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

Example 6 with DatasetVariable

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

the class PublishedDataschemaDatasetVariableResource 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 value = new ExcelContingencyWriter(variables.getFirst(), variables.getSecond()).write(getDatasetVariableContingenciesDto(variables.getFirst(), variables.getSecond()));
    return Response.ok(value.toByteArray()).header("Content-Disposition", String.format("attachment; filename=\"contingency-table-%s-%s.xlsx\"", variableName, crossVariable)).build();
}

Example 7 with DatasetVariable

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

the class HarmonizedDatasetServiceTest method testPopulateHarmonizedVariablesMap.

@Test
public void testPopulateHarmonizedVariablesMap() {
    List<DatasetVariable> l = new ArrayList<DatasetVariable>() {

        {
            add(new DatasetVariable(dataset, Variable.Builder.newVariable("v1", BooleanType.get(), "test").build(), st));
            add(new DatasetVariable(dataset, Variable.Builder.newVariable("v2", BooleanType.get(), "test").build(), st2));
        }
    };
    doReturn(dataset).when(datasetService).findById(anyString());
    when(helper.asyncGetDatasetVariables(any(Supplier.class))).thenReturn(new AsyncResult<>(l));
    doReturn(l).when(datasetService).getDatasetVariables(any(HarmonizationDataset.class));
    doReturn(l).when(datasetService).getDatasetVariables(any(HarmonizationDataset.class), any(StudyTable.class));
    Map<String, List<DatasetVariable>> res = datasetService.populateHarmonizedVariablesMap(dataset);
    assertEquals(2, res.keySet().size());
    assertEquals(2, res.get("testds:v1:Dataschema").size());
    assertEquals(2, res.get("testds:v2:Dataschema").size());
}

Example 8 with DatasetVariable

use of org.obiba.mica.dataset.domain.DatasetVariable 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 9 with DatasetVariable

use of org.obiba.mica.dataset.domain.DatasetVariable 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 10 with DatasetVariable

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

the class AbstractPublishedDatasetResource method getHarmonizedDatasetVariable.

private DatasetVariable getHarmonizedDatasetVariable(String datasetId, String variableId, String variableName) {
    String dataSchemaVariableId = DatasetVariable.IdResolver.encode(datasetId, variableName, DatasetVariable.Type.Dataschema, null, null, null, null);
    DatasetVariable harmonizedDatasetVariable = getDatasetVariableInternal(Indexer.HARMONIZED_VARIABLE_TYPE, variableId, variableName);
    DatasetVariable dataSchemaVariable = getDatasetVariableInternal(Indexer.VARIABLE_TYPE, dataSchemaVariableId, variableName);
    dataSchemaVariable.getAttributes().asAttributeList().forEach(a -> {
        if (!a.getName().startsWith("Mlstr_harmo"))
            harmonizedDatasetVariable.addAttribute(a);
    });
    return harmonizedDatasetVariable;
}