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

Example 1 with HarmonizationDataset

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

the class HarmonizedDatasetService method index.

/**
 * Index the dataset and associated variables.
 *
 * @param id
 */
public void index(@NotNull String id) {
    HarmonizationDataset dataset = findById(id);
    eventBus.post(new DatasetUpdatedEvent(dataset));
}

Example 2 with HarmonizationDataset

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

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

the class HarmonizedDatasetService method indexAll.

public void indexAll(boolean mustIndexVariables) {
    Set<HarmonizationDataset> publishedDatasets = Sets.newHashSet(findAllPublishedDatasets());
    findAllDatasets().forEach(dataset -> {
        try {
            eventBus.post(new DatasetUpdatedEvent(dataset));
            if (publishedDatasets.contains(dataset)) {
                Map<String, List<DatasetVariable>> harmonizationVariables = mustIndexVariables && publishedDatasets.contains(dataset) ? populateHarmonizedVariablesMap(dataset) : null;
                Iterable<DatasetVariable> datasetVariables = mustIndexVariables && publishedDatasets.contains(dataset) ? wrappedGetDatasetVariables(dataset) : null;
                eventBus.post(new DatasetPublishedEvent(dataset, datasetVariables, harmonizationVariables, getCurrentUsername()));
            }
        } catch (Exception e) {
            log.error(String.format("Error indexing dataset %s", dataset), e);
        }
    });
    eventBus.post(new HarmonizationDatasetIndexedEvent());
}

Example 4 with HarmonizationDataset

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

the class HarmonizedDatasetService method publish.

/**
 * Apply dataset publication flag.
 *
 * @param id
 * @param published
 */
@Caching(evict = { @CacheEvict(value = "aggregations-metadata", key = "'dataset'") })
public void publish(@NotNull String id, boolean published, PublishCascadingScope cascadingScope) {
    HarmonizationDataset dataset = findById(id);
    helper.evictCache(dataset);
    if (published) {
        checkIsPublishable(dataset);
        publishState(id);
        Map<String, List<DatasetVariable>> harmonizationVariables = populateHarmonizedVariablesMap(dataset);
        eventBus.post(new DatasetPublishedEvent(dataset, wrappedGetDatasetVariables(dataset), harmonizationVariables, getCurrentUsername(), cascadingScope));
    // helper.asyncBuildDatasetVariablesCache(dataset, harmonizationVariables);
    } else {
        unPublishState(id);
        eventBus.post(new DatasetUnpublishedEvent(dataset));
    }
}

Example 5 with HarmonizationDataset

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

the class PublishedDataschemaDatasetVariableResource method getVariableSummaries.

@GET
@Path("/summary")
@Timed
public List<Math.SummaryStatisticsDto> getVariableSummaries() {
    ImmutableList.Builder<Math.SummaryStatisticsDto> builder = ImmutableList.builder();
    HarmonizationDataset dataset = getDataset(HarmonizationDataset.class, datasetId);
    dataset.getBaseStudyTables().forEach(table -> {
        try {
            String studyId = table.getStudyId();
            builder.add(datasetService.getVariableSummary(dataset, variableName, studyId, table.getProject(), table.getTable()).getWrappedDto());
        } catch (NoSuchVariableException | NoSuchValueTableException e) {
            // case the study has not implemented this dataschema variable
            builder.add(Math.SummaryStatisticsDto.newBuilder().setResource(variableName).build());
        }
    });
    return builder.build();
}