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

Example 26 with DocumentSet

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

the class DataAccessEntityResource method createOrUpdateVariablesSet.

// 
// Private methods
// 
/**
 * Create or update a variables set from user's cart.
 *
 * @param entity
 * @return
 */
protected DocumentSet createOrUpdateVariablesSet(DataAccessEntity entity) {
    DocumentSet set;
    DocumentSet cart = variableSetService.getCartCurrentUser();
    String setId = String.format("dar:%s", entity.getId());
    Optional<DocumentSet> setOpt = variableSetService.getAllCurrentUser().stream().filter(docset -> setId.equals(docset.getName())).findFirst();
    if (setOpt.isPresent()) {
        // reuse and append an existing set with same name
        set = variableSetService.addIdentifiers(setId, Lists.newArrayList(cart.getIdentifiers()));
    } else {
        // create a new one
        set = variableSetService.create(setId, Lists.newArrayList(cart.getIdentifiers()));
    }
    // case an administrator is by-passing the flow
    if (!DataAccessEntityStatus.OPENED.equals(entity.getStatus())) {
        variableSetService.setLock(set, true);
    }
    return set;
}

Example 27 with DocumentSet

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

the class PublishedStudiesSetResource method reportStudies.

@GET
@Path("/documents/_report")
@Produces(MediaType.APPLICATION_OCTET_STREAM)
public Response reportStudies(@PathParam("id") String id, @QueryParam("locale") @DefaultValue("en") String locale) {
    DocumentSet documentSet = getSecuredDocumentSet(id);
    ReportGenerator reporter = new StudyCsvReportGenerator(studySetService.getPublishedStudies(documentSet, true), locale, personService);
    StreamingOutput stream = reporter::write;
    return Response.ok(stream).header("Content-Disposition", "attachment; filename=\"Studies.zip\"").build();
}

Example 28 with DocumentSet

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

the class PublishedStudiesSetResource method importQueryDocuments.

private Mica.DocumentSetDto importQueryDocuments(String id, String query) {
    DocumentSet set = getSecuredDocumentSet(id);
    if (Strings.isNullOrEmpty(query))
        return dtos.asDto(set);
    MicaSearch.JoinQueryResultDto result = makeQuery(QueryType.STUDY, query);
    if (result.hasStudyResultDto() && result.getStudyResultDto().getTotalHits() > 0) {
        List<String> ids = result.getStudyResultDto().getExtension(MicaSearch.StudyResultDto.result).getSummariesList().stream().map(Mica.StudySummaryDto::getId).collect(Collectors.toList());
        getDocumentSetService().addIdentifiers(id, ids);
        set = getSecuredDocumentSet(id);
    }
    return dtos.asDto(set);
}

Example 29 with DocumentSet

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

the class PublishedDatasetVariablesSetResource method reportVariables.

@GET
@Path("/documents/_report")
@Produces(MediaType.APPLICATION_OCTET_STREAM)
public Response reportVariables(@PathParam("id") String id, @QueryParam("locale") @DefaultValue("en") String locale) {
    DocumentSet documentSet = getSecuredDocumentSet(id);
    ReportGenerator reporter = new DatasetVariableCsvReportGenerator(variableSetService.getVariables(documentSet, false), locale);
    StreamingOutput stream = reporter::write;
    return Response.ok(stream).header("Content-Disposition", "attachment; filename=\"Variables.zip\"").build();
}

Example 30 with DocumentSet

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

the class PublishedDatasetVariablesSetResource method createOpalViewsGet.

@GET
@Path("/documents/_opal")
@Produces(MediaType.APPLICATION_OCTET_STREAM)
public Response createOpalViewsGet(@PathParam("id") String id, @QueryParam("ids") String identifiers) {
    DocumentSet set = getSecuredDocumentSet(id);
    if (!subjectAclService.isAdministrator() && !subjectAclService.isDataAccessOfficer())
        throw new AuthorizationException();
    StreamingOutput streamingOutput;
    if (!Strings.isNullOrEmpty(identifiers)) {
        streamingOutput = stream -> variableSetService.createOpalViewsZip(variableSetService.getVariables(Sets.newHashSet(identifiers.split(","))), micaConfigService.getConfig().getOpalViewsGrouping(), new BufferedOutputStream(stream));
    } else {
        streamingOutput = stream -> variableSetService.createOpalViewsZip(variableSetService.getVariables(set), micaConfigService.getConfig().getOpalViewsGrouping(), new BufferedOutputStream(stream));
    }
    return Response.ok(streamingOutput, MediaType.APPLICATION_OCTET_STREAM).header("Content-Disposition", "attachment; filename=\"opal-views-" + id + ".zip\"").build();
}