Examples with Dataset org.obiba.mica.dataset.domain.Dataset used on opensource projects

Example 11 with Dataset

use of org.obiba.mica.dataset.domain.Dataset in project mica2 by obiba.

the class DatasetCacheResolver method resolveCaches.

@Override
public synchronized Collection<? extends Cache> resolveCaches(CacheOperationInvocationContext<?> cacheOperationInvocationContext) {
    Collection<Cache> res = Lists.newArrayList();
    Optional<Object> dataset = Arrays.stream(cacheOperationInvocationContext.getArgs()).filter(o -> o instanceof Dataset).findFirst();
    if (dataset.isPresent()) {
        String cacheName = "dataset-" + ((Dataset) dataset.get()).getId();
        Cache datasetCache = springCacheManager.getCache(cacheName);
        if (datasetCache == null) {
            CacheConfiguration conf = cacheManager.getEhcache("dataset-variables").getCacheConfiguration().clone();
            conf.setName(cacheName);
            cacheManager.addCache(new net.sf.ehcache.Cache(conf));
            net.sf.ehcache.Cache cache = cacheManager.getCache(cacheName);
            cacheManager.replaceCacheWithDecoratedCache(cache, InstrumentedEhcache.instrument(metricRegistry, cache));
            datasetCache = new EhCacheCache(cacheManager.getEhcache(cacheName));
        }
        res.add(datasetCache);
    }
    return res;
}

Example 12 with Dataset

use of org.obiba.mica.dataset.domain.Dataset 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 13 with Dataset

use of org.obiba.mica.dataset.domain.Dataset in project mica2 by obiba.

the class DraftCollectedDatasetsResource method list.

/**
 * Get all {@link org.obiba.mica.dataset.domain.StudyDataset}, optionally filtered by study.
 *
 * @param studyId can be null, in which case all datasets are returned
 * @return
 */
@GET
@Path("/collected-datasets")
@Timed
public List<Mica.DatasetDto> list(@QueryParam("study") String studyId, @QueryParam("query") String query, @QueryParam("from") @DefaultValue("0") Integer from, @QueryParam("limit") Integer limit, @QueryParam("sort") @DefaultValue("id") String sort, @QueryParam("order") @DefaultValue("asc") String order, @QueryParam("filter") @DefaultValue("ALL") String filter, @Context HttpServletResponse response) {
    long totalCount;
    EntityStateFilter entityStateFilter = EntityStateFilter.valueOf(filter);
    List<String> filteredIds = datasetService.getIdsByStateFilter(entityStateFilter);
    Searcher.IdFilter accessibleIdFilter = AccessibleIdFilterBuilder.newBuilder().aclService(subjectAclService).resources(Lists.newArrayList("/draft/collected-dataset")).ids(filteredIds).build();
    if (limit == null)
        limit = MAX_LIMIT;
    if (limit < 0)
        throw new IllegalArgumentException("limit cannot be negative");
    DocumentService.Documents<StudyDataset> datasets = draftCollectedDatasetService.find(from, limit, sort, order, studyId, query, null, null, accessibleIdFilter);
    totalCount = datasets.getTotal();
    response.addHeader("X-Total-Count", Long.toString(totalCount));
    return datasets.getList().stream().map(dataset -> dtos.asDto(dataset, true)).collect(toList());
}

Example 14 with Dataset

use of org.obiba.mica.dataset.domain.Dataset in project mica2 by obiba.

the class DraftHarmonizedDatasetsResource method list.

/**
 * Get all {@link HarmonizationDataset}, optionally filtered by study.
 *
 * @param studyId can be null, in which case all datasets are returned
 * @return
 */
@GET
@Path("/harmonized-datasets")
@Timed
public List<Mica.DatasetDto> list(@QueryParam("study") String studyId, @QueryParam("query") String query, @QueryParam("from") @DefaultValue("0") Integer from, @QueryParam("limit") Integer limit, @QueryParam("sort") @DefaultValue("id") String sort, @QueryParam("order") @DefaultValue("asc") String order, @QueryParam("filter") @DefaultValue("ALL") String filter, @Context HttpServletResponse response) {
    long totalCount;
    EntityStateFilter entityStateFilter = EntityStateFilter.valueOf(filter);
    List<String> filteredIds = datasetService.getIdsByStateFilter(entityStateFilter);
    Searcher.IdFilter accessibleIdFilter = AccessibleIdFilterBuilder.newBuilder().aclService(subjectAclService).resources(Lists.newArrayList("/draft/harmonized-dataset")).ids(filteredIds).build();
    if (limit == null)
        limit = MAX_LIMIT;
    if (limit < 0)
        throw new IllegalArgumentException("limit cannot be negative");
    DocumentService.Documents<HarmonizationDataset> datasets = draftDatasetService.find(from, limit, sort, order, studyId, query, null, null, accessibleIdFilter);
    totalCount = datasets.getTotal();
    response.addHeader("X-Total-Count", Long.toString(totalCount));
    return datasets.getList().stream().map(dataset -> dtos.asDto(dataset, true)).collect(toList());
}

Example 15 with Dataset

use of org.obiba.mica.dataset.domain.Dataset in project mica2 by obiba.

the class PublishedDatasetResource method alternativeStudyDataset.

private StudyDataset alternativeStudyDataset(String id, String project, String table) {
    Dataset dataset = getDataset(id);
    if (!(dataset instanceof StudyDataset))
        throw NoSuchDatasetException.withId(id);
    StudyDataset asStudyDataset = (StudyDataset) dataset;
    asStudyDataset.getStudyTable().setProject(project);
    asStudyDataset.getStudyTable().setTable(table);
    return asStudyDataset;
}