uk.ac.ebi.eva.server.ws.ga4gh.GA4GHBeaconWSServer.java Source code

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Here is the source code for uk.ac.ebi.eva.server.ws.ga4gh.GA4GHBeaconWSServer.java

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/*
 * European Variation Archive (EVA) - Open-access database of all types of genetic
 * variation data from all species
 *
 * Copyright 2014-2016 EMBL - European Bioinformatics Institute
 *
 * 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 uk.ac.ebi.eva.server.ws.ga4gh;

import java.io.IOException;
import java.net.UnknownHostException;
import java.util.Arrays;

import javax.servlet.http.HttpServletResponse;

import org.opencb.biodata.models.feature.Region;
import org.opencb.datastore.core.QueryOptions;
import org.opencb.datastore.core.QueryResult;
import org.opencb.opencga.lib.auth.IllegalOpenCGACredentialsException;
import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RequestParam;
import org.springframework.web.bind.annotation.RestController;

import io.swagger.annotations.Api;
import uk.ac.ebi.eva.lib.datastore.DBAdaptorConnector;
import uk.ac.ebi.eva.server.ws.EvaWSServer;

/**
 *
 * @author Cristina Yenyxe Gonzalez Garcia <cyenyxe@ebi.ac.uk>
 */
@RestController
@RequestMapping(value = "/v1/ga4gh", produces = "application/json")
@Api(tags = { "ga4gh" })
public class GA4GHBeaconWSServer extends EvaWSServer {

    public GA4GHBeaconWSServer() {
    }

    @RequestMapping(value = "/beacon", method = RequestMethod.GET)
    public GA4GHBeaconResponse beacon(@RequestParam("referenceName") String chromosome,
            @RequestParam("start") int start, @RequestParam("allele") String allele,
            @RequestParam("datasetIds") String studies, HttpServletResponse response)
            throws UnknownHostException, IllegalOpenCGACredentialsException, IOException {
        initializeQueryOptions();

        if (start < 0) {
            response.setStatus(HttpServletResponse.SC_BAD_REQUEST);
            return new GA4GHBeaconResponse(chromosome, start, allele, studies,
                    "Please provide a positive number as start position");
        }

        VariantDBAdaptor variantMongoDbAdaptor = DBAdaptorConnector.getVariantDBAdaptor("hsapiens_grch37");

        Region region = new Region(chromosome, start, start + allele.length());
        if (allele.equalsIgnoreCase("INDEL")) {
            queryOptions.put("type", "INDEL");
        } else {
            queryOptions.put("alternate", allele);
        }

        if (studies != null && !studies.isEmpty()) {
            queryOptions.put("studies", Arrays.asList(studies.split(",")));
        }

        QueryResult queryResult = variantMongoDbAdaptor.getAllVariantsByRegion(region, queryOptions);
        //        queryResult.setResult(Arrays.asList(queryResult.getNumResults() > 0));
        //        queryResult.setResultType(Boolean.class.getCanonicalName());
        return new GA4GHBeaconResponse(chromosome, start, allele, studies, queryResult.getNumResults() > 0);
    }

    class GA4GHBeaconResponse {

        private String chromosome;

        private Integer start;

        private String allele;

        private String datasetIds;

        private boolean exists;

        private String errorMessage;

        public GA4GHBeaconResponse(String chromosome, Integer start, String allele, String datasetIds,
                boolean exists) {
            this.chromosome = chromosome;
            this.start = start;
            this.allele = allele;
            this.datasetIds = datasetIds;
            this.exists = exists;
        }

        public GA4GHBeaconResponse(String chromosome, Integer start, String allele, String datasetIds,
                String errorMessage) {
            this.chromosome = chromosome;
            this.start = start;
            this.allele = allele;
            this.datasetIds = datasetIds;
            this.errorMessage = errorMessage;
        }

        public String getChromosome() {
            return chromosome;
        }

        public Integer getStart() {
            return start;
        }

        public String getAllele() {
            return allele;
        }

        public String getDatasetIds() {
            return datasetIds;
        }

        public boolean isExists() {
            return exists;
        }

        public String getErrorMessage() {
            return errorMessage;
        }
    }

}