org.opencb.opencga.catalog.db.mongodb.AbstractCatalogMongoDBAdaptor.java Source code

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Here is the source code for org.opencb.opencga.catalog.db.mongodb.AbstractCatalogMongoDBAdaptor.java

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/*
 * Copyright 2015 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.opencb.opencga.catalog.db.mongodb;

import com.mongodb.client.model.Accumulators;
import com.mongodb.client.model.Aggregates;
import com.mongodb.client.model.Filters;
import com.mongodb.client.model.Projections;
import org.bson.Document;
import org.bson.conversions.Bson;
import org.opencb.commons.datastore.core.Query;
import org.opencb.commons.datastore.core.QueryOptions;
import org.opencb.commons.datastore.core.QueryResult;
import org.opencb.commons.datastore.mongodb.MongoDBCollection;
import org.opencb.opencga.catalog.db.AbstractCatalogDBAdaptor;
import org.slf4j.Logger;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;

/**
 * Created by imedina on 08/01/16.
 */
@Deprecated
public class AbstractCatalogMongoDBAdaptor extends AbstractCatalogDBAdaptor {

    protected AbstractCatalogMongoDBAdaptor(Logger logger) {
        super(logger);
    }

    protected void createOrQuery(Query query, String queryParam, String mongoDbField, List<Bson> andBsonList) {
        if (query != null && query.getString(queryParam) != null && !query.getString(queryParam).isEmpty()) {
            createOrQuery(query.getAsStringList(queryParam), mongoDbField, andBsonList);
        }
    }

    protected void createOrQuery(List<String> queryValues, String mongoDbField, List<Bson> andBsonList) {
        if (queryValues.size() == 1) {
            andBsonList.add(Filters.eq(mongoDbField, queryValues.get(0)));
        } else {
            List<Bson> orBsonList = new ArrayList<>(queryValues.size());
            for (String queryItem : queryValues) {
                orBsonList.add(Filters.eq(mongoDbField, queryItem));
            }
            andBsonList.add(Filters.or(orBsonList));
        }
    }

    protected QueryResult groupBy(MongoDBCollection collection, Bson query, String groupByField, String idField,
            QueryOptions options) {
        if (groupByField == null || groupByField.isEmpty()) {
            return new QueryResult();
        }

        if (groupByField.contains(",")) {
            // call to multiple groupBy if commas are present
            return groupBy(collection, query, Arrays.asList(groupByField.split(",")), idField, options);
        } else {
            Bson match = Aggregates.match(query);
            Bson project = Aggregates.project(Projections.include(groupByField, idField));
            Bson group;
            if (options.getBoolean("count", false)) {
                group = Aggregates.group("$" + groupByField, Accumulators.sum("count", 1));
            } else {
                group = Aggregates.group("$" + groupByField, Accumulators.addToSet("features", "$" + idField));
            }
            return collection.aggregate(Arrays.asList(match, project, group), options);
        }
    }

    protected QueryResult groupBy(MongoDBCollection collection, Bson query, List<String> groupByField,
            String idField, QueryOptions options) {
        if (groupByField == null || groupByField.isEmpty()) {
            return new QueryResult();
        }

        if (groupByField.size() == 1) {
            // if only one field then we call to simple groupBy
            return groupBy(collection, query, groupByField.get(0), idField, options);
        } else {
            Bson match = Aggregates.match(query);

            // add all group-by fields to the projection together with the aggregation field name
            List<String> groupByFields = new ArrayList<>(groupByField);
            groupByFields.add(idField);
            Bson project = Aggregates.project(Projections.include(groupByFields));

            // _id document creation to have the multiple id
            Document id = new Document();
            for (String s : groupByField) {
                id.append(s, "$" + s);
            }
            Bson group;
            if (options.getBoolean("count", false)) {
                group = Aggregates.group(id, Accumulators.sum("count", 1));
            } else {
                group = Aggregates.group(id, Accumulators.addToSet("features", "$" + idField));
            }
            return collection.aggregate(Arrays.asList(match, project, group), options);
        }
    }

}