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

Example 6 with BaseStudy

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

the class PersonDtos method asStudyMembershipDto.

private Mica.PersonDto.MembershipDto asStudyMembershipDto(Person.Membership membership, boolean asDraft) {
    Mica.PersonDto.MembershipDto.Builder builder = Mica.PersonDto.MembershipDto.newBuilder();
    builder.setRole(membership.getRole());
    builder.setParentId(membership.getParentId());
    if (membership.getParentId() != null) {
        BaseStudy study = asDraft ? studyService.findStudy(membership.getParentId()) : publishedStudyService.findById(membership.getParentId());
        if (study != null) {
            builder.addAllParentAcronym(localizedStringDtos.asDto(study.getAcronym()));
            builder.addAllParentName(localizedStringDtos.asDto(study.getName()));
            builder.setExtension(Mica.PersonDto.StudyMembershipDto.meta, Mica.PersonDto.StudyMembershipDto.newBuilder().setType(study.getResourcePath()).build());
        }
    }
    return builder.build();
}

Example 7 with BaseStudy

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

the class StudyDtos method fromDto.

@NotNull
BaseStudy fromDto(@NotNull Mica.StudyDtoOrBuilder dto) {
    Assert.isTrue(dto.hasExtension(Mica.CollectionStudyDto.type) || dto.hasExtension(Mica.HarmonizationStudyDto.type), "StudyDto must of a type extension.");
    BaseStudy study = dto.hasExtension(Mica.CollectionStudyDto.type) ? new Study() : new HarmonizationStudy();
    if (dto.hasId())
        study.setId(dto.getId());
    if (dto.getNameCount() > 0)
        study.setName(localizedStringDtos.fromDto(dto.getNameList()));
    if (dto.getAcronymCount() > 0)
        study.setAcronym(localizedStringDtos.fromDto(dto.getAcronymList()));
    if (dto.hasLogo())
        study.setLogo(attachmentDtos.fromDto(dto.getLogo()));
    if (dto.hasTimestamps())
        TimestampsDtos.fromDto(dto.getTimestamps(), study);
    if (dto.getObjectivesCount() > 0)
        study.setObjectives(localizedStringDtos.fromDto(dto.getObjectivesList()));
    if (dto.hasOpal())
        study.setOpal(dto.getOpal());
    if (dto.getMembershipsCount() > 0) {
        Map<String, List<Membership>> memberships = Maps.newHashMap();
        dto.getMembershipsList().forEach(e -> memberships.put(e.getRole(), e.getMembersList().stream().map(p -> new Membership(personDtos.fromDto(p), e.getRole())).collect(toList())));
        study.setMemberships(memberships);
    }
    if (dto.getPopulationsCount() > 0) {
        study.setPopulations(dto.getPopulationsList().stream().map(populationDtos::fromDto).collect(Collectors.toCollection(TreeSet<org.obiba.mica.study.domain.Population>::new)));
    }
    if (dto.hasContent() && !Strings.isNullOrEmpty(dto.getContent()))
        study.setModel(JSONUtils.toMap(dto.getContent()));
    else
        study.setModel(new HashMap<>());
    return study;
}

Example 8 with BaseStudy

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

the class StudyEntitiesCountService method newQueries.

/**
 * Parse the RQL query and translate each node as a Opal query wrapped in a {@link StudyEntitiesCountQuery}.
 *
 * @param query
 * @param entityType
 * @return
 */
public List<StudyEntitiesCountQuery> newQueries(String query, String entityType) {
    RQLCriteriaOpalConverter converter = applicationContext.getBean(RQLCriteriaOpalConverter.class);
    converter.parse(query);
    Map<BaseStudy, List<RQLCriterionOpalConverter>> studyConverters = converter.getCriterionConverters().stream().filter(// TODO include Dataschema variables
    c -> !c.hasMultipleStudyTables()).collect(Collectors.groupingBy(c -> c.getVariableReferences().getStudy()));
    return studyConverters.keySet().stream().map(study -> newQuery(entityType, study, studyConverters.get(study))).collect(Collectors.toList());
}

Example 9 with BaseStudy

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

the class AbstractPublishedStudyResource method getStudyFileResource.

protected FileResource getStudyFileResource(String id, String fileId) {
    checkAccess(id);
    FileResource fileResource = applicationContext.getBean(FileResource.class);
    BaseStudy study = getStudy(id);
    if (study.hasLogo() && study.getLogo().getId().equals(fileId)) {
        fileResource.setAttachment(study.getLogo());
    } else {
        List<Attachment> attachments = fileSystemService.findAttachments(String.format("^/%s/%s", getStudyPath(id), id), true).stream().filter(a -> a.getId().equals(fileId)).collect(Collectors.toList());
        if (attachments.isEmpty())
            throw NoSuchEntityException.withId(Attachment.class, fileId);
        fileResource.setAttachment(attachments.get(0));
    }
    return fileResource;
}

Example 10 with BaseStudy

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

the class PublishedStudyResource method getStudyDto.

@GET
@Timed
public Mica.StudyDto getStudyDto(@PathParam("id") String id, @QueryParam("locale") String locale) {
    checkAccess(id);
    BaseStudy study = getStudy(id, locale);
    return study instanceof Study ? dtos.asDto((Study) study) : dtos.asDto((HarmonizationStudy) study);
}