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

Example 1 with HarmonizationStudyTable

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

the class CsvHarmonizationVariablesWriter method writeBody.

private void writeBody(CSVWriter writer, HarmonizationDataset dataset, DatasetVariablesHarmonizationsDto harmonizationVariables, String locale) {
    harmonizationVariables.getVariableHarmonizationsList().forEach(variableHarmonization -> {
        List<String> row = Lists.newArrayList();
        dataset.getBaseStudyTables().forEach(table -> {
            final boolean[] found = { false };
            variableHarmonization.getDatasetVariableSummariesList().forEach(summary -> {
                String id = table instanceof StudyTable ? ((StudyTable) table).getStudyId() : ((HarmonizationStudyTable) table).getStudyId();
                Mica.DatasetVariableResolverDto resolver = summary.getResolver();
                if ((resolver.getStudyId().equals(id) && resolver.getProject().equals(table.getProject()) && resolver.getTable().equals(table.getTable()))) {
                    row.add(getStatus(summary, locale));
                    found[0] = true;
                    return;
                }
            });
            if (row.size() == 0 || !found[0]) {
                row.add(EMPTY_STATUS);
            }
        });
        row.add(0, variableHarmonization.getResolver().getName());
        writer.writeNext(row.toArray(new String[row.size()]));
    });
}

Example 2 with HarmonizationStudyTable

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

the class HarmonizedDatasetHelperTest method createHarmonizationStudyTable.

private HarmonizationStudyTable createHarmonizationStudyTable(String studyId) {
    HarmonizationStudyTable table = new HarmonizationStudyTable();
    initTable(studyId, table);
    return table;
}

Example 3 with HarmonizationStudyTable

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

the class DatasetDtos method fromDto.

private Dataset fromDto(@NotNull Mica.HarmonizedDatasetDto dto) {
    Assert.notNull(dto, "HarmonizationDataset dt cannot be null.");
    HarmonizationDataset harmonizationDataset = new HarmonizationDataset();
    if (dto.getStudyTablesCount() > 0) {
        dto.getStudyTablesList().forEach(tableDto -> harmonizationDataset.addStudyTable(fromDto(tableDto)));
    }
    if (dto.getHarmonizationTablesCount() > 0) {
        dto.getHarmonizationTablesList().forEach(tableDto -> harmonizationDataset.addHarmonizationTable(fromDto(tableDto)));
    }
    if (dto.hasHarmonizationTable()) {
        HarmonizationStudyTable harmonizationLink = new HarmonizationStudyTable();
        harmonizationLink.setProject(dto.getHarmonizationTable().getProject());
        harmonizationLink.setTable(dto.getHarmonizationTable().getTable());
        harmonizationLink.setStudyId(dto.getHarmonizationTable().getStudyId());
        harmonizationLink.setPopulationId(dto.getHarmonizationTable().getPopulationId());
        harmonizationDataset.setHarmonizationTable(harmonizationLink);
    }
    return harmonizationDataset;
}

Example 4 with HarmonizationStudyTable

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

the class DatasetDtos method asContingencyDto.

public Mica.DatasetVariableContingencyDto.Builder asContingencyDto(@NotNull OpalTable opalTable, DatasetVariable variable, DatasetVariable crossVariable, @Nullable Search.QueryResultDto results) {
    Mica.DatasetVariableContingencyDto.Builder crossDto = Mica.DatasetVariableContingencyDto.newBuilder();
    if (opalTable instanceof StudyTable)
        crossDto.setStudyTable(asDto((StudyTable) opalTable, true));
    else if (opalTable instanceof HarmonizationStudyTable)
        crossDto.setHarmonizationStudyTable(asDto((HarmonizationStudyTable) opalTable));
    Mica.DatasetVariableAggregationDto.Builder allAggBuilder = Mica.DatasetVariableAggregationDto.newBuilder();
    if (results == null) {
        allAggBuilder.setN(0);
        allAggBuilder.setTotal(0);
        crossDto.setAll(allAggBuilder);
        return crossDto;
    }
    allAggBuilder.setTotal(results.getTotalHits());
    MicaConfig micaConfig = micaConfigService.getConfig();
    int privacyThreshold = micaConfig.getPrivacyThreshold();
    crossDto.setPrivacyThreshold(privacyThreshold);
    boolean privacyChecks = crossVariable.hasCategories() ? validatePrivacyThreshold(results, privacyThreshold) : true;
    boolean totalPrivacyChecks = validateTotalPrivacyThreshold(results, privacyThreshold);
    // add facet results in the same order as the variable categories
    variable.getCategories().forEach(cat -> results.getFacetsList().stream().filter(facet -> facet.hasFacet() && cat.getName().equals(facet.getFacet())).forEach(facet -> {
        boolean privacyCheck = privacyChecks && checkPrivacyThreshold(facet.getFilters(0).getCount(), privacyThreshold);
        Mica.DatasetVariableAggregationDto.Builder aggBuilder = Mica.DatasetVariableAggregationDto.newBuilder();
        aggBuilder.setTotal(totalPrivacyChecks ? results.getTotalHits() : 0);
        aggBuilder.setTerm(facet.getFacet());
        DatasetCategory category = variable.getCategory(facet.getFacet());
        aggBuilder.setMissing(category != null && category.isMissing());
        addSummaryStatistics(crossVariable, aggBuilder, facet, privacyCheck, totalPrivacyChecks);
        crossDto.addAggregations(aggBuilder);
    }));
    // add total facet for all variable categories
    results.getFacetsList().stream().filter(facet -> facet.hasFacet() && "_total".equals(facet.getFacet())).forEach(facet -> {
        boolean privacyCheck = privacyChecks && facet.getFilters(0).getCount() > micaConfig.getPrivacyThreshold();
        addSummaryStatistics(crossVariable, allAggBuilder, facet, privacyCheck, totalPrivacyChecks);
    });
    crossDto.setAll(allAggBuilder);
    return crossDto;
}

Example 5 with HarmonizationStudyTable

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

the class DatasetDtos method fromDto.

private HarmonizationStudyTable fromDto(Mica.DatasetDto.HarmonizationTableDto dto) {
    HarmonizationStudyTable table = new HarmonizationStudyTable();
    table.setStudyId(dto.getStudyId());
    table.setPopulationId(dto.getPopulationId());
    table.setPopulationId(dto.getPopulationId());
    table.setProject(dto.getProject());
    table.setTable(dto.getTable());
    table.setWeight(dto.getWeight());
    table.setName(localizedStringDtos.fromDto(dto.getNameList()));
    table.setDescription(localizedStringDtos.fromDto(dto.getDescriptionList()));
    return table;
}