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

Example 6 with StudyDataset

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

the class DatasetDtosTest method test_study_dataset_dto.

@Test
public void test_study_dataset_dto() throws Exception {
    StudyDataset studyDataset = createStudyDataset();
    Mica.DatasetDto dto = datasetDtos.asDto(studyDataset);
    assertThat(dto.getId(), is("123"));
}

Example 7 with StudyDataset

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

the class DatasetDtosTest method createStudyDataset.

private StudyDataset createStudyDataset() {
    StudyDataset studyDataset = new StudyDataset();
    studyDataset.setId("123");
    return studyDataset;
}

Example 8 with StudyDataset

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

the class DraftCollectedDatasetsResource method create.

@POST
@Path("/collected-datasets")
@Timed
@RequiresPermissions({ "/draft/collected-dataset:ADD" })
public Response create(Mica.DatasetDto datasetDto, @Context UriInfo uriInfo, @Nullable @QueryParam("comment") String comment) {
    Dataset dataset = dtos.fromDto(datasetDto);
    if (!(dataset instanceof StudyDataset))
        throw new IllegalArgumentException("A collected dataset is expected");
    datasetService.save((StudyDataset) dataset, comment);
    return Response.created(uriInfo.getBaseUriBuilder().segment("draft", "collected-dataset", dataset.getId()).build()).build();
}

Example 9 with StudyDataset

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

the class RQLCriteriaOpalConverter method parseField.

private RQLFieldReferences parseField(String path) {
    DatasetVariable.IdResolver resolver = DatasetVariable.IdResolver.from(path);
    if (resolver.getType() == null || DatasetVariable.Type.Collected.equals(resolver.getType())) {
        StudyDataset ds = collectedDatasetService.findById(resolver.getDatasetId());
        BaseStudyTable studyTable = ds.getStudyTable();
        BaseStudy study = studyService.findStudy(studyTable.getStudyId());
        return new RQLFieldReferences(path, ds, studyTable, study, getDatasetVariableInternal(Indexer.VARIABLE_TYPE, path));
    } else if (DatasetVariable.Type.Dataschema.equals(resolver.getType())) {
        HarmonizationDataset ds = harmonizedDatasetService.findById(resolver.getDatasetId());
        BaseStudy study = studyService.findStudy(ds.getHarmonizationTable().getStudyId());
        return new RQLFieldReferences(path, ds, ds.getBaseStudyTables(), study, getDatasetVariableInternal(Indexer.VARIABLE_TYPE, path));
    } else if (DatasetVariable.Type.Harmonized.equals(resolver.getType())) {
        HarmonizationDataset ds = harmonizedDatasetService.findById(resolver.getDatasetId());
        Optional<BaseStudyTable> studyTable = ds.getBaseStudyTables().stream().filter(st -> st.getStudyId().equals(resolver.getStudyId()) && st.getProject().equals(resolver.getProject()) && st.getTable().equals(resolver.getTable())).findFirst();
        if (!studyTable.isPresent())
            throw new IllegalArgumentException("Not a valid variable: " + path);
        BaseStudy study = studyService.findStudy(studyTable.get().getStudyId());
        return new RQLFieldReferences(path, ds, studyTable.get(), study, getDatasetVariableInternal(Indexer.HARMONIZED_VARIABLE_TYPE, path));
    }
    throw new IllegalArgumentException("Not a valid variable: " + path);
}

Example 10 with StudyDataset

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

the class DatasetDtos method fromDto.

@NotNull
public Dataset fromDto(Mica.DatasetDtoOrBuilder dto) {
    Dataset dataset = dto.hasExtension(Mica.HarmonizedDatasetDto.type) ? fromDto(dto.getExtension(Mica.HarmonizedDatasetDto.type)) : dto.hasExtension(Mica.CollectedDatasetDto.type) ? fromDto(dto.getExtension(Mica.CollectedDatasetDto.type)) : new StudyDataset();
    if (dto.hasId())
        dataset.setId(dto.getId());
    dataset.setAcronym(localizedStringDtos.fromDto(dto.getAcronymList()));
    dataset.setName(localizedStringDtos.fromDto(dto.getNameList()));
    dataset.setDescription(localizedStringDtos.fromDto(dto.getDescriptionList()));
    dataset.setEntityType(dto.getEntityType());
    dataset.setPublished(dto.getPublished());
    if (dto.getAttributesCount() > 0) {
        dto.getAttributesList().forEach(attributeDto -> dataset.addAttribute(attributeDtos.fromDto(attributeDto)));
    }
    if (dto.hasContent()) {
        dataset.setModel(JSONUtils.toMap(dto.getContent()));
    }
    return dataset;
}