Examples with StudyTable org.obiba.mica.core.domain.StudyTable used on opensource projects

Example 11 with StudyTable

use of org.obiba.mica.core.domain.StudyTable in project mica2 by obiba.

the class HarmonizedDatasetHelperTest method createStudyTable.

private StudyTable createStudyTable(String studyId) {
    StudyTable table = new StudyTable();
    initTable(studyId, table);
    table.setDataCollectionEventId(RandomStringUtils.random(10, true, true));
    return table;
}

Example 12 with StudyTable

use of org.obiba.mica.core.domain.StudyTable 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 13 with StudyTable

use of org.obiba.mica.core.domain.StudyTable in project mica2 by obiba.

the class CollectedDatasetService method prepareForIndex.

private void prepareForIndex(StudyDataset dataset) {
    if (dataset.hasStudyTable()) {
        StudyTable studyTable = dataset.getStudyTable();
        BaseStudy study = publishedStudyService.findById(dataset.getStudyTable().getStudyId());
        if (study != null) {
            Population population = study.findPopulation(studyTable.getPopulationId());
            if (population != null) {
                studyTable.setPopulationWeight(population.getWeight());
                DataCollectionEvent dataCollectionEvent = population.findDataCollectionEvent(studyTable.getDataCollectionEventId());
                if (dataCollectionEvent != null) {
                    studyTable.setDataCollectionEventWeight(dataCollectionEvent.getWeight());
                }
            }
        }
    }
}

Example 14 with StudyTable

use of org.obiba.mica.core.domain.StudyTable in project mica2 by obiba.

the class PublishedCollectedDatasetVariableResource method getContingencyDto.

private Mica.DatasetVariableContingencyDto getContingencyDto(DatasetVariable var, DatasetVariable crossVar) {
    StudyDataset dataset = getDataset(StudyDataset.class, datasetId);
    StudyTable studyTable = dataset.getSafeStudyTable();
    try {
        return dtos.asContingencyDto(studyTable, var, crossVar, datasetService.getContingencyTable(dataset, var, crossVar)).build();
    } catch (Exception e) {
        log.warn("Unable to retrieve contingency table: " + e.getMessage(), e);
        return dtos.asContingencyDto(studyTable, var, crossVar, null).build();
    }
}