org.opencb.cellbase.mongodb.db.ProteinMongoDBAdaptor.java Source code

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Here is the source code for org.opencb.cellbase.mongodb.db.ProteinMongoDBAdaptor.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.cellbase.mongodb.db;

import com.mongodb.DB;
import com.mongodb.DBObject;
import com.mongodb.QueryBuilder;
import org.opencb.cellbase.core.lib.api.core.ProteinDBAdaptor;
import org.opencb.datastore.core.QueryOptions;
import org.opencb.datastore.core.QueryResult;
import org.opencb.datastore.mongodb.MongoDataStore;

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

/**
 * Created by imedina on 06/03/14.
 */
public class ProteinMongoDBAdaptor extends MongoDBAdaptor implements ProteinDBAdaptor {

    public ProteinMongoDBAdaptor(DB db, String species, String version) {
        super(db, species, version);
        mongoDBCollection = db.getCollection("protein");
    }

    public ProteinMongoDBAdaptor(String species, String assembly, MongoDataStore mongoDataStore) {
        super(species, assembly, mongoDataStore);
        mongoDBCollection2 = mongoDataStore.getCollection("protein");

        logger.info("ProteinMongoDBAdaptor: in 'constructor'");
    }

    @Override
    public QueryResult getAll(QueryOptions options) {
        return null;
    }

    @Override
    public QueryResult getAllById(String id, QueryOptions options) {

        return null;
    }

    @Override
    public List<QueryResult> getAllByIdList(List<String> idList, QueryOptions options) {
        List<DBObject> queries = new ArrayList<>(idList.size());
        for (String id : idList) {
            QueryBuilder builder = QueryBuilder.start("name").is(id);
            queries.add(builder.get());
        }

        //        options = addExcludeReturnFields("transcripts", options);
        return executeQueryList(idList, queries, options);
    }

    @Override
    public QueryResult getAllByAccession(String id, QueryOptions options) {
        return null;
    }

    @Override
    public List<QueryResult> getAllByAccessionList(List<String> idList, QueryOptions options) {
        return null;
    }
}