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

Example 1 with HarmonizationStudy

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

the class DraftHarmonizationStudiesResource method create.

@POST
@Path("/harmonization-studies")
@Timed
@RequiresPermissions({ "/draft/harmonization-study:ADD" })
public Response create(@SuppressWarnings("TypeMayBeWeakened") Mica.StudyDto studyDto, @Context UriInfo uriInfo, @Nullable @QueryParam("comment") String comment) {
    HarmonizationStudy study = (HarmonizationStudy) dtos.fromDto(studyDto);
    harmonizationStudyService.save(study, comment);
    return Response.created(uriInfo.getBaseUriBuilder().path(DraftHarmonizationStudiesResource.class, "study").build(study.getId())).build();
}

Example 2 with HarmonizationStudy

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

the class DraftHarmonizationStudyResource method file.

@Path("/file/{fileId}")
public FileResource file(@PathParam("fileId") String fileId, @QueryParam("key") String key) {
    checkPermission("/draft/harmonization-study", "VIEW", key);
    FileResource fileResource = applicationContext.getBean(FileResource.class);
    HarmonizationStudy study = studyService.findDraft(id);
    if (study.hasLogo() && study.getLogo().getId().equals(fileId)) {
        fileResource.setAttachment(study.getLogo());
    } else {
        List<Attachment> attachments = fileSystemService.findAttachments(String.format("^/harmonization-study/%s", study.getId()), false).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 3 with HarmonizationStudy

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

the class DraftHarmonizationStudyResource method update.

@PUT
@Timed
public Response update(@SuppressWarnings("TypeMayBeWeakened") Mica.StudyDto studyDto, @Nullable @QueryParam("comment") String comment) {
    checkPermission("/draft/harmonization-study", "EDIT");
    // ensure study exists
    studyService.findDraft(id);
    HarmonizationStudy study = (HarmonizationStudy) dtos.fromDto(studyDto);
    HashMap<Object, Object> response = Maps.newHashMap();
    response.put("study", study);
    response.put("potentialConflicts", studyService.getPotentialConflicts(study, false));
    studyService.save(study, comment);
    return Response.ok(response, MediaType.APPLICATION_JSON_TYPE).build();
}

Example 4 with HarmonizationStudy

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

the class HarmonizationStudyService method getPotentialConflicts.

/**
 * @param study
 * @param publishing
 * @return
 */
public Map<String, List<String>> getPotentialConflicts(HarmonizationStudy study, boolean publishing) {
    if (study.getId() != null) {
        HarmonizationStudy oldStudy = publishing ? study : harmonizationStudyRepository.findOne(study.getId());
        if (oldStudy != null) {
            List<String> populationUIDs = publishing ? toListOfPopulationUids(study) : populationsAffected(study, oldStudy);
            if (populationUIDs != null) {
                List<String> networkIds = networkRepository.findByStudyIds(study.getId()).stream().map(AbstractGitPersistable::getId).collect(toList());
                List<String> harmoDatasetIds = findHarmonizedDatasetDependencies(study.getId(), populationUIDs);
                if (!harmoDatasetIds.isEmpty() || !networkIds.isEmpty()) {
                    return new HashMap<String, List<String>>() {

                        {
                            put("harmonizationDataset", harmoDatasetIds);
                            put("network", networkIds);
                        }
                    };
                }
            }
        }
    }
    return null;
}

Example 5 with HarmonizationStudy

use of org.obiba.mica.study.domain.HarmonizationStudy 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;
}