Examples with Study org.obiba.mica.study.domain.Study used on opensource projects

Example 16 with Study

use of org.obiba.mica.study.domain.Study in project mica2 by obiba.

the class StudySeedService method importStudy.

/**
 * Import a Study from a jackson file.
 *
 * @param json
 */
private void importStudy(File json) throws IOException {
    log.info("Seeding study with file: {}", json.getAbsolutePath());
    InputStream inputStream = new FileInputStream(json);
    Study study = objectMapper.readValue(inputStream, Study.class);
    individualStudyService.save(study);
    individualStudyService.publish(study.getId(), true);
}

Example 17 with Study

use of org.obiba.mica.study.domain.Study in project mica2 by obiba.

the class SubjectAclService method studyDeleted.

@Async
@Subscribe
public void studyDeleted(StudyDeletedEvent event) {
    BaseStudy persistable = event.getPersistable();
    removeInstance(persistable instanceof Study ? "/individual-study" : "/harmonization-study", persistable.getId());
}

Example 18 with Study

use of org.obiba.mica.study.domain.Study in project mica2 by obiba.

the class IndividualStudyService method getPotentialConflicts.

public Map<String, List<String>> getPotentialConflicts(Study study, boolean publishing) {
    if (study.getId() != null) {
        Study oldStudy = publishing ? study : studyRepository.findOne(study.getId());
        if (oldStudy != null) {
            List<String> dceUIDs = publishing ? toListOfDceUids(study, true) : populationsOrDceAffected(study, oldStudy, true);
            if (dceUIDs != null) {
                List<String> studyDatasetIds = findStudyDatasetDependencies(dceUIDs);
                List<String> harmoDatasetIds = findHarmonizedDatasetDependencies(dceUIDs);
                List<String> networkIds = networkRepository.findByStudyIds(study.getId()).stream().map(AbstractGitPersistable::getId).collect(toList());
                if (!harmoDatasetIds.isEmpty() || !studyDatasetIds.isEmpty() || !networkIds.isEmpty()) {
                    return new HashMap<String, List<String>>() {

                        {
                            put("harmonizationDataset", harmoDatasetIds);
                            put("studyDataset", studyDatasetIds);
                            put("network", networkIds);
                        }
                    };
                }
            }
        }
    }
    return null;
}

Example 19 with Study

use of org.obiba.mica.study.domain.Study in project mica2 by obiba.

the class IndividualStudyService method getFromCommit.

@Override
public Study getFromCommit(@NotNull Study study, @NotNull String commitId) {
    String studyBlob = gitService.getBlob(study, commitId, Study.class);
    InputStream inputStream = new ByteArrayInputStream(studyBlob.getBytes(StandardCharsets.UTF_8));
    Study restoredStudy;
    try {
        restoredStudy = objectMapper.readValue(inputStream, Study.class);
    } catch (IOException e) {
        throw Throwables.propagate(e);
    }
    return restoredStudy;
}

Example 20 with Study

use of org.obiba.mica.study.domain.Study in project mica2 by obiba.

the class NetworkDtos method asDtoBuilder.

@NotNull
Mica.NetworkDto.Builder asDtoBuilder(@NotNull Network network, boolean asDraft) {
    Mica.NetworkDto.Builder builder = Mica.NetworkDto.newBuilder();
    if (network.hasModel())
        builder.setContent(JSONUtils.toJSON(network.getModel()));
    // 
    builder.setId(network.getId()).addAllName(// 
    localizedStringDtos.asDto(network.getName())).addAllDescription(// 
    localizedStringDtos.asDto(network.getDescription())).addAllAcronym(localizedStringDtos.asDto(network.getAcronym()));
    Mica.PermissionsDto permissionsDto = permissionsDtos.asDto(network);
    NetworkState networkState = networkService.getEntityState(network.getId());
    builder.setPublished(networkState.isPublished());
    if (asDraft) {
        // 
        builder.setTimestamps(TimestampsDtos.asDto(network)).setPublished(// 
        networkState.isPublished()).setExtension(Mica.EntityStateDto.state, entityStateDtos.asDto(networkState).setPermissions(permissionsDto).build());
    }
    builder.setPermissions(permissionsDto);
    List<String> roles = micaConfigService.getConfig().getRoles();
    if (network.getMemberships() != null) {
        List<Mica.MembershipsDto> memberships = network.getMemberships().entrySet().stream().filter(e -> roles.contains(e.getKey())).map(e -> Mica.MembershipsDto.newBuilder().setRole(e.getKey()).addAllMembers(e.getValue().stream().map(m -> personDtos.asDto(m.getPerson(), asDraft)).collect(toList())).build()).collect(toList());
        builder.addAllMemberships(memberships);
    }
    List<BaseStudy> publishedStudies = publishedStudyService.findByIds(network.getStudyIds());
    Set<String> publishedStudyIds = publishedStudies.stream().map(AbstractGitPersistable::getId).collect(Collectors.toSet());
    Sets.SetView<String> unpublishedStudyIds = Sets.difference(ImmutableSet.copyOf(network.getStudyIds().stream().filter(sId -> asDraft && subjectAclService.isPermitted("/draft/individual-study", "VIEW", sId) || subjectAclService.isAccessible("/individual-study", sId)).collect(toList())), publishedStudyIds);
    if (!publishedStudies.isEmpty()) {
        Map<String, Long> datasetVariableCounts = asDraft ? null : datasetVariableService.getCountByStudyIds(Lists.newArrayList(publishedStudyIds));
        publishedStudies.forEach(study -> {
            builder.addStudyIds(study.getId());
            builder.addStudySummaries(studySummaryDtos.asDtoBuilder(study, true, datasetVariableCounts == null ? 0 : datasetVariableCounts.get(study.getId())));
        });
    }
    unpublishedStudyIds.forEach(studyId -> {
        try {
            builder.addStudySummaries(studySummaryDtos.asDto(studyId));
            builder.addStudyIds(studyId);
        } catch (NoSuchEntityException e) {
            log.warn("Study not found in network {}: {}", network.getId(), studyId);
        // ignore
        }
    });
    if (network.getLogo() != null) {
        builder.setLogo(attachmentDtos.asDto(network.getLogo()));
    }
    network.getNetworkIds().stream().filter(nId -> asDraft && subjectAclService.isPermitted("/draft/network", "VIEW", nId) || subjectAclService.isAccessible("/network", nId)).forEach(nId -> {
        try {
            builder.addNetworkSummaries(networkSummaryDtos.asDtoBuilder(nId, asDraft));
            builder.addNetworkIds(nId);
        } catch (NoSuchEntityException e) {
            log.warn("Network not found in network {}: {}", network.getId(), nId);
        // ignore
        }
    });
    return builder;
}