Examples with BaseStudy org.obiba.mica.study.domain.BaseStudy used on opensource projects

Example 11 with BaseStudy

use of org.obiba.mica.study.domain.BaseStudy 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 12 with BaseStudy

use of org.obiba.mica.study.domain.BaseStudy 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 13 with BaseStudy

use of org.obiba.mica.study.domain.BaseStudy in project mica2 by obiba.

the class StudyQuery method processHits.

@Override
public void processHits(QueryResultDto.Builder builder, Searcher.DocumentResults results, QueryScope scope, CountStatsData counts) throws IOException {
    StudyResultDto.Builder resBuilder = StudyResultDto.newBuilder();
    StudyCountStatsBuilder studyCountStatsBuilder = counts == null ? null : StudyCountStatsBuilder.newBuilder(counts);
    Consumer<BaseStudy> addDto = getStudyConsumer(scope, resBuilder, studyCountStatsBuilder);
    List<BaseStudy> publishedStudies = getPublishedDocumentsFromHitsByClassName(results, BaseStudy.class);
    publishedStudies.forEach(addDto::accept);
    builder.setExtension(StudyResultDto.result, resBuilder.build());
}

Example 14 with BaseStudy

use of org.obiba.mica.study.domain.BaseStudy in project mica2 by obiba.

the class VariableQuery method processHit.

/**
 * Fill the variable resolver dto with user-friendly labels about the variable, the dataset and the study.
 *
 * @param resolver
 * @param variable
 * @param studyMap study cache
 * @return
 */
private Mica.DatasetVariableResolverDto processHit(DatasetVariable.IdResolver resolver, DatasetVariable variable, Map<String, BaseStudy> studyMap, Map<String, Network> networkMap) {
    Mica.DatasetVariableResolverDto.Builder builder = dtos.asDto(resolver);
    String studyId = resolver.hasStudyId() ? resolver.getStudyId() : null;
    if (resolver.getType() == DatasetVariable.Type.Collected || resolver.getType() == DatasetVariable.Type.Dataschema || resolver.getType() == DatasetVariable.Type.Harmonized) {
        studyId = variable.getStudyId();
    }
    if (studyId != null) {
        builder.setStudyId(studyId);
        try {
            BaseStudy study;
            if (studyMap.containsKey(studyId)) {
                study = studyMap.get(studyId);
            } else {
                study = publishedStudyService.findById(studyId);
                studyMap.put(studyId, study);
            }
            if (study != null) {
                builder.addAllStudyName(dtos.asDto(study.getName()));
                builder.addAllStudyAcronym(dtos.asDto(study.getAcronym()));
            }
        } catch (NoSuchStudyException e) {
        }
    }
    builder.addAllDatasetAcronym(dtos.asDto(variable.getDatasetAcronym()));
    builder.addAllDatasetName(dtos.asDto(variable.getDatasetName()));
    if (variable.hasAttribute("label", null)) {
        builder.addAllVariableLabel(dtos.asDto(variable.getAttributes().getAttribute("label", null).getValues()));
    }
    return builder.build();
}

Example 15 with BaseStudy

use of org.obiba.mica.study.domain.BaseStudy in project mica2 by obiba.

the class VariableQuery method processHits.

@Override
protected void processHits(MicaSearch.QueryResultDto.Builder builder, Searcher.DocumentResults results, QueryScope scope, CountStatsData counts) throws IOException {
    MicaSearch.DatasetVariableResultDto.Builder resBuilder = MicaSearch.DatasetVariableResultDto.newBuilder();
    Map<String, BaseStudy> studyMap = Maps.newHashMap();
    Map<String, Network> networkMap = Maps.newHashMap();
    for (Searcher.DocumentResult result : results.getDocuments()) {
        if (result.hasSource()) {
            DatasetVariable.IdResolver resolver = DatasetVariable.IdResolver.from(result.getId());
            DatasetVariable variable = objectMapper.readValue(result.getSourceInputStream(), DatasetVariable.class);
            resBuilder.addSummaries(processHit(resolver, variable, studyMap, networkMap));
        }
    }
    builder.setExtension(MicaSearch.DatasetVariableResultDto.result, resBuilder.build());
}