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

Example 16 with HarmonizationDataset

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

the class DatasetDtos method asDtoBuilder.

@NotNull
Mica.DatasetDto.Builder asDtoBuilder(@NotNull HarmonizationDataset dataset, boolean asDraft, boolean studySummary) {
    Mica.DatasetDto.Builder builder = asBuilder(dataset);
    builder.setVariableType(DatasetVariable.Type.Dataschema.name());
    Mica.HarmonizedDatasetDto.Builder hbuilder = Mica.HarmonizedDatasetDto.newBuilder();
    if (dataset.hasHarmonizationTable() && !Strings.isNullOrEmpty(dataset.getHarmonizationTable().getStudyId()) && isStudyTablePermitted(asDraft, "harmonization", dataset.getHarmonizationTable().getStudyId())) {
        hbuilder.setHarmonizationTable(createHarmonizationLinkDtoFromHarmonizationTable(dataset.getHarmonizationTable(), asDraft));
    }
    if (!dataset.getStudyTables().isEmpty()) {
        dataset.getStudyTables().stream().filter(studyTable -> isStudyTablePermitted(asDraft, "individual", studyTable.getStudyId())).forEach(studyTable -> hbuilder.addStudyTables(asDto(studyTable, studySummary)));
    }
    if (!dataset.getHarmonizationTables().isEmpty()) {
        dataset.getHarmonizationTables().stream().filter(studyTable -> isStudyTablePermitted(asDraft, "harmonization", studyTable.getStudyId())).forEach(harmonizationTable -> hbuilder.addHarmonizationTables(asDto(harmonizationTable, studySummary)));
    }
    builder.setExtension(Mica.HarmonizedDatasetDto.type, hbuilder.build());
    Mica.PermissionsDto permissionsDto = permissionsDtos.asDto(dataset);
    if (asDraft) {
        HarmonizationDatasetState state = harmonizationDatasetStateRepository.findOne(dataset.getId());
        if (state != null) {
            builder.setPublished(state.isPublished());
            builder.setExtension(Mica.EntityStateDto.datasetState, entityStateDtos.asDto(state).setPermissions(permissionsDto).build());
        }
    }
    builder.setPermissions(permissionsDto);
    return builder;
}

Example 17 with HarmonizationDataset

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

the class HarmonizedDatasetServiceTest method buildHarmonizationDataset.

private HarmonizationDataset buildHarmonizationDataset(String id, StudyTable... studyTables) {
    HarmonizationDataset ds = new HarmonizationDataset();
    for (StudyTable s : studyTables) {
        ds.addStudyTable(s);
    }
    ds.setId(id);
    ds.setName(new LocalizedString(Locale.CANADA, "dataset" + id));
    return ds;
}

Example 18 with HarmonizationDataset

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

the class HarmonizedDatasetHelperTest method createDataset.

private HarmonizationDataset createDataset(List<String> studyIds, List<String> harmoStudyIds) {
    HarmonizationDataset dataset = new HarmonizationDataset();
    studyIds.forEach(id -> dataset.addStudyTable(createStudyTable(id)));
    harmoStudyIds.forEach(id -> dataset.addHarmonizationTable(createHarmonizationStudyTable(id)));
    return dataset;
}

Example 19 with HarmonizationDataset

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

the class DatasetDtosTest method test_harmonized_dataset_dto.

@Test
public void test_harmonized_dataset_dto() throws Exception {
    when(harmonizationDatasetStateRepository.findOne(anyString())).thenReturn(new HarmonizationDatasetState());
    HarmonizationDataset harmonizationDataset = createHarmonizedDataset();
    Mica.DatasetDto dto = datasetDtos.asDto(harmonizationDataset);
    assertThat(dto.getId(), is("123"));
}

Example 20 with HarmonizationDataset

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

the class DatasetDtosTest method createHarmonizedDataset.

private HarmonizationDataset createHarmonizedDataset() {
    HarmonizationDataset harmonizationDataset = new HarmonizationDataset();
    harmonizationDataset.setId("123");
    HarmonizationStudyTable harmonizationLink = new HarmonizationStudyTable();
    harmonizationLink.setProject("project123");
    harmonizationLink.setTable("table123");
    harmonizationLink.setStudyId("study123");
    harmonizationLink.setPopulationId("population123");
    harmonizationDataset.setHarmonizationTable(harmonizationLink);
    return harmonizationDataset;
}