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

Example 1 with BaseStudy

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

the class SpecificStudyReportGenerator method writeEachLine.

@Override
protected void writeEachLine(CSVWriter writer) {
    for (String studyId : studyIds) {
        BaseStudy publishedStudy = publishedStudyService.findById(studyId);
        if (publishedStudy != null) {
            List<String> publishedStudyDetails = generatePublishedStudyDetails(publishedStudy);
            Iterator<Population> populationIterator = publishedStudy.getPopulations().iterator();
            if (!populationIterator.hasNext()) {
                writer.writeNext(publishedStudyDetails.toArray(new String[publishedStudyDetails.size()]));
            }
            while (populationIterator.hasNext()) {
                List<String> buildingCompleteLine = new ArrayList<>(publishedStudyDetails);
                Population next = populationIterator.next();
                buildingCompleteLine.addAll(generatePopulationDetails(next));
                writer.writeNext(buildingCompleteLine.toArray(new String[buildingCompleteLine.size()]));
            }
        } else {
            BaseStudy draftStudy = studyService.findStudy(studyId);
            if (draftStudy != null) {
                List<String> lineOfDratStudy = generateDraftStudyDetails(draftStudy);
                writer.writeNext(lineOfDratStudy.toArray(new String[lineOfDratStudy.size()]));
            }
        }
    }
}

Example 2 with BaseStudy

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

the class RQLCriteriaOpalConverter method parseField.

private RQLFieldReferences parseField(String path) {
    DatasetVariable.IdResolver resolver = DatasetVariable.IdResolver.from(path);
    if (resolver.getType() == null || DatasetVariable.Type.Collected.equals(resolver.getType())) {
        StudyDataset ds = collectedDatasetService.findById(resolver.getDatasetId());
        BaseStudyTable studyTable = ds.getStudyTable();
        BaseStudy study = studyService.findStudy(studyTable.getStudyId());
        return new RQLFieldReferences(path, ds, studyTable, study, getDatasetVariableInternal(Indexer.VARIABLE_TYPE, path));
    } else if (DatasetVariable.Type.Dataschema.equals(resolver.getType())) {
        HarmonizationDataset ds = harmonizedDatasetService.findById(resolver.getDatasetId());
        BaseStudy study = studyService.findStudy(ds.getHarmonizationTable().getStudyId());
        return new RQLFieldReferences(path, ds, ds.getBaseStudyTables(), study, getDatasetVariableInternal(Indexer.VARIABLE_TYPE, path));
    } else if (DatasetVariable.Type.Harmonized.equals(resolver.getType())) {
        HarmonizationDataset ds = harmonizedDatasetService.findById(resolver.getDatasetId());
        Optional<BaseStudyTable> studyTable = ds.getBaseStudyTables().stream().filter(st -> st.getStudyId().equals(resolver.getStudyId()) && st.getProject().equals(resolver.getProject()) && st.getTable().equals(resolver.getTable())).findFirst();
        if (!studyTable.isPresent())
            throw new IllegalArgumentException("Not a valid variable: " + path);
        BaseStudy study = studyService.findStudy(studyTable.get().getStudyId());
        return new RQLFieldReferences(path, ds, studyTable.get(), study, getDatasetVariableInternal(Indexer.HARMONIZED_VARIABLE_TYPE, path));
    }
    throw new IllegalArgumentException("Not a valid variable: " + path);
}

Example 3 with BaseStudy

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

the class AbstractPublishedStudyResource method getStudy.

protected BaseStudy getStudy(String id, String locale) {
    BaseStudy study = publishedStudyService.findById(id);
    if (study == null)
        throw NoSuchStudyException.withId(id);
    translateModels(locale, study);
    log.debug("Study acronym {}", study.getAcronym());
    return study;
}

Example 4 with BaseStudy

use of org.obiba.mica.study.domain.BaseStudy 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 5 with BaseStudy

use of org.obiba.mica.study.domain.BaseStudy 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;
}