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

Example 6 with HarmonizationDataset

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

the class PublishedDataschemaDatasetVariableResource method getVariableAggregations.

@GET
@Path("/aggregation")
@Timed
public Mica.DatasetVariableAggregationsDto getVariableAggregations() {
    ImmutableList.Builder<Mica.DatasetVariableAggregationDto> builder = ImmutableList.builder();
    HarmonizationDataset dataset = getDataset(HarmonizationDataset.class, datasetId);
    Mica.DatasetVariableAggregationsDto.Builder aggDto = Mica.DatasetVariableAggregationsDto.newBuilder();
    List<Future<Math.SummaryStatisticsDto>> results = Lists.newArrayList();
    dataset.getBaseStudyTables().forEach(table -> results.add(helper.getVariableFacet(dataset, variableName, table)));
    for (int i = 0; i < dataset.getBaseStudyTables().size(); i++) {
        BaseStudyTable opalTable = dataset.getBaseStudyTables().get(i);
        Future<Math.SummaryStatisticsDto> futureResult = results.get(i);
        try {
            builder.add(dtos.asDto(opalTable, futureResult.get()).build());
        } catch (Exception e) {
            log.warn("Unable to retrieve statistics: " + e.getMessage(), e);
            builder.add(dtos.asDto(opalTable, null).build());
        }
    }
    List<Mica.DatasetVariableAggregationDto> aggsDto = builder.build();
    Mica.DatasetVariableAggregationDto allAggDto = CombinedStatistics.mergeAggregations(aggsDto);
    aggDto.setN(allAggDto.getN());
    aggDto.setTotal(allAggDto.getTotal());
    if (allAggDto.hasStatistics())
        aggDto.setStatistics(allAggDto.getStatistics());
    aggDto.addAllFrequencies(allAggDto.getFrequenciesList());
    aggDto.addAllAggregations(aggsDto);
    return aggDto.build();
}

Example 7 with HarmonizationDataset

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

the class PublishedDataschemaDatasetVariableResource method getDatasetVariableContingenciesDto.

private Mica.DatasetVariableContingenciesDto getDatasetVariableContingenciesDto(DatasetVariable var, DatasetVariable crossVar) {
    HarmonizationDataset dataset = getDataset(HarmonizationDataset.class, datasetId);
    Mica.DatasetVariableContingenciesDto.Builder crossDto = Mica.DatasetVariableContingenciesDto.newBuilder();
    List<Future<Search.QueryResultDto>> results = Lists.newArrayList();
    dataset.getBaseStudyTables().forEach(table -> results.add(helper.getContingencyTable(dataset, var, crossVar, table)));
    Multimap<String, Mica.DatasetVariableAggregationDto> termAggregations = LinkedListMultimap.create();
    for (int i = 0; i < dataset.getBaseStudyTables().size(); i++) {
        BaseStudyTable opalTable = dataset.getBaseStudyTables().get(i);
        Future<Search.QueryResultDto> futureResult = results.get(i);
        try {
            Mica.DatasetVariableContingencyDto studyTableCrossDto = dtos.asContingencyDto(opalTable, var, crossVar, futureResult.get()).build();
            termAggregations.put(null, studyTableCrossDto.getAll());
            studyTableCrossDto.getAggregationsList().forEach(termAggDto -> termAggregations.put(termAggDto.getTerm(), termAggDto));
            crossDto.addContingencies(studyTableCrossDto);
        } catch (Exception e) {
            log.warn("Unable to retrieve contingency table: " + e.getMessage(), e);
            crossDto.addContingencies(dtos.asContingencyDto(opalTable, var, crossVar, null));
        }
    }
    // Merge aggregations by term (=variable category) + all terms aggregation.
    Mica.DatasetVariableContingencyDto.Builder allContingencies = Mica.DatasetVariableContingencyDto.newBuilder();
    termAggregations.asMap().entrySet().forEach(entry -> {
        Mica.DatasetVariableAggregationDto merged = CombinedStatistics.mergeAggregations(entry.getValue());
        if (entry.getKey() == null) {
            allContingencies.setAll(merged);
        } else {
            allContingencies.addAggregations(merged);
        }
    });
    crossDto.setAll(allContingencies);
    return crossDto.build();
}

Example 8 with HarmonizationDataset

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

the class PublishedHarmonizedDatasetResource method getVariableHarmonizationsAsCsv.

