org.obiba.mica.search.queries.StudyQuery.java Source code

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Here is the source code for org.obiba.mica.search.queries.StudyQuery.java

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/*
 * Copyright (c) 2018 OBiBa. All rights reserved.
 *
 * This program and the accompanying materials
 * are made available under the terms of the GNU Public License v3.0.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

package org.obiba.mica.search.queries;

import com.google.common.collect.Lists;
import org.obiba.mica.core.domain.DefaultEntityBase;
import org.obiba.mica.micaConfig.service.helper.AggregationMetaDataProvider;
import org.obiba.mica.search.aggregations.StudyTaxonomyMetaDataProvider;
import org.obiba.mica.spi.search.*;
import org.obiba.mica.study.domain.BaseStudy;
import org.obiba.mica.study.domain.HarmonizationStudy;
import org.obiba.mica.study.domain.Study;
import org.obiba.mica.study.service.IndividualStudyService;
import org.obiba.mica.study.service.HarmonizationStudyService;
import org.obiba.mica.web.model.Dtos;
import org.obiba.mica.web.model.Mica;
import org.obiba.mica.web.model.MicaSearch;
import org.springframework.context.annotation.Scope;
import org.springframework.stereotype.Component;

import javax.annotation.Nullable;
import javax.inject.Inject;
import java.io.IOException;
import java.util.*;
import java.util.function.Consumer;
import java.util.stream.Collectors;

import static org.obiba.mica.search.CountStatsDtoBuilders.StudyCountStatsBuilder;
import static org.obiba.mica.web.model.MicaSearch.QueryResultDto;
import static org.obiba.mica.web.model.MicaSearch.StudyResultDto;

@Component
@Scope("request")
public class StudyQuery extends AbstractDocumentQuery {

    @Inject
    private IndividualStudyService individualStudyService;

    @Inject
    private HarmonizationStudyService harmonizationStudyService;

    @Inject
    private Dtos dtos;

    @Inject
    private StudyTaxonomyMetaDataProvider studyTaxonomyMetaDataProvider;

    private static final String JOIN_FIELD = "id";

    @Override
    public String getSearchIndex() {
        return Indexer.PUBLISHED_STUDY_INDEX;
    }

    @Override
    public String getSearchType() {
        return Indexer.STUDY_TYPE;
    }

    @Nullable
    @Override
    protected Searcher.IdFilter getAccessibleIdFilter() {
        if (isOpenAccess())
            return null;
        return new Searcher.IdFilter() {
            @Override
            public Collection<String> getValues() {
                List<String> ids = individualStudyService.findPublishedIds().stream()
                        .filter(s -> subjectAclService.isAccessible("/individual-study", s))
                        .collect(Collectors.toList());
                ids.addAll(harmonizationStudyService.findPublishedIds().stream()
                        .filter(s -> subjectAclService.isAccessible("/harmonization-study", s))
                        .collect(Collectors.toList()));
                return ids;
            }
        };
    }

    @Override
    protected List<AggregationMetaDataProvider> getAggregationMetaDataProviders() {
        return Arrays.asList(studyTaxonomyMetaDataProvider);
    }

    @Override
    protected List<String> getMandatorySourceFields() {
        return Lists.newArrayList("id", "className", "populations.id", "populations.dataCollectionEvents.id");
    }

    @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());
    }

    private Consumer<BaseStudy> getStudyConsumer(QueryScope scope, StudyResultDto.Builder resBuilder,
            StudyCountStatsBuilder studyCountStatsBuilder) {

        return scope == QueryScope.DETAIL ? (study) -> {
            Mica.StudySummaryDto.Builder summaryBuilder = dtos.asSummaryDtoBuilder(study);
            if (mode == QueryMode.LIST) {
                summaryBuilder.clearPopulationSummaries();
            }
            if (studyCountStatsBuilder != null) {
                summaryBuilder
                        .setExtension(MicaSearch.CountStatsDto.studyCountStats, studyCountStatsBuilder.build(study))
                        .build();
            }
            resBuilder.addSummaries(summaryBuilder.build());
        } : (study) -> resBuilder.addDigests(dtos.asDigestDtoBuilder(study).build());
    }

    @Nullable
    @Override
    protected Properties getAggregationsProperties(List<String> filter) {
        Properties properties = getAggregationsProperties(filter, taxonomyService.getStudyTaxonomy());
        if (!properties.containsKey(JOIN_FIELD))
            properties.put(JOIN_FIELD, "");
        return properties;
    }

    @Override
    public Map<String, Integer> getStudyCounts() {
        return getDocumentCounts(JOIN_FIELD);
    }

    public Map<String, Integer> getHarmonizationStudyCounts() {
        return getDocumentCountsFilteredByClassName(JOIN_FIELD, HarmonizationStudy.class.getSimpleName());
    }

    public Map<String, Integer> getIndividualStudyCounts() {
        return getDocumentCountsFilteredByClassName(JOIN_FIELD, Study.class.getSimpleName());
    }

    @Override
    protected List<String> getJoinFields() {
        return Arrays.asList(JOIN_FIELD);
    }
}