    int privacyThreshold = micaConfig.getPrivacyThreshold();
    crossDto.setPrivacyThreshold(privacyThreshold);
    boolean privacyChecks = !crossVariable.hasCategories() || validatePrivacyThreshold(results, privacyThreshold);
    boolean totalPrivacyChecks = validateTotalPrivacyThreshold(results, privacyThreshold);
    // add facet results in the same order as the variable categories
    List<String> catNames = variable.getValueType().equals(BooleanType.get().getName()) ? Lists.newArrayList("true", "false") : variable.getCategories().stream().map(DatasetCategory::getName).collect(Collectors.toList());
    catNames.forEach(catName -> results.getFacetsList().stream().filter(facet -> facet.hasFacet() && catName.equals(facet.getFacet())).forEach(facet -> {
        boolean privacyCheck = privacyChecks && checkPrivacyThreshold(facet.getFilters(0).getCount(), privacyThreshold);
        Mica.DatasetVariableAggregationDto.Builder aggBuilder = Mica.DatasetVariableAggregationDto.newBuilder();
        aggBuilder.setTotal(totalPrivacyChecks ? results.getTotalHits() : 0);
        aggBuilder.setTerm(facet.getFacet());
        DatasetCategory category = variable.getCategory(facet.getFacet());
        aggBuilder.setMissing(category != null && category.isMissing());
        addSummaryStatistics(crossVariable, aggBuilder, facet, privacyCheck, totalPrivacyChecks);
        crossDto.addAggregations(aggBuilder);
    }));
    // add total facet for all variable categories
    results.getFacetsList().stream().filter(facet -> facet.hasFacet() && "_total".equals(facet.getFacet())).forEach(facet -> {
        boolean privacyCheck = privacyChecks && facet.getFilters(0).getCount() >= micaConfig.getPrivacyThreshold();
        addSummaryStatistics(crossVariable, allAggBuilder, facet, privacyCheck, totalPrivacyChecks);
    });
    crossDto.setAll(allAggBuilder);
    return crossDto;
}

Example 63 with NotNull

use of javax.validation.constraints.NotNull in project mica2 by obiba.

the class DatasetDtos method asDtoBuilder.

@NotNull
Mica.DatasetDto.Builder asDtoBuilder(@NotNull StudyDataset dataset, boolean asDraft, boolean studySummary) {
    Mica.DatasetDto.Builder builder = asBuilder(dataset);
    builder.setVariableType(DatasetVariable.Type.Collected.name());
    if (dataset.hasStudyTable() && !Strings.isNullOrEmpty(dataset.getStudyTable().getStudyId()) && isStudyTablePermitted(asDraft, "individual", dataset.getStudyTable().getStudyId())) {
        Mica.CollectedDatasetDto.Builder sbuilder = Mica.CollectedDatasetDto.newBuilder().setStudyTable(asDto(dataset.getStudyTable(), studySummary));
        builder.setExtension(Mica.CollectedDatasetDto.type, sbuilder.build());
    }
    Mica.PermissionsDto permissionsDto = permissionsDtos.asDto(dataset);
    if (asDraft) {
        StudyDatasetState state = studyDatasetStateRepository.findOne(dataset.getId());
        if (state != null) {
            builder.setPublished(state.isPublished());
            Mica.EntityStateDto.Builder stateBuilder = entityStateDtos.asDto(state).setPermissions(permissionsDto);
            builder.setExtension(Mica.EntityStateDto.datasetState, stateBuilder.setPermissions(permissionsDto).setRequireIndexing(state.isRequireIndexing()).build());
        }
    }
    builder.setPermissions(permissionsDto);
    return builder;
}

Example 64 with NotNull

use of javax.validation.constraints.NotNull in project mica2 by obiba.

the class NetworkDtos method fromDto.

@NotNull
Network fromDto(@NotNull Mica.NetworkDtoOrBuilder dto) {
    Network network = new Network();
    if (dto.hasId()) {
        network.setId(dto.getId());
    }
    network.setName(localizedStringDtos.fromDto(dto.getNameList()));
    network.setDescription(localizedStringDtos.fromDto(dto.getDescriptionList()));
    network.setAcronym(localizedStringDtos.fromDto(dto.getAcronymList()));
    if (dto.getStudyIdsCount() > 0) {
        dto.getStudyIdsList().forEach(network::addStudyId);
    }
    if (dto.getAttachmentsCount() > 0) {
        dto.getAttachmentsList().stream().filter(Mica.AttachmentDto::getJustUploaded).findFirst().ifPresent(a -> network.setLogo(attachmentDtos.fromDto(a)));
    }
    if (dto.hasLogo()) {
        network.setLogo(attachmentDtos.fromDto(dto.getLogo()));
    }
    if (dto.getNetworkIdsCount() > 0) {
        network.setNetworkIds(Lists.newArrayList(Sets.newHashSet(dto.getNetworkIdsList())));
    }
    if (dto.getMembershipSortOrderCount() > 0) {
        Map<String, List<String>> membershipSortOrder = new HashMap<>();
        dto.getMembershipSortOrderList().forEach(membership -> {
            membershipSortOrder.put(membership.getRole(), membership.getPersonIdsList());
        });
        network.setMembershipSortOrder(membershipSortOrder);
    }
    if (dto.hasContent() && !Strings.isNullOrEmpty(dto.getContent()))
        network.setModel(JSONUtils.toMap(dto.getContent()));
    else
        network.setModel(new HashMap<>());
    return network;
}

Example 65 with NotNull

use of javax.validation.constraints.NotNull in project mica2 by obiba.

the class ProjectDtos method asDto.

@NotNull
public Mica.ProjectDto asDto(@NotNull Project project, boolean asDraft) {
    Mica.ProjectDto.Builder builder = Mica.ProjectDto.newBuilder().addAllTitle(// 
    localizedStringDtos.asDto(project.getTitle())).addAllSummary(localizedStringDtos.asDto(project.getSummary()));
    if (project.hasModel())
        builder.setContent(JSONUtils.toJSON(project.getModel()));
    if (project.hasDataAccessRequestId()) {
        try {
            DataAccessRequest request = dataAccessRequestService.findById(project.getDataAccessRequestId());
            Mica.DataAccessRequestSummaryDto.Builder darBuilder = Mica.DataAccessRequestSummaryDto.newBuilder();
            darBuilder.setId(project.getDataAccessRequestId());
            darBuilder.setStatus(request.getStatus().name());
            darBuilder.setApplicant(request.getApplicant());
            darBuilder.setViewable(subjectAclService.isPermitted("/data-access-request", "VIEW", request.getId()));
            builder.setRequest(darBuilder);
        } catch (NoSuchElementException e) {
        // ignore
        }
    }
    if (!project.isNew())
        builder.setId(project.getId());
    Mica.PermissionsDto permissionsDto = permissionsDtos.asDto(project);
    if (asDraft) {
        ProjectState projectState = projectService.getEntityState(project.getId());
        // 
        builder.setTimestamps(TimestampsDtos.asDto(project)).setPublished(// 
        projectState.isPublished()).setExtension(Mica.EntityStateDto.projectState, entityStateDtos.asDto(projectState).setPermissions(permissionsDto).build());
    }
    builder.setPermissions(permissionsDto);
    builder.setTimestamps(TimestampsDtos.asDto(project));
    return builder.build();
}