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

Example 1 with DatasetVariable

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

the class CollectedDatasetService method indexDatasets.

private void indexDatasets(Set<StudyDataset> publishedDatasets, List<StudyDataset> datasets, boolean mustIndexVariables) {
    datasets.forEach(dataset -> {
        try {
            eventBus.post(new DatasetUpdatedEvent(dataset));
            if (publishedDatasets.contains(dataset)) {
                prepareForIndex(dataset);
                Iterable<DatasetVariable> variables = mustIndexVariables && publishedDatasets.contains(dataset) ? wrappedGetDatasetVariables(dataset) : null;
                eventBus.post(new DatasetPublishedEvent(dataset, variables, getCurrentUsername()));
            }
        } catch (Exception e) {
            log.error(String.format("Error indexing dataset %s", dataset), e);
        }
    });
}

Example 2 with DatasetVariable

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

the class CollectedDatasetService 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) {
    StudyDataset dataset = findById(id);
    helper.evictCache(dataset);
    if (published) {
        checkIsPublishable(dataset);
        Iterable<DatasetVariable> variables = wrappedGetDatasetVariables(dataset);
        publishState(id);
        prepareForIndex(dataset);
        eventBus.post(new DatasetPublishedEvent(dataset, variables, getCurrentUsername(), cascadingScope));
    // helper.asyncBuildDatasetVariablesCache(dataset, variables);
    } else {
        unPublishState(id);
        eventBus.post(new DatasetUnpublishedEvent(dataset));
    }
}

Example 3 with DatasetVariable

use of org.obiba.mica.dataset.domain.DatasetVariable 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 DatasetVariable

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

the class PublishedCollectedDatasetVariableResource method getContingencyCsv.

@GET
@Path("/contingency/_export")
@Produces("text/csv")
@Timed
public Response getContingencyCsv(@QueryParam("by") String crossVariable) throws IOException {
    Pair<DatasetVariable, DatasetVariable> variables = getContingencyVariables(crossVariable);
    ByteArrayOutputStream res = new CsvContingencyWriter(variables.getFirst(), variables.getSecond()).write(getContingencyDto(variables.getFirst(), variables.getSecond()));
    return Response.ok(res.toByteArray()).header("Content-Disposition", String.format("attachment; filename=\"contingency-table-%s-%s.csv\"", variableName, crossVariable)).build();
}

Example 5 with DatasetVariable

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

the class PublishedCollectedDatasetVariableResource method getContingencyExcel.

@GET
@Path("/contingency/_export")
@Produces("application/vnd.openxmlformats-officedocument.spreadsheetml.sheet")
@Timed
public Response getContingencyExcel(@QueryParam("by") String crossVariable) throws IOException {
    Pair<DatasetVariable, DatasetVariable> variables = getContingencyVariables(crossVariable);
    ByteArrayOutputStream res = new ExcelContingencyWriter(variables.getFirst(), variables.getSecond()).write(getContingencyDto(variables.getFirst(), variables.getSecond()));
    return Response.ok(res.toByteArray()).header("Content-Disposition", String.format("attachment; filename=\"contingency-table-%s-%s.xlsx\"", variableName, crossVariable)).build();
}