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

Example 11 with StudyDataset

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

the class DatasetDtos method fromDto.

private Dataset fromDto(@NotNull Mica.CollectedDatasetDto dto) {
    Assert.notNull(dto, "StudyDataset dt cannot be null.");
    StudyDataset studyDataset = new StudyDataset();
    Optional.ofNullable(dto).ifPresent(ext -> studyDataset.setStudyTable(fromDto(ext.getStudyTable())));
    return studyDataset;
}

Example 12 with StudyDataset

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

the class CollectedDatasetServiceTest method buildStudyDataset.

private StudyDataset buildStudyDataset() {
    StudyDataset ds = new StudyDataset();
    StudyTable st = new StudyTable();
    st.setProject("proj");
    st.setTable("tab");
    ds.setStudyTable(st);
    ds.setName(new LocalizedString(Locale.CANADA, "test"));
    return ds;
}

Example 13 with StudyDataset

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

the class DraftCollectedDatasetResource method update.

@PUT
public Response update(Mica.DatasetDto datasetDto, @Context UriInfo uriInfo, @Nullable @QueryParam("comment") String comment) {
    checkPermission("/draft/collected-dataset", "EDIT");
    if (!datasetDto.hasId() || !datasetDto.getId().equals(id))
        throw new IllegalArgumentException("Not the expected dataset id");
    Dataset dataset = dtos.fromDto(datasetDto);
    if (!(dataset instanceof StudyDataset))
        throw new IllegalArgumentException("A study dataset is expected");
    datasetService.save((StudyDataset) dataset, comment);
    return Response.noContent().build();
}

Example 14 with StudyDataset

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

the class CollectedDatasetService method processVariablesForStudyDataset.

public List<DatasetVariable> processVariablesForStudyDataset(StudyDataset dataset, Iterable<DatasetVariable> variables) {
    if (!dataset.hasStudyTable()) {
        return Lists.newArrayList(variables);
    }
    StudyTable studyTable = dataset.getStudyTable();
    BaseStudy study = studyService.findStudy(dataset.getStudyTable().getStudyId());
    Population population = study.findPopulation(studyTable.getPopulationId());
    if (population == null) {
        return Lists.newArrayList(variables);
    }
    int populationWeight = population.getWeight();
    DataCollectionEvent dataCollectionEvent = population.findDataCollectionEvent(studyTable.getDataCollectionEventId());
    if (dataCollectionEvent == null) {
        return Lists.newArrayList(variables);
    }
    int dataCollectionEventWeight = dataCollectionEvent.getWeight();
    return StreamSupport.stream(variables.spliterator(), false).map(datasetVariable -> {
        datasetVariable.setPopulationWeight(populationWeight);
        datasetVariable.setDataCollectionEventWeight(dataCollectionEventWeight);
        return datasetVariable;
    }).collect(toList());
}

Example 15 with StudyDataset

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

the class CollectedDatasetService method saveInternal.

private void saveInternal(StudyDataset dataset, String comment) {
    StudyDataset saved = prepareSave(dataset);
    StudyDatasetState studyDatasetState = findEntityState(dataset, StudyDatasetState::new);
    if (!dataset.isNew())
        ensureGitRepository(studyDatasetState);
    studyDatasetState.incrementRevisionsAhead();
    studyDatasetStateRepository.save(studyDatasetState);
    saved.setLastModifiedDate(DateTime.now());
    studyDatasetRepository.save(saved);
    gitService.save(saved, comment);
    eventBus.post(new DatasetUpdatedEvent(saved));
}