Examples with EntityStateFilter org.obiba.mica.core.domain.EntityStateFilter used on opensource projects

Example 1 with EntityStateFilter

use of org.obiba.mica.core.domain.EntityStateFilter in project mica2 by obiba.

the class StudyStatesResource method listCollectionStudyStates.

@GET
@Path("/study-states")
@Timed
public List<Mica.StudySummaryDto> listCollectionStudyStates(@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("type") String type, @QueryParam("exclude") List<String> excludes, @QueryParam("filter") @DefaultValue("ALL") String filter, @Context HttpServletResponse response) {
    Stream<? extends EntityState> result;
    long totalCount;
    EntityStateFilter entityStateFilter = EntityStateFilter.valueOf(filter);
    List<String> filteredIds = Strings.isNullOrEmpty(type) ? studyService.getIdsByStateFilter(entityStateFilter) : getStudyServiceByType(type).getIdsByStateFilter(entityStateFilter);
    Searcher.IdFilter accessibleIdFilter = AccessibleIdFilterBuilder.newBuilder().aclService(subjectAclService).resources(getPermissionResources(type)).ids(filteredIds).build();
    String ids = excludes.stream().map(s -> "id:" + s).collect(Collectors.joining(" "));
    if (!Strings.isNullOrEmpty(ids)) {
        if (Strings.isNullOrEmpty(query))
            query = String.format("NOT(%s)", ids);
        else
            query += String.format(" AND NOT(%s)", ids);
    }
    if (limit == null)
        limit = MAX_LIMIT;
    if (limit < 0)
        throw new IllegalArgumentException("limit cannot be negative");
    DocumentService.Documents<Study> studyDocuments = draftStudyService.find(from, limit, sort, order, null, query, null, null, accessibleIdFilter);
    totalCount = studyDocuments.getTotal();
    response.addHeader("X-Total-Count", Long.toString(totalCount));
    return studyDocuments.getList().stream().map(study -> dtos.asDto(study, studyService.getEntityState(study.getId()))).collect(toList());
}

Example 2 with EntityStateFilter

use of org.obiba.mica.core.domain.EntityStateFilter in project mica2 by obiba.

the class DraftProjectsResource method list.

@GET
@Path("/projects")
@Timed
public Mica.ProjectsDto list(@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) {
    EntityStateFilter entityStateFilter = EntityStateFilter.valueOf(filter);
    List<String> filteredIds = projectService.getIdsByStateFilter(entityStateFilter);
    Searcher.IdFilter accessibleIdFilter = AccessibleIdFilterBuilder.newBuilder().aclService(subjectAclService).resources(Lists.newArrayList("/draft/project")).ids(filteredIds).build();
    if (limit == null)
        limit = MAX_LIMIT;
    if (limit < 0)
        throw new IllegalArgumentException("limit cannot be negative");
    DocumentService.Documents<Project> projectDocuments = draftProjectService.find(from, limit, sort, order, null, query, null, null, accessibleIdFilter);
    long totalCount = projectDocuments.getTotal();
    List<Mica.ProjectDto> result = projectDocuments.getList().stream().map(n -> dtos.asDto(n, true)).collect(toList());
    Mica.ProjectsDto.Builder builder = Mica.ProjectsDto.newBuilder();
    builder.setFrom(from).setLimit(limit).setTotal(Long.valueOf(totalCount).intValue());
    builder.addAllProjects(result);
    if (subjectAclService.isPermitted("/draft/project", "ADD")) {
        builder.addActions("ADD");
    }
    return builder.build();
}

Example 3 with EntityStateFilter

use of org.obiba.mica.core.domain.EntityStateFilter in project mica2 by obiba.

the class DraftNetworksResource method list.

@GET
@Path("/networks")
@Timed
public List<Mica.NetworkSummaryDto> 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("exclude") List<String> excludes, @QueryParam("filter") @DefaultValue("ALL") String filter, @Context HttpServletResponse response) {
    Stream<Network> result;
    long totalCount;
    EntityStateFilter entityStateFilter = EntityStateFilter.valueOf(filter);
    List<String> filteredIds = networkService.getIdsByStateFilter(entityStateFilter);
    Searcher.IdFilter accessibleIdFilter = AccessibleIdFilterBuilder.newBuilder().aclService(subjectAclService).resources(Lists.newArrayList("/draft/network")).ids(filteredIds).build();
    if (limit == null)
        limit = MAX_LIMIT;
    if (limit < 0)
        throw new IllegalArgumentException("limit cannot be negative");
    String ids = excludes.stream().map(s -> "id:" + s).collect(Collectors.joining(" "));
    if (!Strings.isNullOrEmpty(ids)) {
        if (Strings.isNullOrEmpty(query))
            query = String.format("NOT(%s)", ids);
        else
            query += String.format(" AND NOT(%s)", ids);
    }
    DocumentService.Documents<Network> networkDocuments = draftNetworkService.find(from, limit, sort, order, studyId, query, null, null, accessibleIdFilter);
    totalCount = networkDocuments.getTotal();
    response.addHeader("X-Total-Count", Long.toString(totalCount));
    return networkDocuments.getList().stream().map(network -> dtos.asSummaryDto(network, true)).collect(toList());
}

Example 4 with EntityStateFilter

use of org.obiba.mica.core.domain.EntityStateFilter 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 5 with EntityStateFilter

use of org.obiba.mica.core.domain.EntityStateFilter 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());
}