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

Example 1 with HarmonizationDatasetState

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

the class HarmonizedDatasetService method saveInternal.

// 
// Private methods
// 
@SuppressWarnings("OverlyLongMethod")
private void saveInternal(HarmonizationDataset dataset, String comment) {
    HarmonizationDataset saved = prepareSave(dataset);
    HarmonizationDatasetState harmonizationDatasetState = findEntityState(dataset, HarmonizationDatasetState::new);
    if (!dataset.isNew())
        ensureGitRepository(harmonizationDatasetState);
    harmonizationDatasetState.incrementRevisionsAhead();
    harmonizationDatasetStateRepository.save(harmonizationDatasetState);
    saved.setLastModifiedDate(DateTime.now());
    harmonizationDatasetRepository.save(saved);
    gitService.save(saved, comment);
    helper.getPublishedVariables(saved);
}

Example 2 with HarmonizationDatasetState

use of org.obiba.mica.dataset.domain.HarmonizationDatasetState 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 3 with HarmonizationDatasetState

use of org.obiba.mica.dataset.domain.HarmonizationDatasetState 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"));
}