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

Example 21 with StudyDataset

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

the class VariableSetService method toOpalTableFullName.

private List<String> toOpalTableFullName(Dataset dataset) {
    if (dataset instanceof StudyDataset) {
        OpalTable opalTable = ((StudyDataset) dataset).getSafeStudyTable();
        return Lists.newArrayList(opalTable.getProject() + "." + opalTable.getTable());
    } else {
        HarmonizationDataset harmoDataset = (HarmonizationDataset) dataset;
        // one for each study and harmo tables
        List<String> tableNames = Lists.newArrayList();
        tableNames.addAll(harmoDataset.getStudyTables().stream().map(st -> st.getProject() + "." + st.getTable()).collect(Collectors.toList()));
        tableNames.addAll(harmoDataset.getHarmonizationTables().stream().map(ht -> ht.getProject() + "." + ht.getTable()).collect(Collectors.toList()));
        return tableNames;
    }
}

Example 22 with StudyDataset

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

the class CollectedDatasetServiceTest method buildStudyDataset.

private StudyDataset buildStudyDataset() {
    StudyDataset ds = new StudyDataset();
    StudyTable st = new StudyTable();
    st.setProject("proj");
    st.setTable("tab");
    ds.setStudyTable(st);
    ds.setName(new LocalizedString(Locale.CANADA, "test"));
    return ds;
}

Example 23 with StudyDataset

use of org.obiba.mica.dataset.domain.StudyDataset 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 24 with StudyDataset

use of org.obiba.mica.dataset.domain.StudyDataset 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;
}

Example 25 with StudyDataset

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

the class DraftCollectedDatasetResource method update.

@PUT
public Response update(Mica.DatasetDto datasetDto, @Context UriInfo uriInfo, @Nullable @QueryParam("comment") String comment) {
    checkPermission("/draft/collected-dataset", "EDIT");
    if (!datasetDto.hasId() || !datasetDto.getId().equals(id))
        throw new IllegalArgumentException("Not the expected dataset id");
    Dataset dataset = dtos.fromDto(datasetDto);
    if (!(dataset instanceof StudyDataset))
        throw new IllegalArgumentException("A study dataset is expected");
    datasetService.save((StudyDataset) dataset, comment);
    return Response.noContent().build();
}