@GET
@Path("/variables/harmonizations/_export")
@Produces("text/csv")
@Timed
public Response getVariableHarmonizationsAsCsv(@PathParam("id") String id, @QueryParam("sort") @DefaultValue("index") String sort, @QueryParam("order") @DefaultValue("asc") String order, @QueryParam("locale") @DefaultValue("en") String locale) throws IOException {
    HarmonizationDataset dataset = getDataset(HarmonizationDataset.class, id);
    Mica.DatasetVariablesHarmonizationsDto harmonizationVariables = getVariableHarmonizationsInternal(id, 0, 999999, sort, order, false);
    CsvHarmonizationVariablesWriter writer = new CsvHarmonizationVariablesWriter(Lists.newArrayList("maelstrom", "Mlstr_harmo"));
    ByteArrayOutputStream values = writer.write(dataset, harmonizationVariables, locale);
    return Response.ok(values.toByteArray(), "text/csv").header("Content-Disposition", "attachment; filename=\"" + id + ".csv\"").build();
}

Example 9 with HarmonizationDataset

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

the class PublishedHarmonizedDatasetResource method getVariable.

@Path("/study/{study}/population/{population}/data-collection-event/{dce}/variable/{variable}")
public PublishedHarmonizedDatasetVariableResource getVariable(@PathParam("id") String id, @PathParam("study") String studyId, @PathParam("population") String populationId, @PathParam("dce") String dceId, @PathParam("variable") String variable) {
    checkAccess(id);
    PublishedHarmonizedDatasetVariableResource resource = applicationContext.getBean(PublishedHarmonizedDatasetVariableResource.class);
    resource.setDatasetId(id);
    resource.setVariableName(variable);
    resource.setStudyId(studyId);
    HarmonizationDataset dataset = getDataset(HarmonizationDataset.class, id);
    dataset.getStudyTables().stream().filter(t -> t.appliesTo(studyId, populationId, dceId)).forEach(t -> {
        resource.setTableType(t instanceof StudyTable ? DatasetVariable.OPAL_STUDY_TABLE_PREFIX : DatasetVariable.OPAL_HARMONIZATION_TABLE_PREFIX);
    });
    return resource;
}

Example 10 with HarmonizationDataset

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

the class RQLCriteriaOpalConverter method parseField.

private RQLFieldReferences parseField(String path) {
    DatasetVariable.IdResolver resolver = DatasetVariable.IdResolver.from(path);
    if (resolver.getType() == null || DatasetVariable.Type.Collected.equals(resolver.getType())) {
        StudyDataset ds = collectedDatasetService.findById(resolver.getDatasetId());
        BaseStudyTable studyTable = ds.getStudyTable();
        BaseStudy study = studyService.findStudy(studyTable.getStudyId());
        return new RQLFieldReferences(path, ds, studyTable, study, getDatasetVariableInternal(Indexer.VARIABLE_TYPE, path));
    } else if (DatasetVariable.Type.Dataschema.equals(resolver.getType())) {
        HarmonizationDataset ds = harmonizedDatasetService.findById(resolver.getDatasetId());
        BaseStudy study = studyService.findStudy(ds.getHarmonizationTable().getStudyId());
        return new RQLFieldReferences(path, ds, ds.getBaseStudyTables(), study, getDatasetVariableInternal(Indexer.VARIABLE_TYPE, path));
    } else if (DatasetVariable.Type.Harmonized.equals(resolver.getType())) {
        HarmonizationDataset ds = harmonizedDatasetService.findById(resolver.getDatasetId());
        Optional<BaseStudyTable> studyTable = ds.getBaseStudyTables().stream().filter(st -> st.getStudyId().equals(resolver.getStudyId()) && st.getProject().equals(resolver.getProject()) && st.getTable().equals(resolver.getTable())).findFirst();
        if (!studyTable.isPresent())
            throw new IllegalArgumentException("Not a valid variable: " + path);
        BaseStudy study = studyService.findStudy(studyTable.get().getStudyId());
        return new RQLFieldReferences(path, ds, studyTable.get(), study, getDatasetVariableInternal(Indexer.HARMONIZED_VARIABLE_TYPE, path));
    }
    throw new IllegalArgumentException("Not a valid variable: " + path);
}